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plant functional genomics
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Discovery Of Drought-Responsive Transposable Element-Related Peach miRNAs

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Frontiers | Engineering the Plant Factory for the Production of Biologics and Small-Molecule Medicines

Frontiers | Engineering the Plant Factory for the Production of Biologics and Small-Molecule Medicines | unverlab | Scoop.it
Plant gene transfer achieved in the early ‘80s paved the way for the exploitation of the potential of gene engineering to add novel agronomic traits and/or to design plants as factories for hig
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Frontiers | Regulation of Isoflavone Biosynthesis by miRNAs in Two Contrasting Soybean Genotypes at Different Seed Developmental Stages | Plant Metabolism and Chemodiversity

Frontiers | Regulation of Isoflavone Biosynthesis by miRNAs in Two Contrasting Soybean Genotypes at Different Seed Developmental Stages | Plant Metabolism and Chemodiversity | unverlab | Scoop.it
Owing to the presence of nutritionally important, health-promoting bioactive compounds, especially isoflavones, soybean has acquired the status of a functional food. miRNAs are tiny riboregulator of gene expression by either decreasing and/or increasing the expression of their corresponding target genes. Despite several works on identification and functional characterization of plant miRNAs, the role of miRNAs in the regulation of isoflavones metabolism is still a virgin field. In the present study, we identified a total of 31 new miRNAs along with their 245 putative target genes from soybean seed-specific ESTs using computational approach. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that miRNA putatively regulates metabolism and genetic information processing. Out of that, a total of 5 miRNAs (Gma-miRNA12, Gma-miRNA24, Gma-miRNA26, Gma-miRNA28 and Gma-miRNA29) were predicted and validated for their probable role during isoflavone biosynthesis. We also validated their five target genes using RA-PCR, which is as good as 5’RLM-RACE. Temporal regulation (35DAF, 45DAF, 55DAF and 65DAF) of miRNAs and their targets showed differential expression schema. Differential expression of Gma-miR26 and Gma-miRNA28 along with their corresponding target genes (Glyma.10G197900 and Glyma.09G127200) showed a direct relationship with the total isoflavone content. Therefore, understanding the miRNA-based genetic regulation of isoflavone pathway would assist in selection and manipulation to get high-performing soybean genotypes with better isoflavone yield.
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MicroRNA exocytosis by large dense-core vesicle fusion

MicroRNA exocytosis by large dense-core vesicle fusion | unverlab | Scoop.it
Neurotransmitters and peptide hormones are secreted into outside the cell by a vesicle fusion process.
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PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs)

PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs) | unverlab | Scoop.it
MicroRNAs (miRNA) are small endogenous RNA molecules, which regulate target gene expression at post-transcriptional level. Besides, miRNA activity can be controlled by a newly discovered regulatory mechanism called endogenous target mimicry (eTM). In target mimicry, eTMs bind to the corresponding miRNAs to block the binding of specific transcript leading to increase mRNA expression. Thus, miRNA-eTM-target-mRNA regulation modules involving a wide range of biological processes; an increasing need for a comprehensive eTM database arose. Except miRSponge with limited number of Arabidopsis eTM data no available database and/or repository was developed and released for plant eTMs yet. Here, we present an online plant eTM database, called PeTMbase (http://petmbase.org), with a highly efficient search tool. To establish the repository a number of identified eTMs was obtained utilizing from high-throughput RNA-sequencing data of 11 plant species. Each transcriptome libraries is first mapped to corresponding plant genome, then long non-coding RNA (lncRNA) transcripts are characterized. Furthermore, additional lncRNAs retrieved from GREENC and PNRD were incorporated into the lncRNA catalog. Then, utilizing the lncRNA and miRNA sources a total of 2,728 eTMs were successfully predicted. Our regularly updated database, PeTMbase, provides high quality information regarding miRNA:eTM modules and will aid functional genomics studies particularly, on miRNA regulatory networks.
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BMC Genomics | Abstract | Isolation and expression analysis of cDNAs that are associated with alternate bearing in Olea europaea L. cv. Ayval[latin small letter dotless i]k

Olive cDNA libraries to isolate candidate genes that can help enlightening the molecular mechanism of periodicity and / or fruit production were constructed and analyzed.
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Transcriptome-wide identification of R2R3-MYB transcription factors in barley with their boron responsive expression analysis - Online First - Springer

Transcriptome-wide identification of R2R3-MYB transcription factors in barley with their boron responsive expression analysis - Online First - Springer | unverlab | Scoop.it
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Proteome changes in wild and modern wheat leaves upon drought stress by two-dimensional electrophoresis and nanoLC-ESI–MS/MS - Online First - Springer

Proteome changes in wild and modern wheat leaves upon drought stress by two-dimensional electrophoresis and nanoLC-ESI–MS/MS - Online First - Springer | unverlab | Scoop.it
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BMC Plant Biology | Abstract | Genome-wide identification of alternate bearing-associated microrna (mirna) in olive (Olea europaea L.)

