-
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 -
Marine Life Science & Technology May 2023Ciliates in the class Prostomatea play an important role in the global microbial loop due to their significant abundances and broad feeding strategies at the foundation...
Morphological and molecular examination of the ciliate family Lagynusidae (Protista, Ciliophora, Prostomatea) with descriptions of two new genera and two new species from China.
Ciliates in the class Prostomatea play an important role in the global microbial loop due to their significant abundances and broad feeding strategies at the foundation of food webs. Despite their importance in ecosystems, the taxonomy and systematics of this group of ciliates has long been poorly understood, with this being especially true for members of the family Lagynusidae. Here we examine four lagynusids collected from sandy beaches in China, using silver-staining and 18S rRNA gene sequencing techniques. These investigations revealed two new genera and two new species and provided details for two little known forms: gen. nov., sp. nov., (as reported by Penard. Études sur les infusoires d'eau douce. Georg and Cie, Genève, 1922) gen. nov., comb. nov., sp. nov., and (Engelmann in Z Wiss Zool 11:347-393, 1862) Quennerstedt (Acta Univ Lund 4:1-48, 1867). gen. nov. can be morphologically distinguished by having more than three dikinetidal perioral kineties. gen. nov. differs from the closely related genus in the absence of a conspicuous neck-like region. The ciliature of is revealed here for the first time, which demonstrates the classification of this species within Lagynusidae. Furthermore, (Jiang et al., 2021) comb. nov. is established according to the new finding. The results of our phylogenetic analyses based on the 18S rRNA gene support the establishment of two new genera and indicate that Lagynusidae is monophyletic, which further strengthens its valid taxonomic status.
PubMed: 37275546
DOI: 10.1007/s42995-023-00174-1 -
Molecular Phylogenetics and Evolution Nov 2023Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of...
Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of oligotrichs and choreotrichs are inconsistent with previous results based on morphological features, probably hindered by the limited information from a single gene locus. Here we provide 53 new sequences from small subunit ribosomal RNA (SSU rDNA), ITS1-5.8S rDNA-ITS2, and large subunit ribosomal RNA (LSU rDNA) gene loci in 25 oligotrich and choreotrich species. We also predict RNA secondary structures for the ITS2 regions in 55 species, 48 species of which are reported for the first time. Based on these novel data, we make a more comprehensive phylogenetic reconstruction, revealing consistency between morphological taxonomy and an updated phylogenetic system for oligotrichs and choreotrichs. With the addition of data from ciliature patterns and genes, the phylogenetic analysis of the subclass Oligotrichia suggests three evolutionary trajectories, among which: 1) Novistrombidium asserts an ancestral ciliary pattern in Oligotrichia; 2) the subgenera division of Novistrombidium and Parallelostrombidium are fully supported; 3) the three families (Tontoniidae, Pelagostrombidiidae and Cyrtostrombidiidae) all evolved from the most diverse family Strombidiidae, which explains why strombidiids consistently form polyphyletic clades. In the subclass Choreotrichia, Strombidinopsis likely possesses an ancestral position to other choreotrichs, and both phylogenetic analysis and RNA secondary structure prediction support the hypothesis that tintinnids may have evolved from Strombidinopsis. The results presented here offer an updated hypothesis for the evolutionary history of oligotrichs and choreotrichs based on new evidence obtained by expanding sampling of molecular information across multiple gene loci.
Topics: Humans; Phylogeny; Ciliophora; DNA, Ribosomal; RNA; RNA, Ribosomal
PubMed: 37648182
DOI: 10.1016/j.ympev.2023.107911 -
Molecular Phylogenetics and Evolution Sep 2023Peritrichs are one of the largest groups within the class Oligohymenophorea. They have a worldwide distribution and a high degree of species diversity. Using the...
Comparative genomics provides insights into the phylogeny and environmental adaptations of Peritrichia (Protista, Ciliophora) - A potential resource for environmental pollution control and bioremediation.
Peritrichs are one of the largest groups within the class Oligohymenophorea. They have a worldwide distribution and a high degree of species diversity. Using the single-cell genome sequencing technique, we obtained the genomes of five sessilid peritrichs. Combining both genomic and transcriptomic data of other publicly available oligohymenophorean ciliates (including the genomes of three sessilid peritrichs from our team's previous study), we conducted a comparative genomics study. Our phylogenomic analyses using both maximum likelihood and Bayesian inference methods recovered the subclass Peritrichia and each of its two orders (Sessilida and Mobilida) as being monophyletic. The non-monophyly of two families (Vorticellidae and Zoothamniidae) was also well supported in both trees. Molecular clock analysis showed that the origin of the subclass Peritrichia was estimated to be during the late Proterozoic. We also analyzed the stop codon usage of 44 oligohymenophoreans. The results showed that most of these species used TGA as the biased stop codon and reassigned the other two stop codons (TAA and TAG) to code amino acids. In addition, we found that the presence of a typical peritrich lorica is a plesiomorphic character of the family Vaginicolidae. Through GO enrichment analysis for group-specific orthogroups of Vaginicolidae, we successfully identified the biological process and molecular function GO terms that were linked with the typical peritrich lorica, including three glycosaminoglycan-related and two chitin-related GO terms. Finally, our enrichment analyses of significantly expanded gene families in Peritrichia found that sessilids were more tolerant to environmental stress (mainly organic matter) than mobilids, suggesting that peritrich lineages (especially sessilids) may have the potential for application in environmental pollution control and bioremediation. Together, the results presented in this study will facilitate wider genome-scale phylogenetic analyses of Peritrichia and deepen the understanding of their unique advantages for environmental pollution control bioremediation.
