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Biodiversity Data Journal 2022The species checklists for Bhutan published in the Global Biodiversity Information Facility (GBIF) were originally collated for the publication 'Biodiversity Statistics...
BACKGROUND
The species checklists for Bhutan published in the Global Biodiversity Information Facility (GBIF) were originally collated for the publication 'Biodiversity Statistics of Bhutan 2017, A Preliminary Baseline' (BSB 2017). This document was published in 2019 and is the first comprehensive overview of Bhutan's species richness, recording more than 11,000 species across all five kingdoms. Collation of biodiversity checklists has been limited in Bhutan. Thus, this paper and its associated data provide an overview of all species from the kingdoms Plantae, Animalia, Fungi, Chromista and Eubacteria in the country that have been recorded in scientific publications.
NEW INFORMATION
The checklists showcase 11,175 species from the kingdoms Plantae, Animalia, Fungi, Chromista and Eubacteria. Research conducted into identifying species from the kingdoms Protista and Archaebacteria revealed zero records. These checklists include at least 33 species new to science and 566 species new to Bhutan, discovered between 2009 and 2017. Unidentified species are not taken into account in this publication.
PubMed: 36761637
DOI: 10.3897/BDJ.10.e83798 -
Methods in Molecular Biology (Clifton,... 2022Physarum polycephalum is a protist slime mould that exhibits a high degree of responsiveness to its environment through a complex network of tubes and cytoskeletal...
Physarum polycephalum is a protist slime mould that exhibits a high degree of responsiveness to its environment through a complex network of tubes and cytoskeletal components that coordinate behavior across its unicellular, multinucleated body. Physarum has been used to study decision making, problem solving, and mechanosensation in aneural biological systems. The robust generative and repair capacities of Physarum also enable the study of whole-body regeneration within a relatively simple model system. Here we describe methods for growing, imaging, quantifying, and sampling Physarum that are adapted for investigating regeneration and repair.
Topics: Adaptation, Physiological; Models, Biological; Physarum polycephalum
PubMed: 35359302
DOI: 10.1007/978-1-0716-2172-1_3 -
Cancer Letters Jun 2021Hippo pathway is a master regulator of development, cell proliferation, stem cell function, tissue regeneration, homeostasis, and organ size control. Hippo pathway... (Review)
Review
Hippo pathway is a master regulator of development, cell proliferation, stem cell function, tissue regeneration, homeostasis, and organ size control. Hippo pathway relays signals from different extracellular and intracellular events to regulate cell behavior and functions. Hippo pathway is conserved from Protista to eukaryotes. Deregulation of the Hippo pathway is associated with numerous cancers. Alteration of the Hippo pathway results in cell invasion, migration, disease progression, and therapy resistance in cancers. However, the function of the various components of the mammalian Hippo pathway is yet to be elucidated in detail especially concerning tumor biology. In the present review, we focused on the Hippo pathway in different model organisms, its regulation and deregulation, and possible therapeutic targets for cancer treatment.
Topics: Animals; Antineoplastic Agents; Caenorhabditis elegans Proteins; Drosophila Proteins; Drug Resistance, Neoplasm; Epigenesis, Genetic; Exosomes; Fungal Proteins; Gene Expression Regulation, Neoplastic; Hippo Signaling Pathway; Humans; Intracellular Signaling Peptides and Proteins; Molecular Targeted Therapy; Neoplasms; Protein Serine-Threonine Kinases; Signal Transduction; Tumor Microenvironment
PubMed: 33737002
DOI: 10.1016/j.canlet.2021.03.006 -
BMC Ecology and Evolution Oct 2022Na,K-ATPase is a key protein in maintaining membrane potential that has numerous additional cellular functions. Its catalytic subunit (α), found in a wide range of...
BACKGROUND
Na,K-ATPase is a key protein in maintaining membrane potential that has numerous additional cellular functions. Its catalytic subunit (α), found in a wide range of organisms from prokaryotes to complex eukaryote. Several studies have been done to identify the functions as well as determining the evolutionary relationships of the α-subunit. However, a survey of a larger collection of protein sequences according to sequences similarity and their attributes is very important in revealing deeper evolutionary relationships and identifying specific amino acid differences among evolutionary groups that may have a functional role.
RESULTS
In this study, 753 protein sequences using phylogenetic tree classification resulted in four groups: prokaryotes (I), fungi and various kinds of Protista and some invertebrates (II), the main group of invertebrates (III), and vertebrates (IV) that was consisted with species tree. The percent of sequences that acquired a specific motif for the α/β subunit assembly increased from group I to group IV. The vertebrate sequences were divided into four groups according to isoforms with each group conforming to the evolutionary path of vertebrates from fish to tetrapods. Data mining was used to identify the most effective attributes in classification of sequences. Using 1252 attributes extracted from the sequences, the decision tree classified them in five groups: Protista, prokaryotes, fungi, invertebrates and vertebrates. Also, vertebrates were divided into four subgroups (isoforms). Generally, the count of different dipeptides and amino acid ratios were the most significant attributes for grouping. Using alignment of sequences identified the effective position of the respective dipeptides in the separation of the groups. So that GC is apparently involved in the separation of vertebrates from the four other organism groups, and DH, FK, and KC were involved in separation vertebrate isoform types.
