Multi class intracellular protein targeting predictions in diatoms and other algae with complex plastids: ASAFind 2.0 [PDF]
arXiv, 2023 Cells of diatoms and related algae with complex plastids of red algal origin are highly compartmentalized. These plastids are surrounded by four envelope membranes, which also define the periplastidic compartment (PPC), the space between the second and third membranes.
arxiv
Comparison of different versions of SignalP and TargetP for diatom plastid protein predictions with ASAFind [PDF]
Matters (ISSN: 2297-8240), e202005000001 (2020), 2023 Plastid targeted proteins of diatoms and related algae can be predicted with high sensitivity and specificity using the ASAFind method published in 2015. ASAFind predictions rely on SignalP predictions of endoplasmic reticulum (ER) targeting signal peptides. Recently (in 2019), a new version of SignalP was released, SignalP 5.0.
arxiv
Comparative Analysis of Plastid Genomes Using Pangenome Research ToolKit (PGR-TK) [PDF]
arXiv, 2023 Plastid genomes (plastomes) of angiosperms are of great interest among biologists. High-throughput sequencing is making many such genomes accessible, increasing the need for tools to perform rapid comparative analysis. This exploratory analysis investigates whether the Pangenome Research Tool Kit (PGR-TK) is suitable for analyzing plastomes.
arxiv
How a simple chloroplast psbA gene mutation changed world agriculture [PDF]
arXiv, 2023 Atrazine as a weed control tactic profoundly changed world agriculture. Long-term use revealed resistant biotypes, R, with a single base pair mutation of the chloroplast psbA gene. The R phenotype emerged from a sequential cascade of pleiotropic effects from the plastid to the whole plant.
arxiv
A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data [PDF]
arXiv, 2013 Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this complex information.
arxiv
Reconstruction of the 3D structure and developmental history of plant cells and tissues [PDF]
arXiv, 2012 Modern spatial microscopy has provided developmental biology with powerful research tools. However, the recent significant technological breakthroughs have inevitably led to technical "bottlenecks" for the application of the new procedures to other tasks. We have developed a protocol for the 3D reconstruction of plant organelles and tissues from stacks
arxiv
Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation [PDF]
arXiv, 2019 Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment.
arxiv
On Certain Plastids, with Special Reference to the Protein Bodies of Zea, Ricinus, and Conopholis [PDF]
, 1921 David M. Mottier
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The Control of Plastid Pigment Formation by a Virescent Gene, Pale-Yellow-1, of maize. [PDF]
, 1956 Robert E. Kay, Bernard O. Phinney
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The Mitochondrial Genome of Cathaya argyrophylla Reaches 18.99 Mb: Analysis of Super-Large Mitochondrial Genomes in Pinaceae [PDF]
arXivMitochondrial genomes in the Pinaceae family are notable for their large size and structural complexity. In this study, we sequenced and analyzed the mitochondrial genome of Cathaya argyrophylla, an endangered and endemic Pinaceae species, uncovering a genome size of 18.99 Mb, meaning the largest mitochondrial genome reported to date.
arxiv