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Nature Methods Jun 2015Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular...
Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular data. We provide an open-source software pipeline, which we call MS-DIAL, for DIA-based identification and quantification of small molecules by mass spectral deconvolution. For a reversed-phase LC-MS/MS analysis of nine algal strains, MS-DIAL using an enriched LipidBlast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between the algal strains.
Topics: Chlorophyta; Chromatography, Liquid; Gene Expression Regulation, Plant; Lipid Metabolism; Lipids; Metabolome; Software; Species Specificity; Tandem Mass Spectrometry
PubMed: 25938372
DOI: 10.1038/nmeth.3393 -
Journal of Phycology Apr 2020Snow or glacial algae are found on all continents, and most species are in the Chlamydomonadales (Chlorophyta) and Zygnematales (Streptophyta). Other algal groups... (Review)
Review
Snow or glacial algae are found on all continents, and most species are in the Chlamydomonadales (Chlorophyta) and Zygnematales (Streptophyta). Other algal groups include euglenoids, cryptomonads, chrysophytes, dinoflagellates, and cyanobacteria. They may live under extreme conditions of temperatures near 0°C, high irradiance levels in open exposures, low irradiance levels under tree canopies or deep in snow, acidic pH, low conductivity, and desiccation after snow melt. These primary producers may color snow green, golden-brown, red, pink, orange, or purple-grey, and they are part of communities that include other eukaryotes, bacteria, archaea, viruses, and fungi. They are an important component of the global biosphere and carbon and water cycles. Life cycles in the Chlamydomonas-Chloromonas-Chlainomonas complex include migration of flagellates in liquid water and formation of resistant cysts, many of which were identified previously as other algae. Species differentiation has been updated through the use of metagenomics, lipidomics, high-throughput sequencing (HTS), multi-gene analysis, and ITS. Secondary metabolites (astaxanthin in snow algae and purpurogallin in glacial algae) protect chloroplasts and nuclei from damaging PAR and UV, and ice binding proteins (IBPs) and polyunsaturated fatty acids (PUFAs) reduce cell damage in subfreezing temperatures. Molecular phylogenies reveal that snow algae in the Chlamydomonas-Chloromonas complex have invaded the snow habitat at least twice, and some species are polyphyletic. Snow and glacial algae reduce albedo, accelerate the melt of snowpacks and glaciers, and are used to monitor climate change. Selected strains of these algae have potential for producing food or fuel products.
Topics: Chlamydomonas; Chlorophyceae; Chlorophyta; Ecosystem; Ice Cover
PubMed: 31825096
DOI: 10.1111/jpy.12952 -
Trends in Plant Science Sep 2018The evolution of sex determination continues to pose major questions in biology. Sex-determination mechanisms control reproductive cell differentiation and development... (Review)
Review
The evolution of sex determination continues to pose major questions in biology. Sex-determination mechanisms control reproductive cell differentiation and development of sexual characteristics in all organisms, from algae to animals and plants. While the underlying processes defining sex (meiosis and recombination) are conserved, sex-determination mechanisms are highly labile. In particular, a flow of new discoveries has highlighted several fascinating features of the previously understudied haploid UV sex determination and related mating systems found in diverse photosynthetic taxa including green algae, bryophytes, and brown algae. Analyses integrating information from these systems and contrasting them with classical XY and ZW systems are providing exciting insights into both the universality and the diversity of sex-determining chromosomes across eukaryotes.
Topics: Biological Evolution; Bryopsida; Chlorophyta; Haploidy; Meiosis; Phaeophyceae; Reproduction; Sex Chromosomes
PubMed: 30007571
DOI: 10.1016/j.tplants.2018.06.005 -
Plant Physiology Dec 2023Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings,... (Review)
Review
Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.
