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Fulltext Identification, Growth Profile and Probiotic Properties of Autochthonous Intestinal Bacteria of Sagor catfish (Hexanematichthys sagor)

Pang Sing T, Julian R, Hatai K

Biocontrol Sci, 2019;24(1):1-11.
PMID: 30880308 DOI: 10.4265/bio.24.1

　The prevalence of antibiotic resistant bacteria in aquaculture has reached alarming proportions and intensified the search for microbe derived antimicrobial compounds. This study isolated bacteria from the intestine of Sagor catfish (Hexanematichthys sagor) and screened it for antagonistic properties. Five out of 334 bacterial isolates inhibited growth of fish pathogens. The 5 bacterial strains included relatives of Shewanella haliotis, Myroides odoratimimus, Vibrio harveyi, Vibrio alginolyticus and Alcaligenes faecalis. The growth profiles and probiotic properties of these bacteria were examined. The results showed that the isolate 9 (3) 7.5.2.1, whose closest relative was S. haliotis exhibited growth and probiotic advantage compared to the other bacterial strains, such as highest doubling time and the ability to survive at all experimental temperatures (18 to 60℃) , and bile concentrations (0.01 to 1.00%) and pH (pH2 to 9) . While the bacteria with probiotic properties were successfully isolated. Further study is necessary to examine the efficiency of the probiotic candidate bacteria in boosting fish immunity against pathogens.
Fulltext A Central Bioactive Region of LTBP-2 Stimulates the Expression of TGF-β1 in Fibroblasts via Akt and p38 Signalling Pathways

Sideek MA, Smith J, Menz C, Adams JRJ, Cowin AJ, Gibson MA

Int J Mol Sci, 2017 Oct 09;18(10).
PMID: 28991210 DOI: 10.3390/ijms18102114

Latent transforming growth factor-β-1 binding protein-2 (LTBP-2) belongs to the LTBP-fibrillin superfamily of extracellular proteins. Unlike other LTBPs, LTBP-2 does not covalently bind transforming growth factor-β1 (TGF-β1) but appears to be implicated in the regulation of TGF-β1 bioactivity, although the mechanisms are largely unknown. In experiments originally designed to study the displacement of latent TGF-β1 complexes from matrix storage, we found that the addition of exogenous LTBP-2 to cultured human MSU-1.1 fibroblasts caused an increase in TGF-β1 levels in the medium. However, the TGF-β1 increase was due to an upregulation of TGF-β1 expression and secretion rather than a displacement of matrix-stored TGF-β1. The secreted TGF-β1 was mainly in an inactive form, and its concentration peaked around 15 h after addition of LTBP-2. Using a series of recombinant LTBP-2 fragments, the bioactivity was identified to a small region of LTBP-2 consisting of an 8-Cys motif flanked by four epidermal growth factor (EGF)-like repeats. The LTBP-2 stimulation of TGF-β expression involved the phosphorylation of both Akt and p38 mitogen-activated protein kinase (MAPK) signalling proteins, and specific inactivation of each protein individually blocked TGF-β1 increase. The search for the cell surface receptor mediating this LTBP-2 activity proved inconclusive. Inhibitory antibodies to integrins β1 and αVβ5 showed no reduction of LTBP-2 stimulation of TGF-β1. However, TGF-β1 upregulation was partially inhibited by anti-αVβ3 integrin antibodies, suggestive of a direct or indirect role for this integrin. Overall, the study indicates that LTBP-2 can directly upregulate cellular TGF-β1 expression and secretion by interaction with cells via a short central bioactive region. This may be significant in connective tissue disorders involving aberrant TGF-β1 signalling.
Fulltext Cobalt containing glass fibres and their synergistic effect on the HIF-1 pathway for wound healing applications

Solanki AK, Autefage H, Rodriguez AR, Agarwal S, Penide J, Mahat M, et al.

Front Bioeng Biotechnol, 2023;11:1125060.
PMID: 36970616 DOI: 10.3389/fbioe.2023.1125060

