Mitogenome features and phylogenetic analysis of red algae, Grateloupia cornea (Rhodophyta, Halymeniales).

The mitogenome is an important tool for taxonomic and evolutionary investigation. Here, a few complete mitogenomes of red algae have been reported. We have reported the complete mitogenome sequences of Grateloupia cornea Okamura, 1913 (Rhodophyta, Halymeniales). The genome is 30,595 bp in circumference, and has a strongly biased [AT] = 66.9%. Like most other Grateloupia species, it has a group II intron in the cox1 gene. Maximum likelihood and maximum parsimony analyses showed that G. cornea is more closely related to G. asiatica. This shows that the group II intron in the cox1 ORF present in most species of Grateloupia was present in their common ancestor, and uniquely lost in G. asiatica. The seven Grateloupia species with known mitogenome sequences remain monophyletic, with the genus Polyopes as sister taxon. The complete mitochondrial genome data will be valuable for future research on comparative mitochondrial genome analysis, an extensive understanding of gene content and organization, evolution of the cox1 intron in Rhodophyta as well as phylogenetic analysis.

Complete Mitochondrial Genome and Its Phylogenetic Position in Red Algae Fushitsunagia catenata from South Korea.

The mitogenome is an important tool in taxonomic and evolutionary studies. Only a few complete mitogenomes have been reported for red algae. Herein, we reported the complete mitochondrial genome sequence of Fushitsunagia catenata (Harvey) Filloramo, G.V. and Saunders, G.W. 2016, a monospecific genus. The genome was 25,889 bp in circumference and had a strongly biased AT of 70.4%. It consisted of 2 rRNAs, 23 tRNAs, and 24 protein-coding genes (PCGs). nad5 (1986 bp) was the largest and atp9 (231 bp) was the smallest PCG. All PCGs used ATG as an initiation codon and TAA as a termination codon, except TAG, which was the termination codon used in the sdh3, rps3, and rps11 genes. The general structure and gene content of the present findings were almost identical to those of other red algae genomes, particularly those of the Rhodymeniales order. The maximum likelihood analysis showed that F. catenata was closely related to Rhodymenia pseudopalmata. The mitochondrial genome data presented in this study will enhance our understanding of evolution in Rhodophyta species.

Optimization of K2CO3 exposure conditions using response surface methodology for CO2 capture with 2-methylpiperazine and monoethanolamine as promoters.

In this study, the optimization of potassium carbonate (K2CO3) exposure conditions for CO2 capture with the use of 2-methypiperazine (2MPz) and monoethanolamine (MEA) as promoters was investigated. The tested operating conditions for the CO2 capture process included the pH, temperature, K2CO3 dose, gas flow rate, and pressure, and their effect on the CO2 absorption/desorption rate and CO2 absorption efficiency was assessed. Response surface methodology (RSM) was also employed to determine the equations for the optimal long-term operating conditions. The results showed that the CO2 absorption rate and efficiency increased under K2CO3 exposure with an increase in the pressure and loading rate. Moreover, for the temperature the absorption efficiency first increase and then decreases with increase in temperature, however, the with increase in temperature the faster absorption were observed with lower absorption loading rate. Furthermore, pH had a more complex effect due to its variable effects on the speciation of bicarbonate ions (HCO3-) and carbonate ions (CO32-). Under higher pH conditions, there was an increase in the concentration of HCO3-, which has a higher CO2 loading capacity than CO32-. Contouring maps were also used to visualize the effect of different exposure conditions on the CO2 absorption rate and efficiency and the role of 2MPz and MEA as promoters in the K2CO3 solution for CO2 absorption. The results showed that the mean CO2 absorption rate was 6.76 × 10-4 M/L/s with an R2 of 0.9693 for the K2CO3 solution containing 2MPz. The highest absorption rate (6.56-7.20 × 10-4 M/L/s) was observed at a temperature of 298-313 K, a pressure of >2 bar, a pH of 8-9, and a loading rate of 80-120 L/h for a concentration of 1-3 M K2CO3 and 0.05-1.5 M 2MPz. The CO2 absorption efficiency exhibited a variation of 56-70% under the same conditions.

Adiponectin restores the obesity-induced impaired immunomodulatory function of mesenchymal stromal cells via glycolytic reprogramming.