Topics: Chlorophyta; Polysaccharides; Extracellular Matrix; Plants; Glycoproteins
PubMed: 37399237
DOI: 10.1093/plphys/kiad384 -
Microbiology (Reading, England) Nov 2009The presence and deteriorating action of micro-organisms on monuments and stone works of art have received considerable attention in the last few years. Knowledge of the... (Review)
Review
The presence and deteriorating action of micro-organisms on monuments and stone works of art have received considerable attention in the last few years. Knowledge of the microbial populations living on stone materials is the starting point for successful conservation treatment and control. This paper reviews the literature on cyanobacteria and chlorophyta that cause deterioration of stone cultural heritage (outdoor monuments and stone works of art) in European countries of the Mediterranean Basin. Some 45 case studies from 32 scientific papers published between 1976 and 2009 were analysed. Six lithotypes were considered: marble, limestone, travertine, dolomite, sandstone and granite. A wide range of stone monuments in the Mediterranean Basin support considerable colonization of cyanobacteria and chlorophyta, showing notable biodiversity. About 172 taxa have been described by different authors, including 37 genera of cyanobacteria and 48 genera of chlorophyta. The most widespread and commonly reported taxa on the stone cultural heritage in the Mediterranean Basin are, among cyanobacteria, Gloeocapsa, Phormidium and Chroococcus and, among chlorophyta, Chlorella, Stichococcus and Chlorococcum. The results suggest that cyanobacteria and chlorophyta colonize a wide variety of substrata and that this is related primarily to the physical characteristics of the stone surface, microclimate and environmental conditions and secondarily to the lithotype.
Topics: Biodegradation, Environmental; Biodiversity; Calcium Carbonate; Chlorophyta; Construction Materials; Cyanobacteria; Mediterranean Region; Sculpture; Silicon Dioxide
PubMed: 19778965
DOI: 10.1099/mic.0.032508-0 -
Marine Drugs Dec 2016With the advent of modern biotechnology, microorganisms from diverse lineages have been used to produce bio-based feedstocks and bioactive compounds. Many of these... (Review)
Review
With the advent of modern biotechnology, microorganisms from diverse lineages have been used to produce bio-based feedstocks and bioactive compounds. Many of these compounds are currently commodities of interest, in a variety of markets and their utility warrants investigation into improving their production through strain development. In this review, we address the issue of strain improvement in a group of organisms with strong potential to be productive "cell factories": the photosynthetic microalgae. Microalgae are a diverse group of phytoplankton, involving polyphyletic lineage such as green algae and diatoms that are commonly used in the industry. The photosynthetic microalgae have been under intense investigation recently for their ability to produce commercial compounds using only light, CO₂, and basic nutrients. However, their strain improvement is still a relatively recent area of work that is under development. Importantly, it is only through appropriate engineering methods that we may see the full biotechnological potential of microalgae come to fruition. Thus, in this review, we address past and present endeavors towards the aim of creating productive algal cell factories and describe possible advantageous future directions for the field.
Topics: Animals; Biotechnology; Chlorophyta; Genetic Engineering; Humans; Microalgae; Photosynthesis
PubMed: 27983586
DOI: 10.3390/md14120225 -
Biomolecules Jul 2019Photosynthesis is a biochemical process essential for life, serving as the ultimate source of chemical energy for phototrophic and heterotrophic life forms. Since the... (Review)
Review
Photosynthesis is a biochemical process essential for life, serving as the ultimate source of chemical energy for phototrophic and heterotrophic life forms. Since the machinery of the photosynthetic electron transport chain is quite complex and is unlikely to have evolved multiple independent times, it is believed that this machinery has been transferred to diverse eukaryotic organisms by endosymbiotic events involving a eukaryotic host and a phototrophic endosymbiont. Thus, photoautotrophy, as a benefit, is transmitted through the evolution of plastids. However, many eukaryotes became secondarily heterotrophic, reverting to hetero-osmotrophy, phagotrophy, or parasitism. Here, I briefly review the constructive evolution of plastid endosymbioses and the consequential switch to reductive evolution involving losses of photosynthesis and plastids and the evolution of parasitism from a photosynthetic ancestor.
Topics: Chlorophyta; Electron Transport; Heterotrophic Processes; Symbiosis
PubMed: 31288476
DOI: 10.3390/biom9070266 -
Genes Aug 2022Considering the phylogenetic differences in the taxonomic framework of the Chaetophorales as determined by the use of nuclear molecular markers or chloroplast genes, the...
