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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 -
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 -
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 -
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 -
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 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 -
Frontiers in Microbiology 2021Strombidiids are common free-living ciliates that have colonized coastal and open oceanic waters across the world. In recent years, numerous new taxa and gene sequences...
Strombidiids are common free-living ciliates that have colonized coastal and open oceanic waters across the world. In recent years, numerous new taxa and gene sequences of strombidiids have been reported, revealing a large diversity of both their morphologic and genetic features. Here, we compare the taxonomic characters of all genera in the family Strombidiidae, provide a key to their identification, and investigate their molecular phylogeny. In addition, we analyze their regional distribution based on faunal data accumulated in China and attempt to infer their global distribution based on SSU rRNA gene sequence data. The current work revises the systematics of strombidiids based on morphologic, phylogenetic, and biogeographic evidence and provides a genus-level review of marine strombidiids.
PubMed: 34603227
DOI: 10.3389/fmicb.2021.700940 -
Computational and Structural... 2022In this paper, we present the results of a systematic statistical analysis of the fungal glycome in comparison with the prokaryotic and protistal glycomes as described...
In this paper, we present the results of a systematic statistical analysis of the fungal glycome in comparison with the prokaryotic and protistal glycomes as described in the scientific literature and presented in the Carbohydrate Structure Database (CSDB). The monomeric and dimeric compositions of glycans, their non-carbohydrate modifications, glycosidic linkages, sizes of structures, branching degree and net charge are assessed. The obtained information can help elucidating carbohydrate molecular markers for various fungal classes which, in its turn, can be demanded for the development of diagnostic tools and carbohydrate-based vaccines against pathogenic fungi. It can also be useful for revealing specific glycosyltransferases active in a particular fungal species.
PubMed: 36249563
DOI: 10.1016/j.csbj.2022.09.040 -
Frontiers in Microbiology 2022Hybridization is an important evolutionary process that can fuel diversification formation of hybrid species or can lead to fusion of previously separated lineages by...
Hybridization is an important evolutionary process that can fuel diversification formation of hybrid species or can lead to fusion of previously separated lineages by forming highly diverse species complexes. We provide here the first molecular evidence of hybridization in wild populations of ciliates, a highly diverse group of free-living and symbiotic eukaryotic microbes. The impact of hybridization was studied on the model of , an obligate endosymbiont of the digestive tube of earthworms, using split decomposition analyses and species networks, 2D modeling of the nuclear rRNA molecules and compensatory base change analyses as well as multidimensional morphometrics. Gene flow slowed down and eventually hampered the diversification of -dwelling plagiotomids, which collapsed into a single highly variable biological entity, the complex. Disruption of the species boundaries was suggested also by the continuum of morphological variability in the phenotypic space. On the other hand, hybridization conspicuously increased diversity in the nuclear rDNA cistron and somewhat weakened the host structural specificity of the complex, whose members colonize a variety of phylogenetically closely related anecic and epigeic earthworms. By contrast, another recorded species, sp. n., showed no signs of introgression, no variability in the rDNA cistron, and very high host specificity. These contrasting eco-evolutionary patterns indicate that hybridization might decrease the alpha-diversity by dissolving species boundaries, weaken the structural host specificity by broadening ecological amplitudes, and increase the nuclear rDNA variability by overcoming concerted evolution within the species complex.
PubMed: 36569075
DOI: 10.3389/fmicb.2022.1067315 -
Frontiers in Microbiology 2021During an investigation on freshwater peritrichs, a new colonial sessilid ciliate, n. sp., was isolated from aquatic plants in an artificial freshwater pond in Qingdao,...
Integrative Studies on a New Ciliate n. sp. (Protista, Ciliophora, Peritrichia) Based on the Morphological and Molecular Data, With Notes on the Phylogeny and Systematics of the Family Epistylididae.
During an investigation on freshwater peritrichs, a new colonial sessilid ciliate, n. sp., was isolated from aquatic plants in an artificial freshwater pond in Qingdao, China. Specimen observations of this species were performed both and using silver staining. n. sp. is characterized by the appearance of the mature colony, which is up to 2 cm high and contains more than 1,000 zooids, the asymmetric horn-shaped zooids, strongly everted and multi-layered peristomial lip, the slightly convex peristomial disc, and the well-developed haplokinety and polykinety, which make more than four circuits of the peristome before descending into the infundibulum. The small subunit ribosomal DNA (SSU rDNA), 5.8s rDNA and its flank internal transcribed spacers (ITS1-5.8s rDNA-ITS2), and large subunit ribosomal DNA (LSU rDNA) are sequenced and used for phylogenetic analyses which reveal that the family Epistylididae Kahl, 1933 is non-monophyletic whereas the genus is monophyletic and nests within the basal clade of the sessilids. The integrative results support the assertion that the genus represents a separate lineage from other epistylidids, suggesting a further revision of the family Epistylididae is needed. We revise including the transfer into this genus of a taxon formerly assigned to , which we raise to species rank, i.e., (Nenninger, 1948) n. grad. & n. comb. (original combination f. Nenninger, 1948). In addition, we provide a key to the identification of the species of .
PubMed: 34394066
DOI: 10.3389/fmicb.2021.718757