CONCLUSION
The application of phylogenetic and decision tree analysis for Na,K-ATPase, provides a better understanding of the evolutionary changes according to the amino acid sequence and its related properties that could lead to the identification of effective attributes in the separation of sequences in different groups of phylogenetic tree. In this study, key evolution-related dipeptides are identified which can guide future experimental studies.
Topics: Animals; Sodium-Potassium-Exchanging ATPase; Phylogeny; Computational Biology; Vertebrates; Invertebrates; Sodium; Dipeptides; Amino Acids
PubMed: 36289471
DOI: 10.1186/s12862-022-02071-0 -
Antioxidants & Redox Signaling Sep 2008Excessive hydrogen peroxide is harmful for almost all cell components, so its rapid and efficient removal is of essential importance for aerobically living organisms.... (Review)
Review
Excessive hydrogen peroxide is harmful for almost all cell components, so its rapid and efficient removal is of essential importance for aerobically living organisms. Conversely, hydrogen peroxide acts as a second messenger in signal-transduction pathways. H(2)O(2) is degraded by peroxidases and catalases, the latter being able both to reduce H(2)O(2) to water and to oxidize it to molecular oxygen. Nature has evolved three protein families that are able to catalyze this dismutation at reasonable rates. Two of the protein families are heme enzymes: typical catalases and catalase-peroxidases. Typical catalases comprise the most abundant group found in Eubacteria, Archaeabacteria, Protista, Fungi, Plantae, and Animalia, whereas catalase-peroxidases are not found in plants and animals and exhibit both catalatic and peroxidatic activities. The third group is a minor bacterial protein family with a dimanganese active site called manganese catalases. Although catalyzing the same reaction (2 H(2)O(2)--> 2 H(2)O+ O(2)), the three groups differ significantly in their overall and active-site architecture and the mechanism of reaction. Here, we present an overview of the distribution, phylogeny, structure, and function of these enzymes. Additionally, we report about their physiologic role, response to oxidative stress, and about diseases related to catalase deficiency in humans.
Topics: Amino Acid Sequence; Bacteria; Catalase; Evolution, Molecular; Humans; Models, Molecular; Molecular Sequence Data; Phylogeny; Protein Structure, Tertiary; Sequence Homology, Amino Acid
PubMed: 18498226
DOI: 10.1089/ars.2008.2046 -
Nucleic Acids Research Jul 2012Homing endonucleases (HEs) are highly specific DNA-cleaving enzymes that are encoded by invasive DNA elements (usually mobile introns or inteins) within the genomes of... (Review)
Review
Homing endonucleases (HEs) are highly specific DNA-cleaving enzymes that are encoded by invasive DNA elements (usually mobile introns or inteins) within the genomes of phage, bacteria, archea, protista and eukaryotic organelles. Six unique structural HE families, that collectively span four distinct nuclease catalytic motifs, have been characterized to date. Members of each family display structural homology and functional relationships to a wide variety of proteins from various organisms. The biological functions of those proteins are highly disparate and include non-specific DNA-degradation enzymes, restriction endonucleases, DNA-repair enzymes, resolvases, intron splicing factors and transcription factors. These relationships suggest that modern day HEs share common ancestors with proteins involved in genome fidelity, maintenance and gene expression. This review summarizes the results of structural studies of HEs and corresponding proteins from host organisms that have illustrated the manner in which these factors are related.
Topics: Amino Acid Motifs; Colicins; DNA Repair Enzymes; DNA Restriction Enzymes; Endodeoxyribonucleases; Evolution, Molecular; Gene Expression Regulation; Proteins
PubMed: 22406833
DOI: 10.1093/nar/gks226 -
Evidence-based Complementary and... 2022Systemic arterial hypertension is one of the most common cardiovascular risks, corresponding to 45% of deaths involving CVDs. The use of natural products, such as... (Review)
Review
BACKGROUND
Systemic arterial hypertension is one of the most common cardiovascular risks, corresponding to 45% of deaths involving CVDs. The use of natural products, such as medicinal plants, belongs to a millennial part of human therapeutics history and has been employed as an alternative anti-hypertensive treatment.