Considering the phylogenetic differences in the taxonomic framework of the Chaetophorales as determined by the use of nuclear molecular markers or chloroplast genes, the current study was the first to use phylotranscriptomic analyses comparing the transcriptomes of 12 Chaetophorales algal species. The results showed that a total of 240,133 gene families and 143 single-copy orthogroups were identified. Based on the single-copy orthogroups, supergene analysis and the coalescent-based approach were adopted to perform phylotranscriptomic analysis of the Chaetophorales. The phylogenetic relationships of most species were consistent with those of phylogenetic analyses based on the chloroplast genome data rather than nuclear molecular markers. The Schizomeriaceae and the Aphanochaetaceae clustered into a well-resolved basal clade in the Chaetophorales by either strategy. Evolutionary analyses of divergence time and substitution rate also revealed that the closest relationships existed between the Schizomeriaceae and Aphanochaetaceae. All species in the Chaetophorales exhibited a large number of expanded and contracted gene families, in particular the common ancestor of the Schizomeriaceae and Aphanochaetaceae. The only terrestrial alga, , had the greatest number of expanded gene families, which were associated with increased fatty acid biosynthesis. Phylotranscriptomic and evolutionary analyses all robustly identified the unique taxonomic relationship of Chaetophorales consistent with chloroplast genome data, proving the advantages of high-throughput data in phylogeny.
Topics: Base Sequence; Chlorophyceae; Chlorophyta; DNA, Chloroplast; Evolution, Molecular; Phylogeny
PubMed: 36011300
DOI: 10.3390/genes13081389 -
The Plant Journal : For Cell and... Aug 2014Algae are found in all aquatic and many terrestrial habitats. They are dominant in phytoplankton and biofilms thereby contributing massively to global primary... (Review)
Review
Algae are found in all aquatic and many terrestrial habitats. They are dominant in phytoplankton and biofilms thereby contributing massively to global primary production. Since algae comprise photosynthetic representatives of the various protoctist groups their physiology and appearance is highly diverse. This diversity is also mirrored in their characteristic life cycles that exhibit various facets of ploidy and duration of the asexual phase as well as gamete morphology. Nevertheless, sexual reproduction in unicellular and colonial algae usually has as common motive that two specialized, sexually compatible haploid gametes establish physical contact and fuse. To guarantee mating success, processes during sexual reproduction are highly synchronized and regulated. This review focuses on sex pheromones of algae that play a key role in these processes. Especially, the diversity of sexual strategies as well as of the compounds involved are the focus of this contribution. Discoveries connected to algal pheromone chemistry shed light on the role of key evolutionary processes, including endosymbiotic events and lateral gene transfer, speciation and adaptation at all phylogenetic levels. But progress in this field might also in the future provide valid tools for the manipulation of aquaculture and environmental processes.
Topics: Chlorophyta; Pheromones; Reproduction; Stramenopiles
PubMed: 24597605
DOI: 10.1111/tpj.12496 -
Molecules (Basel, Switzerland) May 2022In this study, we aimed to isolate bacteria capable of degrading the polysaccharide ulvan from the green algae sp. (Chlorophyta, Ulvales, Ulvaceae) in marine...
In this study, we aimed to isolate bacteria capable of degrading the polysaccharide ulvan from the green algae sp. (Chlorophyta, Ulvales, Ulvaceae) in marine environments. We isolated 13 ulvan-degrading bacteria and observed high diversity at the genus level. Further, the genera , , , and , which can degrade ulvan, were successfully isolated for the first time from marine environments. Among the 13 isolates, only one isolate ( sp.) showed the ability not only to produce externally expressed ulvan lyase, but also to be periplasmic or on the cell surface. From the results of the full-genome analysis, lyase was presumed to be a member of the PL25 (BNR4) family of ulvan lyases, and the bacterium also contained the sequence for glycoside hydrolase (GH43, GH78 and GH88), which is characteristic of other ulvan-degrading bacteria. Notably, this bacterium has a unique ulvan lyase gene not previously reported.
Topics: Chlorophyta; Flavobacteriaceae; Polysaccharides; Ulva
PubMed: 35684358
DOI: 10.3390/molecules27113420