Topics: Animals; Phylogeny; Bayes Theorem; Biodegradation, Environmental; Oligohymenophorea; Ciliophora; Genomics; Polyplacophora
PubMed: 37263457
DOI: 10.1016/j.ympev.2023.107835 -
Scientific Reports Jul 2019Assembling composite DNA modules from custom DNA parts has become routine due to recent technological breakthroughs such as Golden Gate modular cloning. Using Golden...
Assembling composite DNA modules from custom DNA parts has become routine due to recent technological breakthroughs such as Golden Gate modular cloning. Using Golden Gate, one can efficiently assemble custom transcription units and piece units together to generate higher-order assemblies. Although Golden Gate cloning systems have been developed to assemble DNA plasmids required for experimental work in model species, they are not typically applicable to organisms from other kingdoms. Consequently, a typical molecular biology laboratory working across kingdoms must use multiple cloning strategies to assemble DNA constructs for experimental assays. To simplify the DNA assembly process, we developed a multi-kingdom (MK) Golden Gate assembly platform for experimental work in species from the kingdoms Fungi, Eubacteria, Protista, Plantae, and Animalia. Plasmid backbone and part overhangs are consistent across the platform, saving both time and resources in the laboratory. We demonstrate the functionality of the system by performing a variety of experiments across kingdoms including genome editing, fluorescence microscopy, and protein interaction assays. The versatile MK system therefore streamlines the assembly of modular DNA constructs for biological assays across a range of model organisms.
Topics: Animals; Bacteria; Cloning, Molecular; Female; Gene Editing; Humans; Oocytes; Organisms, Genetically Modified; Plants; Plasmids; Proteins; Recombinant Proteins; Transcription, Genetic; Transgenes; Trypanosoma; Xenopus laevis; Yeasts
PubMed: 31300661
DOI: 10.1038/s41598-019-46171-2 -
Journal of Experimental Psychology.... Jul 2021Since the beginning of the 21st century, the Minimal Cognition approach has emerged vigorously, focusing on the study of the adaptive behavior of the simplest organisms,... (Review)
Review
Since the beginning of the 21st century, the Minimal Cognition approach has emerged vigorously, focusing on the study of the adaptive behavior of the simplest organisms, including bacteria, assuming that they are sentient and information-processing entities. Although Minimal Cognition has occasionally used Pavlovian methods to try to demonstrate Associative Learning, neither the Psychology of Learning nor the Comparative Psychology traditions are prominent in the movement. However, the Psychology of Learning approach, with its highly sophisticated experimental designs, has done a great deal of research on Associative Learning in animals and carried out several studies on plants and unicellular organisms. The present work offers a comprehensive review of these experimental results, among invertebrates, plants and unicellular organisms (paramecia and the amoeba ) showing that, while there are increasing instances of Associative Learning in many invertebrate (and also many with no data) there is no adequate evidence of it in unicellular protists (despite more than a century of experiments with paramecia and amoeba) or in plants (despite recent results that so claim). We then consider the alternative offered by Minimal Cognition and suggest some complementary ideas, from a Comparative Developmental Psychology approach, which we call "Minimal Development." (PsycInfo Database Record (c) 2021 APA, all rights reserved).
Topics: Animals; Association Learning; Cognition; Conditioning, Classical; Invertebrates; Learning
PubMed: 34618525
DOI: 10.1037/xan0000306 -
BMC Microbiology May 2022The genus Euplotes Ehrenberg, 1830, one of the most complicated and confused taxa, contains about 160 nominal species. It was once proposed to be divided into four...
BACKGROUND
The genus Euplotes Ehrenberg, 1830, one of the most complicated and confused taxa, contains about 160 nominal species. It was once proposed to be divided into four genera, two of which were proved to be non-monophyletic. At least 19 new species have been discovered in the past decade, implying that there is a large undiscovered diversity of this genus.
RESULTS
The morphology of two new freshwater euplotid ciliates, Euplotes chongmingensis n. sp. and E. paramieti n. sp., isolated from Shanghai, China, were investigated using live observations, protargol staining, and Chatton-Lwoff silver staining method. Euplotes chongmingensis is characterized by its small size (40-50 × 25-35 μm), about 24 adoral membranelles, 10 frontoventral cirri, two marginal and two caudal cirri, eight dorsolateral kineties with 11-16 dikinetids in the mid-dorsolateral kinety and a double type of silverline system. Euplotes paramieti n. sp. is 180-220 × 110-155 μm in vivo and strongly resembles E. amieti but having a difference of 57 bp in their SSU rRNA gene sequences. Phylogenetic analyses based on SSU rRNA gene sequence data were used to determine the systematic positions of these new taxa.
CONCLUSIONS
The description of two new freshwater taxa and their SSU rRNA gene sequences improve knowledge of biodiversity and enrich the database of euplotids. Furthermore, it offers a reliable reference for environmental monitoring and resource investigations.
Topics: China; Ciliophora; DNA, Protozoan; Euplotes; Genes, rRNA; Phylogeny
PubMed: 35578180
DOI: 10.1186/s12866-022-02543-9