scholarly journals A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses

2018 ◽  
Author(s):  
Felix Hausera ◽  
Paulo H. O. Ceciliatoa ◽  
Yi-Chen Lin ◽  
DanDan Guo ◽  
JD Gregerson ◽  
...  
Keyword(s):  
Genetic Screens ◽  
Resource Center ◽  
New Genes ◽  
Redundant Genes ◽  
Forward Genetic Screens ◽  
Genes Encoding ◽  
Arabidopsis Biological Resource Center ◽  
Redundant Gene ◽  
Aba Insensitive ◽  
Arabidopsis Biological Resource

AbstractThe identification of homologous genes with functional overlap in forward genetic screens is severely limited. Here we report the generation of over 14,000 amiRNA-expressing plants that enable screens of the functionally redundant gene space in Arabidopsis. A protocol is developed here for isolating robust and reproducible amiRNA-mutants. Examples of validation approaches and essential controls are presented for two new amiRNA mutants that exhibit genetically redundant phenotypes and circumvent double mutant lethality. In a forward genetic screen for abscisic acid (ABA)-mediated inhibition of seed germination, amiRNAs that target combinations of known redundant ABA receptor and SnRK2 kinase genes were rapidly isolated, providing a strong proof of principle for this approach. A new ABA insensitive amiRNA line is isolated, which targets three genes encoding avirulence-induced gene2-like (AIG2) genes. A thermal imaging screen for plants with impaired stomatal opening in response to low CO2 exposure led here to isolation of a new amiRNA targeting two essential proteasomal subunits, PAB1 and PAB2. The seed library of 14,000 T2 amiRNA lines generated here provides a new platform for forward genetic screens and is being made available to the Arabidopsis Biological Resource Center (ABRC) and optimized procedures for amiRNA screening and controls are described.HighlightThe generation of over 14,000 amiRNA-expressing plants is reported that are being made publicly available enabling screens of redundant genes in Arabidopsis. Identification of known and new genes is reported.

scholarly journals Uncovering the Genomic Potential of the Amazon River Microbiome to Degrade Rainforest Organic Matter

2020 ◽  
Author(s):  
Célio Dias Santos Júnior ◽  
Hugo Sarmento ◽  
Fernando Pellon de Miranda ◽  
Flávio Henrique-Silva ◽  
Ramiro Logares
Keyword(s):  
Organic Matter ◽  
Future Research ◽  
Amazon River ◽  
Terrestrial Organic Matter ◽  
River Waters ◽  
Gene Catalogue ◽  
Redundant Genes ◽  
Hemicellulose Degradation ◽  
Genes Encoding ◽  
Redundant Gene

Abstract Background: The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analyzing 106 metagenomes from 30 sampling points distributed along the river.Results: We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.Conclusions: Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers.

Following Phenotypes: An Exploration of Mendelian Genetics Using Arabidopsis Plants

2018 ◽  
Vol 80 (4) ◽  
pp. 291-300
Author(s):  
Courtney G. Price ◽  
Emma M. Knee ◽  
Julie A. Miller ◽  
Diana Shin ◽  
James Mann ◽  
...  
Keyword(s):  
School Level ◽  
High School Level ◽  
Resource Center ◽  
Mendelian Genetics ◽  
Hands On ◽  
Two Generations ◽  
Hands On Learning ◽  
Arabidopsis Biological Resource Center ◽  
Mutant Phenotypes ◽  
Arabidopsis Biological Resource

Arabidopsis thaliana, a model system for plant research, serves as the ideal organism for teaching a variety of basic genetic concepts including inheritance, genetic variation, segregation, and dominant and recessive traits. Rapid advances in the field of genetics make understanding foundational concepts, such as Mendel's laws, ever more important to today's biology student. Coupling these concepts with hands-on learning experiences better engages students and deepens their understanding of the topic. In our article, we present a teaching module from the Arabidopsis Biological Resource Center as a tool to engage students in lab inquiry exploring Mendelian genetics. This includes a series of protocols and assignments that guide students through growing two generations of Arabidopsis, making detailed observations of mutant phenotypes, and determining the inheritance of specific traits, thus providing a hands-on component to help teach genetics at the middle and high school level.

scholarly journals Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Célio Dias Santos-Júnior ◽  
Hugo Sarmento ◽  
Fernando Pellon de Miranda ◽  
Flávio Henrique-Silva ◽  
Ramiro Logares
Keyword(s):  
Organic Matter ◽  
Future Research ◽  
Amazon River ◽  
Terrestrial Organic Matter ◽  
River Waters ◽  
Gene Catalogue ◽  
Redundant Genes ◽  
Hemicellulose Degradation ◽  
Genes Encoding ◽  
Redundant Gene

Abstract Background The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river. Results We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course. Conclusions Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers.