Alternate bearing is a widespread phenomenon among crop plants, defined as the tendency of certain fruit trees to produce a high-yield crop one year (
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PLOS ONE: Genome-Wide Identification of miRNAs Responsive to Drought in Peach (Prunus persica) by High-Throughput Deep Sequencing

PLOS ONE: Genome-Wide Identification of miRNAs Responsive to Drought in Peach (Prunus persica) by High-Throughput Deep Sequencing | unverlab | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Genome sequencing in your doctors surgery? | Genome Engineering

Genome sequencing in your doctors surgery? | Genome Engineering | unverlab | Scoop.it
Following on from the news of genome sequencing in just 50 hours, a team of researchers at Columbia University and the National Institute of Standards and Technology (NIST) are using nanoscale technology that could lead ...
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Orhan Ozcan's comment, October 5, 2012 3:27 PM
I have seen far more better instrument at http://www.ieee.org/conferences_events/conferences/conferencedetails/index.html?Conf_ID=18584 . They have micro scissors indicating you are still cutting cancerous tissue ( knowing cancer genome still coming ). METU did not give me funding to go there as it is EE congress so I talked with comittee and I worked as a presentation technician and microphone stuff :) inorder to get scholarship
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European Food Safety Authority Finds Controversial GM Study Wanting - ScienceInsider

European Food Safety Authority Finds Controversial GM Study Wanting - ScienceInsider | unverlab | Scoop.it
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CropLife International (2017)

CropLife International (2017) | unverlab | Scoop.it
Why did you want to be a plant scientist?

I became a scientist because I grew up being extremely curious about the natural world. I wanted to know how living organisms function. How they became the way they are. Plant pathology came later after realized that I may as well study a field of biology that is important to the human condition. This inspires me to narrow the gap between fundamental and applied research. My aim is to perform cutting-edge research and significantly advance knowledge on economically important plant pathogen systems. In contrast, much research focuses on model systems and is therefore further steps away from practical applications.

Can you explain what your job involves?

As an academic scientist, I am in the business of knowledge. My job is to generate new knowledge to advance science, and to influence others to pursue new directions, generate more knowledge and apply it to address practical problems. My job is also to communicate scientific knowledge and discoveries to my peers and to a broader audience, including the general public.

 

What are the plant diseases that you are working on?

I work primarily on blight and blast diseases. Throughout my career, I have worked primarily on the Irish potato famine pathogen Phytophthora infestans. More recently, I was inspired by the sense of urgency brought upon by the February 2016 Bangladeshi wheat blast epidemic to expand my research to blast fungi. I aim to apply the concepts and ideas I developed throughout my career to a problem with an immediate impact on global food security.

Can you describe how damaging these diseases can be for farmers?

Plant diseases are a major constraint for achieving food security. Losses caused by fungal plant pathogens alone account for enough to feed several billion people. Magnaporthe oryzae, the causal agent of blast disease of cereals, is among the most destructive plant pathogens, causing losses in rice production that, if mitigated, could feed up to 740 million people. This pathogen has emerged since the 1980s as an important pathogen of wheat seriously limiting the potential for wheat production in South America. In 2016, wheat blast was detected for the first time in Asia with reports of a severe epidemic in Bangladesh. The outbreak is particularly worrisome because wheat blast has already spread further to India, and is threatening major wheat producing areas in neighboring South Asian countries. Global trade and a warming climate are contributing to the spread and establishment of blast diseases as a global problem for cereal production and a present and clear danger to food security.

Why is your profession important in the challenge to feed the world?

Plant pathology delivers science-driven solutions to plant diseases. In particular, genetic solutions through disease resistant crop varieties can be sustainable and environmentally friendly.

What inspires you about your job?

Knowledge and people. The thrill of learning something new every day is addictive. Sharing the experience with others –be they students, colleagues, stakeholders or members of the public – is priceless.


Via Kamoun Lab @ TSL
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CRISPR/Cas9: an RNA‐guided highly precise synthetic tool for plant genome editing

CRISPR/Cas9: an RNA‐guided highly precise synthetic tool for plant genome editing | unverlab | Scoop.it
CRISPR/Cas 9 is a newly developed and naturally occurred genome editing tool, which is originally used by bacteria for immune defence. In the past years, it has been quickly employed and modified t
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miRNA-based drought regulation in wheat

miRNA-based drought regulation in wheat | unverlab | Scoop.it
MicroRNAs (miRNAs) are a class of small non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. Drought is a common environmental stress i
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A high-efficiency CRISPR/Cas9 system for targeted mutagenesis in Cotton (Gossypium hirsutum L.)

A high-efficiency CRISPR/Cas9 system for targeted mutagenesis in Cotton (Gossypium hirsutum L.) | unverlab | Scoop.it
The complex allotetraploid genome is one of major challenges in cotton for repressing gene expression.
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Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology

Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology | unverlab | Scoop.it
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease system is a powerful RNA-guided genome editing tool.
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PLOS ONE: Nutrition Metabolism Plays an Important Role in the Alternate Bearing of the Olive Tree (Olea europaea L.)

PLOS ONE: Nutrition Metabolism Plays an Important Role in the Alternate Bearing of the Olive Tree (Olea europaea L.) | unverlab | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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PLOS ONE: Boron Stress Responsive MicroRNAs and Their Targets in Barley

PLOS ONE: Boron Stress Responsive MicroRNAs and Their Targets in Barley | unverlab | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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BMC Plant Biology

BMC Plant Biology | unverlab | Scoop.it
Turgay Unver's insight:

Genome-wide identification of alternate bearing-associated microRNAs (miRNAs) in olive (Olea europaea L.) paper is HOTTOPIC


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Olea Europea

Olea Europea | unverlab | Scoop.it
Turgay Unver's insight:

Ministry Of Development Of The Republic Of Turkey and (TÜBİTAK) The Scientific and Technological Research Council of Turkey supports the OLIVE GENOME PROJECT!!!

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Baby's genome in less than 50 hours | Genome Engineering

Baby's genome in less than 50 hours | Genome Engineering | unverlab | Scoop.it
A team at Children's Mercy Hospital in Kansas has sequenced a baby's genome in just 50 hours, from blood sample to results – whole genome sequencing (WGS) can take up to four to six weeks.
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Genomics and the future of food safety

Genomics and the future of food safety | unverlab | Scoop.it
Outlines research into using DNA to improve food safety and traceability systems in Canada and the United States.
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