OBJECTIVE
The present review aims to prospect some natural products already experimentally assayed against arterial hypertension through scientific virtual libraries and patent documents over the past 20 years. . This is a systematic review of the adoption of the PRISMA protocol and a survey of the scientific literature that synthesizes the results from published articles between 2001 and 2020 concerning the use of medicinal plants in the management of hypertension, including which parts of the plant or organism are used, as well as the mechanisms of action underlying the anti-hypertensive effect. Furthermore, a technological prospection was also carried out in patent offices from different countries in order to check technologies based on natural products claimed for the treatment or prevention of hypertension. . Scientific articles where a natural product had been experimentally assayed for anti-hypertensive activity (part of plants, plant extracts, and products derived from other organisms) were included. . The selected abstracts of the articles and patent documents were submitted to a rigorous reading process. Those articles and patents that were not related to anti-hypertensive effects and claimed potential applications were excluded from the search.
RESULTS
Eighty specimens of biological species that showed anti-hypertensive activity were recovered, with 01 representative from the kingdom Fungi and 02 from the kingdom Protista, with emphasis on the families Asteraceae and Lamiaceae, with 6 representatives each. Leaves and aerial parts were the most used parts of the plants for the extraction of anti-hypertensive products, with maceration being the most used extraction method. Regarding phytochemical analyses, the most described classes of biomolecules in the reviewed works were alkaloids, terpenes, coumarins, flavonoids, and peptides, with the reduction of oxidative stress and the release of NO among the mechanisms of action most involved in this process. Regarding the number of patent filings, China was the country that stood out as the main one, with 813 registrations.
CONCLUSION
The anti-hypertensive activity of natural products is still little explored in Western countries. Besides, China and India have shown more results in this area than other countries, confirming the strong influence of traditional medicine in these countries.
PubMed: 35769156
DOI: 10.1155/2022/8499625 -
Scientific Data Jul 2022The Country Compendium of the Global Register of Introduced and Invasive Species (GRIIS) is a collation of data across 196 individual country checklists of alien...
The Country Compendium of the Global Register of Introduced and Invasive Species (GRIIS) is a collation of data across 196 individual country checklists of alien species, along with a designation of those species with evidence of impact at a country level. The Compendium provides a baseline for monitoring the distribution and invasion status of all major taxonomic groups, and can be used for the purpose of global analyses of introduced (alien, non-native, exotic) and invasive species (invasive alien species), including regional, single and multi-species taxon assessments and comparisons. It enables exploration of gaps and inferred absences of species across countries, and also provides one means for updating individual GRIIS Checklists. The Country Compendium is, for example, instrumental, along with data on first records of introduction, for assessing and reporting on invasive alien species targets, including for the Convention on Biological Diversity and Sustainable Development Goals. The GRIIS Country Compendium provides a baseline and mechanism for tracking the spread of introduced and invasive alien species across countries globally. Design Type(s) Data integration objective ● Observation design Measurement Type(s) Alien species occurrence ● Evidence of impact invasive alien species assessment objective Technology Type(s) Agent expert ● Data collation Factor Type(s) Geographic location ● Origin / provenance ● Habitat Sample Characteristics - Organism Animalia ● Bacteria ● Chromista ● Fungi ● Plantae ● Protista (Protozoa) ● Viruses Sample Characteristics - Location Global countries.
Topics: Biodiversity; Ecosystem; Eukaryota; Fungi; Introduced Species; Plants
PubMed: 35810161
DOI: 10.1038/s41597-022-01514-z -
International Journal For Parasitology Oct 2011Perkinsus marinus (Phylum Perkinsozoa) is a protozoan parasite that has devastated natural and farmed oyster populations in the USA, significantly affecting the... (Review)
Review
Perkinsus marinus (Phylum Perkinsozoa) is a protozoan parasite that has devastated natural and farmed oyster populations in the USA, significantly affecting the shellfish industry and the estuarine environment. The other two genera in the phylum, Parvilucifera and Rastrimonas, are parasites of microeukaryotes. The Perkinsozoa occupies a key position at the base of the dinoflagellate branch, close to its divergence from the Apicomplexa, a clade that includes parasitic protista, many harbouring a relic plastid. Thus, as a taxon that has also evolved toward parasitism, the Perkinsozoa has attracted the attention of biologists interested in the evolution of this organelle, both in its ultrastructure and the conservation, loss or transfer of its genes. A review of the recent literature reveals mounting evidence in support of the presence of a relic plastid in P. marinus, including the presence of multimembrane structures, characteristic metabolic pathways and proteins with a bipartite N-terminal extension. Further, these findings raise intriguing questions regarding the potential functions and unique adaptation of the putative plastid and/or plastid genes in the Perkinsozoa. In this review we analyse the above-mentioned evidence and evaluate the potential future directions and expected benefits of addressing such questions. Given the rapidly expanding molecular/genetic resources and methodological toolbox for Perkinsus spp., these organisms should complement the currently established models for investigating plastid evolution within the Chromalveolata.
Topics: Alveolata; Amino Acid Sequence; Animals; Evolution, Molecular; Humans; Microscopy, Electron; Models, Biological; Molecular Sequence Data; Ostreidae; Plastids; Sequence Alignment; United States
PubMed: 21889509
DOI: 10.1016/j.ijpara.2011.07.008