Arabidopsis Biological Resource Center

1994 ◽  
Vol 12 (3) ◽  
pp. 242-244 ◽  
Author(s):  
Randy Scholl ◽  
Mary Anderson
Keyword(s):  
Biological Resource ◽  
Resource Center ◽  
Arabidopsis Biological Resource Center ◽  
Arabidopsis Biological Resource

scholarly journals Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter

2020 ◽  
Author(s):  
Célio Dias Santos Júnior ◽  
Hugo Sarmento ◽  
Fernando Pellon de Miranda ◽  
Flávio Henrique-Silva ◽  
Ramiro Logares
Keyword(s):  
Organic Matter ◽  
Future Research ◽  
Amazon River ◽  
Terrestrial Organic Matter ◽  
River Waters ◽  
Gene Catalogue ◽  
Redundant Genes ◽  
Hemicellulose Degradation ◽  
Genes Encoding ◽  
Redundant Gene

Abstract Background The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analyzing 106 metagenomes from 30 sampling points distributed along the river.Results We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.Conclusions Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers.

scholarly journals Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Vikas D. Trivedi ◽  
Pramod Kumar Jangir ◽  
Rakesh Sharma ◽  
Prashant S. Phale
Keyword(s):  
Draft Genome ◽  
Degradation Pathway ◽  
Evolutionary Analysis ◽  
Extradiol Dioxygenase ◽  
Transfer Event ◽  
New Family ◽  
New Genes ◽  
Catabolic Genes ◽  
Soil Isolate ◽  
Genes Encoding

Abstract Carbaryl (1-naphthyl N-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. Soil isolate, Pseudomonas sp. strain C5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. The draft genome analysis of strain C5pp reveals that the carbaryl catabolic genes are organized into three putative operons, ‘upper’, ‘middle’ and ‘lower’. The sequence and functional analysis led to identification of new genes encoding: i) hitherto unidentified 1-naphthol 2-hydroxylase, sharing a common ancestry with 2,4-dichlorophenol monooxygenase; ii) carbaryl hydrolase, a member of a new family of esterase; and iii) 1,2-dihydroxy naphthalene dioxygenase, uncharacterized type-II extradiol dioxygenase. The ‘upper’ pathway genes were present as a part of a integron while the ‘middle’ and ‘lower’ pathway genes were present as two distinct class-I composite transposons. These findings suggest the role of horizontal gene transfer event(s) in the acquisition and evolution of the carbaryl degradation pathway in strain C5pp. The study presents an example of assembly of degradation pathway for carbaryl.

scholarly journals Identification of plant stress-responsive determinants in arabidopsis by large-scale forward genetic screens

2006 ◽  
Vol 57 (5) ◽  
pp. 1119-1128 ◽  
Author(s):  
Hisashi Koiwa ◽  
Ray A. Bressan ◽  
Paul M. Hasegawa
Keyword(s):  
Large Scale ◽  
Plant Stress ◽  
Genetic Screens ◽  
Forward Genetic Screens

scholarly journals Dendrites with specialized glial attachments develop by retrograde extension using SAX-7 and GRDN-1

2019 ◽  
Author(s):  
Elizabeth R. Cebul ◽  
Ian G. McLachlan ◽  
Maxwell G. Heiman
Keyword(s):  
Glial Cell ◽  
Molecular Mechanism ◽  
Mammalian Brain ◽  
Cytoplasmic Protein ◽  
Genetic Screens ◽  
Sense Organs ◽  
Adhesion Protein ◽  
C Elegans ◽  
Dendrite Development ◽  
Forward Genetic Screens

ABSTRACTDendrites develop elaborate morphologies in concert with surrounding glia, but the molecules that coordinate dendrite and glial morphogenesis are mostly unknown.C. elegansoffers a powerful model for identifying such factors. Previous work in this system examined dendrites and glia that develop within epithelia, similar to mammalian sense organs. Here, we focus on the neurons BAG and URX, which are not part of an epithelium but instead form membranous attachments to a single glial cell at the nose, reminiscent of dendrite-glia contacts in the mammalian brain. We show that these dendrites develop by retrograde extension, in which the nascent dendrite endings anchor to the presumptive nose and then extend by stretch during embryo elongation. Using forward genetic screens, we find that dendrite development requires the adhesion protein SAX-7/L1CAM and the cytoplasmic protein GRDN-1/CCDC88C to anchor dendrite endings at the nose. SAX-7 acts in neurons and glia, while GRDN-1 acts in glia to non-autonomously promote dendrite extension. Thus, this work shows how glial factors can help to shape dendrites, and identifies a novel molecular mechanism for dendrite growth by retrograde extension.

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