Obesity has been known to negatively modulate the life-span and immunosuppressive potential of mesenchymal stromal cells (MSC). However, it remains unclear what drives the compromised potency of obese MSC. In this study, we examined the involvement of adiponectin, an adipose tissue-derived hormone, in obesity-induced impaired therapeutic function of MSC. Diet-induced obesity leads to a decrease in serum adiponectin, accompanied by impairment of survival and immunomodulatory effects of adipose-derived MSC (ADSC). Interestingly, priming with globular adiponectin (gAcrp) improved the immunomodulatory potential of obese ADSC. Similar effects were also observed in lean ADSC. In addition, gAcrp potentiated the therapeutic effectiveness of ADSC in a mouse model of DSS-induced colitis. Mechanistically, while obesity inhibited the glycolytic capacity of MSC, gAcrp treatment induced a metabolic shift toward glycolysis through activation of adiponectin receptor type 1/p38 MAPK/hypoxia inducible factor-1α axis. These findings suggest that activation of adiponectin signaling is a promising strategy for enhancing the therapeutic efficacy of MSC against immune-mediated disorders.

Efficacy of White Spot Syndrome Virus Protein VP28-Expressing Chlorella vulgaris as an Oral Vaccine for Shrimp.

The white spot syndrome virus (WSSV) is the causative agent of white spot disease, which kills shrimp within a few days of infection. Although WSSV has a mortality rate of almost 100% and poses a serious threat to the shrimp farming industry, strategies for its prevention and treatment are extremely limited. In this study, we examined the efficacy of VP28, a recombinant WSSV protein expressed in Chlorella vulgaris (C. vulgaris), as an oral shrimp vaccine. When compared with the control group, in which WSSV had a cumulative mortality of 100%, shrimp treated with 5% VP28-expressing C. vulgaris in their feed only had a 20% cumulative mortality rate 12 days after the WSSV challenge. When compared with the nonvaccinated group, the transcription of anti-lipopolysaccharide factor, C-type lectin, and prophenoloxidase genes, which are involved in shrimp defense against WSSV infection, was upregulated 29.6 fold, 15.4 fold, and 11.5 fold, respectively. These findings highlight C. vulgaris as a potential host for industrial shrimp vaccine production.

Role of inorganic foulants in the aging and deterioration of low-pressure membranes during the chemical cleaning process in surface water treatment: A review.

Low-pressure membrane (LPM) filtration, including microfiltration (MF) and ultrafiltration (UF), is a promising technology for the treatment of surface water for drinking and other purposes. Various configurations and operational sequences have been developed to ensure the sustainable provision of clean water by overcoming fouling problems. In the literature, various periodic physical and/or chemical approaches to the cleaning of LPMs have been reported, but little data is available on the aging of MF/UF membranes that results from the interaction between the foulants and the cleaning agent. Periodic physical cleaning of the membrane is expected to return the membrane to its original performance capacity, but it only recovers to a certain level because the remaining foulants cause irreversible fouling. Chemical cleaning can then be employed to recover the membrane from this irreversible fouling but, in the process, it can cause irrecoverable damage to the membrane. In this review, the foulants responsible for irrecoverable damage to MF/UF membranes are summarized, and their interaction with cleaning agents and other foulants is described. The impact of these foulants on various membrane parameters, including filtration efficiency, flux decline, permeability, membrane characterization, and membrane integrity are also summarized and discussed in detail. In addition, mitigation options and future prospects are also discussed with regard to increasing the operational life span of a membrane in a cost-effective manner. Ultimately, this review suggests an advanced control system based on membrane-foulant interactions under the impact of various operational parameters to mitigate the integrity loss of membranes.

Complete Mitogenome Sequencing, Annotation, and Phylogeny of Grateloupia turuturu, a Red Alga with Intronic cox1 Gene.

The mitochondrial genome (mitogenome) is essential for identifying species and tracing genetic variation, gene patterns, and evolutionary studies. Here, the mitogenome of Grateloupia turuturu was sequenced on the Illumina sequencing platform. This circular mitogenome (28,265 bp) contains 49 genes, including three rRNAs, twenty transfer RNAs (tRNAs), and twenty-six protein-coding genes (PCGs). Nucleotide composition indicates biased AT (68.8%) content. A Group II intronic sequence was identified between two exons of the cox1 gene, and this sequence comprises an open reading frame (ORF) that encodes a hypothetical protein. The gene content, annotation, and genetic makeup are identical to those of Halymeniaceae members. The complete mitogenome sequences of the Grateloupia and Polyopes species were used in a phylogenetic analysis, which revealed that these two genera are monophyletic and that G. turuturu and G. elliptica are closely related. This newly constructed mitogenome will help us better understand the general trends in the development of cox1 introns in Halymeniaceae, as well as the evolution of red algal mitogenomes within the Rhodophyta and among diverse algal species.