Introduction and Methods: Chronic wounds are a major healthcare problem, but their healing may be improved by developing biomaterials which can stimulate angiogenesis, e.g. by activating the Hypoxia Inducible Factor (HIF) pathway. Here, novel glass fibres were produced by laser spinning. The hypothesis was that silicate glass fibres that deliver cobalt ions will activate the HIF pathway and promote the expression of angiogenic genes. The glass composition was designed to biodegrade and release ions, but not form a hydroxyapatite layer in body fluid. Results and Discussion: Dissolution studies demonstrated that hydroxyapatite did not form. When keratinocyte cells were exposed to conditioned media from the cobalt-containing glass fibres, significantly higher amounts of HIF-1α and Vascular Endothelial Growth Factor (VEGF) were measured compared to when the cells were exposed to media with equivalent amounts of cobalt chloride. This was attributed to a synergistic effect of the combination of cobalt and other therapeutic ions released from the glass. The effect was also much greater than the sum of HIF-1α and VEGF expression when the cells were cultured with cobalt ions and with dissolution products from the Co-free glass, and was proven to not be due to a rise in pH. The ability of the glass fibres to activate the HIF-1 pathway and promote VEGF expression shows the potential for their use in chronic wound dressings.
Fulltext Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study

Biscarini F, Masetti G, Muller I, Verhasselt HL, Covelli D, Colucci G, et al.

J Clin Endocrinol Metab, 2023 Jul 14;108(8):2065-2077.
PMID: 36683389 DOI: 10.1210/clinem/dgad030

CONTEXT: Gut bacteria can influence host immune responses but little is known about their role in tolerance-loss mechanisms in Graves disease (GD; hyperthyroidism caused by autoantibodies, TRAb, to the thyrotropin receptor, TSHR) and its progression to Graves orbitopathy (GO).
OBJECTIVE: This work aimed to compare the fecal microbiota in GD patients, with GO of varying severity, and healthy controls (HCs).
METHODS: Patients were recruited from 4 European countries (105 GD patients, 41 HCs) for an observational study with cross-sectional and longitudinal components.
RESULTS: At recruitment, when patients were hyperthyroid and TRAb positive, Actinobacteria were significantly increased and Bacteroidetes significantly decreased in GD/GO compared with HCs. The Firmicutes to Bacteroidetes (F:B) ratio was significantly higher in GD/GO than in HCs. Differential abundance of 15 genera was observed in patients, being most skewed in mild GO. Bacteroides displayed positive and negative correlations with TSH and free thyroxine, respectively, and was also significantly associated with smoking in GO; smoking is a risk factor for GO but not GD. Longitudinal analyses revealed that the presence of certain bacteria (Clostridiales) at diagnosis correlated with the persistence of TRAb more than 200 days after commencing antithyroid drug treatment.
CONCLUSION: The increased F:B ratio observed in GD/GO mirrors our finding in a murine model comparing TSHR-immunized with control mice. We defined a microbiome signature and identified changes associated with autoimmunity as distinct from those due to hyperthyroidism. Persistence of TRAb is predictive of relapse; identification of these patients at diagnosis, via their microbiome, could improve management with potential to eradicate Clostridiales.
Fulltext Antifungal Prospect of Bacillus cereus Postbiotic on Crustacean Pathogen, Lagenidium thermophilum

Elliecpearl Jasca J, Annita Seok KY, Suraini L, Chun YA, Julian R, Sano M, et al.

Biocontrol Sci, 2021;26(4):201-205.
PMID: 35013016 DOI: 10.4265/bio.26.201

Pathogenic marine fungi, Lagenidium thermophilum is known causative agent in the crustacean industry. Current disinfection practice in hatchery has risks and negative impacts which prompts suitable substitute to synthetic antifungal agents. Thus, this study was conducted to evaluate the antifungal potential of postbiotic from four potential probiotics towards marine oomycetes, L. thermophilum IPMB 1401. The screening test showed that the Lactobacillus plantarum GS12 and Bacillus cereus GS15 postbiotics were positive for antifungal activity on L. thermophilum IPMB 1401. These two bacterial extracts have minimum inhibitory concentration （MIC） at 50%. The toxicity assay on MIC level of the postbiotic revealed that the cumulative mortality of brine shrimp nauplii exposed to B. cereus postbiotic was significantly lower compared to L. plantarum GS12 postbiotic and formalin. This indicates a high potential of B. cereus GS15 as a prospect for alternative control method for fungal infections in the crustacean culture industry.
Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies

Doorenweerd C, San Jose M, Leblanc L, Barr N, Geib SM, Chung AYC, et al.

Mol Ecol Resour, 2024 Aug;24(6):e13987.
PMID: 38956928 DOI: 10.1111/1755-0998.13987

The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.
Fulltext Phylogenomics and the rise of the angiosperms

Zuntini AR, Carruthers T, Maurin O, Bailey PC, Leempoel K, Brewer GE, et al.

Nature, 2024 May;629(8013):843-850.
PMID: 38658746 DOI: 10.1038/s41586-024-07324-0

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.