Proteome profiling of vascular sap regarding Eucalyptus grandis, Eucalyptus urophylla, and Eucalyptus camaldulensis.

The plant vascular system is a key element for long-distance communication. Understanding its composition may provide valuable information on how plants grow and develop themselves. In this study, a quantitative proteome dataset of the vascular sap proteome of three commercially important Eucalyptus species was shown.

Proteomics research in forest trees: A 2012-2022 update.

This review is a compilation of proteomic studies on forest tree species published in the last decade (2012-2022), mostly focused on the most investigated species, including , and . Improvements in equipment, platforms, and methods in addition to the increasing availability of genomic data have favored the biological knowledge of these species at the molecular, organismal, and community levels. Integration of proteomics with physiological, biochemical and other large-scale omics in the direction of the Systems Biology, will provide a comprehensive understanding of different biological processes, from growth and development to responses to biotic and abiotic stresses.

Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population.

As one of the world's top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety var.

Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae.

Hybridization is common and considered as an important evolutionary force to increase intraspecific genetic diversity. Detecting hybridization events is crucial for understanding the evolutionary history of species and further improving molecular breeding. The studies on identifying hybridization events through the phylogenomic approach are still limited.

Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity.

Tea is one of the three most popular nonalcoholic beverages globally and has extremely high economic and cultural value. Currently, the classification, taxonomy, and evolutionary history of the tea family are largely elusive, including phylogeny, divergence, speciation, and diversity. For understanding the evolutionary history and dynamics of species diversity in Theaceae, a robust phylogenetic framework based on 1785 low-copy and 79,103 multi-copy nuclear genes from 91 tea plant genomes and transcriptome datasets had been reconstructed.

The Eucalyptus grandis chloroplast proteome: Seasonal variations in leaf development.

Chloroplast metabolism is very sensitive to environmental fluctuations and is intimately related to plant leaf development. Characterization of the chloroplast proteome dynamics can contribute to a better understanding on plant adaptation to different climate scenarios and leaf development processes. Herein, we carried out a discovery-driven analysis of the Eucalyptus grandis chloroplast proteome during leaf maturation and throughout different seasons of the year.

Using Proteomic Approaches to Unravel the Response of to Blood Feeding and Infection With .

Among the -borne pathogens, , the main aetiological agent of cat scratch disease (CSD), is of increasing comparative biomedical importance. Despite the importance of as an emergent pathogen, prevention of the diseases caused by this agent in cats, dogs and humans mostly relies on the use of ectoparasiticides. A vaccine targeting both flea fitness and pathogen competence is an attractive choice requiring the identification of flea proteins/metabolites with a dual effect.

Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry.

Eucalyptus species are widely used in the forestry industry, and a significant increase in the number of sequences available in database repositories has been observed for these species. In proteomics, a protein is identified by correlating the theoretical fragmentation spectrum derived from genomic/transcriptomic data against the experimental fragmentation mass spectrum acquired from large-scale analysis of protein mixtures. Proteogenomics is an alternative approach that can identify novel proteins encoded by regions previously considered as non-coding.

Revisiting the stem proteome of Eucalyptus grandis and Eucalyptus globulus: Identification of temperature-induced changes.

Eucalyptus grandis and Eucalyptus globulus are important species for the Brazilian forestry industry. E. grandis plantations are mainly found in tropical regions, yet E.

Metallomics-based platforms for comparing the human blood serum profiles between bipolar disorder and schizophrenia patients.

Rationale: An evaluation of bipolar disorder (BD) and schizophrenia (SCZ) was carried out, from a metallomics point of view, using native conditions, attempting to preserve the interaction between metals and biomolecules.

Method: For this task, blood serum samples from healthy individuals and patients were compared. In addition, the profiles of metal ions and metalloids involved in the pathologies were quantified, and a comparison was carried out of the protein profile in serum samples of healthy individuals and diseased patients.

Insights into temperature modulation of the Eucalyptus globulus and Eucalyptus grandis antioxidant and lignification subproteomes.

Eucalyptus grandis and Eucalyptus globulus are among the most widely cultivated trees, differing in lignin composition and plantation areas, as E. grandis is mostly cultivated in tropical regions while E. globulus is preferred in temperate areas.

Carbon assimilation in Eucalyptus urophylla grown under high atmospheric CO concentrations: A proteomics perspective.

Unlabelled: Photosynthetic organisms may be drastically affected by the future climate projections of a considerable increase in CO concentrations. Growth under a high concentration of CO could stimulate carbon assimilation-especially in C3-type plants. We used a proteomics approach to test the hypothesis of an increase in the abundance of the enzymes involved in carbon assimilation in Eucalyptus urophylla plants grown under conditions of high atmospheric CO.

Quantitative proteomic analysis of Araucaria angustifolia (Bertol.) Kuntze cell lines with contrasting embryogenic potential.

GeLC–MS/MS based label free proteomic profiling was used in the large scale identification and quantification of proteins from Brazilian pine (Araucaria angustifolia) embryogenic cell (EC) lines that showed different propensities to form somatic embryos. Using a predicted protein sequence database that was derived from A. angustifolia RNA-Seq data, 2398 non-redundant proteins were identified.

Eucalyptus urograndis stem proteome is responsive to short-term cold stress.

Eucalyptus urograndis is a hybrid eucalyptus of major economic importance to the Brazilian pulp and paper industry. Although widely used in forest nurseries around the country, little is known about the biochemical changes imposed by environmental stress in this species. In this study, we evaluated the changes in the stem proteome after short-term stimulation by exposure to low temperature.

Acute-phase protein behavior in dairy cattle herd naturally infected with Trypanosoma vivax.

Trypanosoma vivax is a hemoprotozoon that causes disease in cattle and is difficult to diagnose. The host-parasite relationship in cattle that are infected by T. vivax has only been poorly studied.

Structure, Organization, and Expression of the Alpha Prolamin Multigenic Family Bring New Insights into the Evolutionary Relationships among Grasses.

Prolamins are the major seed storage proteins of grasses. In maize and related species, prolamins are classified into α-, β-, γ-, and δ-subclasses by their solubility properties. α-prolamins are encoded by multigene families and have a secondary structure that consists of tandem α-helix repeats.

Large-scale proteome comparative analysis of developing rhizomes of the ancient vascular plant equisetum hyemale.

Horsetail (Equisetum hyemale) is a widespread vascular plant species, whose reproduction is mainly dependent on the growth and development of the rhizomes. Due to its key evolutionary position, the identification of factors that could be involved in the existence of the rhizomatous trait may contribute to a better understanding of the role of this underground organ for the successful propagation of this and other plant species. In the present work, we characterized the proteome of E.

Protein identification pipeline for the homology-driven proteomics.

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ Orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download.

Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification.

Only a small fraction of spectra acquired in LC-MS/MS runs matches peptides from target proteins upon database searches. The remaining, operationally termed background, spectra originate from a variety of poorly controlled sources and affect the throughput and confidence of database searches. Here, we report an algorithm and its software implementation that rapidly removes background spectra, regardless of their precise origin.