Field experiments on chemical and biological changes of thin-layer oyster shells capping sediments in dense aquaculture area.

Thin-layer oyster shell capping has been proposed as a method for improving contaminated coastal environments. Field experiments were conducted to investigate the effects of oyster shell capping on nutrient concentrations, microorganisms, and macrobenthic communities. The concentration of PO4-Pin the experimental area decreased by approximately 38% more than in the control, due to phosphorus fixation of oyster shells and the presence of Proteobacteria. Ammonia-oxidizing bacteria such as the order Pirellulales (phylum Planctomycetes) were related to the low ratio of NH3-N found in dissolved inorganic nitrogen in the experimental area, indicating nitrification promotion. The reduction in annular benthic organisms observed in the experimental area indicates a decline in sediment organic matter, which could potentially mitigate eutrophication. Oyster shell capping was confirmed to be an effective material for restoring coastal sediments by improving their chemical and biological properties.

Structural and performance variation of PES/PVDF membranes after exposure to the pretreated feed water of CECs.

In this study, the removal efficiency of chemicals of emerging concerns (CECs) was evaluated under exposure to various doses of UV/H2O2-based oxidation processes in combination with membrane filtration for three cleaning cycles. Polyethersulphone (PES) and polyvinylidene fluoride (PVDF) materials based membranes were used for this study. The chemical cleaning of the membranes was performed by immersion of the membranes into 1 N HCl followed by adding 3000 mg.L-1 NaOCl for 1hr. Degradation and filtration performance was evaluated using Liquid Chromatography with tandem mass spectrometry (LC-MS/MS) and total organic carbon (TOC) analysis. Membrane fouling analysis for assessing the comparative performance of PES and PVDF membranes was determined by specific fouling and fouling indices evaluation. Membrane characterization results show that the alkynes and carbonyl group formation are due to dehydrofluorination and oxidation of PVDF and PES membranes under the attack of foulants and cleaning chemicals, which resulted in a reduction of fluoride percentage and an increase in sulfur percentage in the PVDF and PES membranes. A decrease in the hydrophilicity of the membranes in underexposed conditions was observed and is consistent with an increase in dose. Degradation results of CECs follow with the highest removal efficiency of chlortetracycline (CTC) followed by atenolol (ATL), acetaminophen (ACT), and caffeine (CAF) degradation due to attack on the aromatic ring and the carbonyl group of CECs by OH exposure. Membrane exposed at 3 mg.L-1 dose of UV/H2O2-based CECs shows minimum alteration with higher filtration efficiency and lower fouling, particularly in PES membranes.

Methionine consumption by cancer cells drives a progressive upregulation of PD-1 expression in CD4 T cells.

Programmed cell death protein 1 (PD-1), expressed on tumor-infiltrating T cells, is a T cell exhaustion marker. The mechanisms underlying PD-1 upregulation in CD4 T cells remain unknown. Here we develop nutrient-deprived media and a conditional knockout female mouse model to study the mechanism underlying PD-1 upregulation. Reduced methionine increases PD-1 expression on CD4 T cells. The genetic ablation of SLC43A2 in cancer cells restores methionine metabolism in CD4 T cells, increasing the intracellular levels of S-adenosylmethionine and yielding H3K79me2. Reduced H3K79me2 due to methionine deprivation downregulates AMPK, upregulates PD-1 expression and impairs antitumor immunity in CD4 T cells. Methionine supplementation restores H3K79 methylation and AMPK expression, lowering PD-1 levels. AMPK-deficient CD4 T cells exhibit increased endoplasmic reticulum stress and Xbp1s transcript levels. Our results demonstrate that AMPK is a methionine-dependent regulator of the epigenetic control of PD-1 expression in CD4 T cells, a metabolic checkpoint for CD4 T cell exhaustion.

Natural Variations in the Benthic Environment and Bacterial Communities of Coastal Sediments around Aquaculture Farms in South Korea.

The aim of this study was to examine the possible seasonal variations in the nutrients (dissolved inorganic nitrogen-DIN and phosphorus) and benthic bacterial communities in marine aquaculture surrounding sediments. The study areas were Geoje, Tongyeong, and Changwon bays in Korea, which are famous for oysters (Magallana gigas), Halocynthia roretzi, and warty sea squirt (Styela clava) farming, respectively. The study sites included semi-enclosed coastal areas with a low seawater exchange rate. Subtidal sediment samples were collected seasonally from the area surrounding the aquacultures between April and December 2020. Seasonal variations in nutrients were observed, with the highest concentration of DIN in August. For phosphorus, site-specific variations were also observed. To investigate the variations in benthic bacterial communities, the advanced technique of 16S rRNA gene amplicon sequencing was applied, and the results indicated a seasonal variation pattern and predominance of Proteobacteria (59.39-69.73%), followed by Bacteroidetes (6.55-12.85%) and Chloroflexi (2.04-4.50%). This study provides a reference for future studies on natural variations in the benthic environment and bacterial communities in the areas surrounding aquacultures. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-023-01067-8.

Analysis of the complete mitochondrial genome sequence of Japanese butterflyfish, Chaetodon nippon (Chaetodontiformes, Chaetodontidae).

Japanese butterflyfish (Chaetodon nippon) belong to the family Chaetodontidae and order Chaetodontiformes. It has circular mitochondrial genome of 16,507 bp in length with 55.4% of A + T content and has 37 genes, including 22 tRNA, 2 rRNA, and 13 protein-coding genes, in addition to a control region. The results of phylogenetic analysis indicated that the C. nippon, C. wiebeli, C. auripes, C. auriga, C. octofasciatus, C. speculum, and C. modestus are closely related to each other. The findings of this study will provide useful genetic information for further phylogenetic and taxonomic classifications of Chaetodontidae.

The complete sequence of the mitochondrial DNA and phylogenetic analysis of the marine red alga Grateloupia elliptica (Rhodophyta: Halymeniales).

Grateloupia elliptica (Holmes, 1896) is a red alga belonging to the order Halymeniales and phylum Rhodophyta. In this study, the complete mitochondrial DNA (mtDNA) of G. elliptica has been described. The complete circular mtDNA of G. elliptica was 28,503 bp in length, with an A + T content of 68.78%; it encoded a total of 49 genes, including 20 tRNA, three rRNA, and 26 protein-coding (CDS) genes. Phylogenetic analysis based on complete mitochondrial genomes revealed that G. elliptica was most closely related to G. angusta. The complete mitochondrial sequence of G. elliptica will enrich the mitochondrial genome database and provide useful resources for population genetics and evolution analyses.

The effectiveness and adsorption mechanism of iron-carbon nanotube composites for removing phosphate from aqueous environments.

This study successfully employed iron-carbon nanotubes (Fe-CNT) to recover phosphate (P) from water. We examined the effects of various iron concentrations denoted by Fe-CNT-1 and Fe-CNT-2 on P removal and compared them with pristine carbon nanotubes (CNTs). The adsorption capacity of Fe-CNTs was much better than pristine CNTs. According to the high adsorption capacity, Fe-CNT-2 sample was very effective for P recovery and exhibits ∼7 times higher P removal efficiency than that of pristine CNTs. The characterization of the as-obtained adsorbent (Fe-CNT-2) and pristine CNTs were performed using X-ray diffraction, Brunauer-Emmett-Teller method, Field emission scanning electron microscope coupled with energy-dispersive spectroscopy detector (FESEM-EDS), X-ray photoelectron spectroscopy and Transmission electron microscopy. Results demonstrated that iron oxide nanoparticles were successfully deposited on the surface of CNT. The adsorption kinetics and isotherm studies for P removal showed pseudo-second-order rate constants (R2 > 0.99) and the Langmuir isotherm (R2 > 0.99) respectively, thus revealing that the nature of adsorption was chemisorption. The estimated Langmuir adsorption capacity of Fe-CNT-2 was 36.5 mgP/g or 112 mg PO4/g at an equilibrium time of 3 h. The ionic strength provided by SO42-, NO3-, and Cl- demonstrated no considerable influence on phosphate adsorption. Moreover, the P adsorbed Fe-CNT-2 was efficiently recovered with different concentrations of desorbing reagents, such as NaOH and NaCO32-. Moreover, the findings of X-ray photoelectron spectroscopy (XPS) analysis demonstrated that OH group played a major role in the P removal by Fe-CNT-2. The findings of this study demonstrate that Fe-CNT-2 had a great deal of application as an effective and stable adsorbent for the P recovery from aquatic environments.

Mitigation of biofouling with co-deposition of polydopamine and curcumin on the surface of a thin-film composite membrane.

Reverse osmosis (RO) membrane has been widely used in various water treatment fields as an efficient desalination technology, but serious biofouling problem arises in the actual application process. Curcumin is known as a natural compound that can reduce biofouling by inhibiting the growth of microorganisms based on quorum sensing. Dopamine, a molecule with excellent adhesion and functionalization on the material's surface, has high research value for applying a curcumin coating to the membrane surface. Curcumin degrades under alkaline conditions, whereas dopamine must polymerize under alkaline conditions. Simultaneously, a coating may adversely affect curcumin. Therefore, a two-step coating process was considered by self-polymerizing dopamine on the thin-film composite membrane surface and then dip-coating curcumin attached to the polydopamine layer. Furthermore, the effect of time and concentration on the surface modification before and after membrane modification was investigated. The highest permeability of 1.39 L/m2/hr/bar was achieved with the modified membranes. The number of gram-positive bacteria decreased from 6.71 × 106 to 9.67 × 105 CFU/mL. This result is meaningful for antifouling through modification of the membrane surface. Use of curcumin can be applied to reduce biofouling and extend the lifetime of the membrane without pretreatment or membrane cleaning.

Complete mitochondrial genome of brown-banded butterflyfish Chaetodon modestus (Chaetodontiformes, Chaetodontidae) and phylogenetic analysis.

The complete mitochondrial genome of the Chaetodon modestus (Temminck and Schlegel, 1844) was first determined in this study, which is 16,490 bp in length, containing 13 protein-coding genes, two rRNA genes, and 22 tRNA. Out of 37 mitochondrial genes, except for ND6 and eight tRNA (Pro, Glu, Ser, Tyr, Cys, Asn, Ala, Gln) genes were encoded on the L-strand, the others were encoded on the H-strand. The overall base composition includes A (28.0%), T (28.7%), G (16.7%), ad C (26.6%). The phylogenetic tree was built using the maximum-likelihood approach to provide a relationship within Chaetodontidae, which might be valuable for species management.

The complete mitochondrial genome of threadfin butterflyfish, Chaetodon auriga (Chaetodontiformes: Chaetodontidae) and phylogenetic analysis.

Chaetodon auriga (Forsskal, 1775) belongs to the family Chaetodontidae and the order Chaetodontiformes. Here, we report the complete mitochondrial genome of C. auriga assembled using the Illumina MiSeq platform. The circular mitochondrial genome of C. auriga is 16,527 bp long, has an A + T content of 54.53%, and contains 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes), and a non-coding region. The overall nucleotide composition was A: 28.19%, T: 26.34%, G: 16.27%, and C: 29.20%. The mitochondrial genome of C. auriga contributes to revealing the phylogenetic relationships among species of the Chaetodontidae family.

Temperature dependent cellular, and epigenetic regulatory mechanisms underlying the antiviral immunity in sevenband grouper to nervous necrosis virus infection.

Changes in the thermal optima of fish impacts changes in the physiology and immune response associated with infections. The present study showed that at suboptimal temperatures (17 °C), the host tries to evade viral infection by downregulating the inflammatory response through enhanced neuronal protection. There was significantly less abundance of IgM + B cells in the 17 °C group compared to that in the 25 °C group. An increased macrophage population (Iba1+) during the survival phase in fish challenged at 25 °C demonstrated inflammation. Optimal temperature challenge activated virus-induced senescence in brain cells, demonstrated with a heterochromatin-associated H3K9me3 histone mark. There was an abundant expression of anti-inflammatory cytokines in the brain of fish at the suboptimal challenge. Besides the cytokines, the expression of BDNF was significantly higher in the suboptimally challenged group, suggesting that its neuronal protection activity following NNV infection is mediated through TGFß. The suboptimal challenge resulted in H3k9ac displaying transcriptional competency, activation of trained immunity H3K4me3, and enrichment of H3 histone-lysine-4 monomethylation (H3K4me1), resulting in a robust re-stimulatory immune response. The observations from the H4 modifications showed that besides H4K12ac and H4K20m3, all the assayed modifications were significantly higher in suboptimal convalescent fishes. The suboptimally challenged fish acquired more methylation along cytosine residues than the optimally infected fish. Together, these observations suggest that optimal temperature results in an immune priming effect, whereas the protection enabled in suboptimal convalescent fishes is operated through epigenetically controlled trained immune functions.

Complete mitochondrial genome and phylogenetic analysis of the marine red alga Polyopes affinis (Rhodophyta: Halymeniales).

Polyopes affinis ((Harvey) Kawaguchi & Wang, 2002) is a red alga in the order Halymeniales of the phylum Rhodophyta. The entire mitogenome of P. affinis was sequenced and compared to related Halymeniales species. The entire circular-mitogenome is 25,988 bp long, has 27.59% GC content, and comprises 25 protein-coding genes (CDS), 23 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. In terms of gene synteny and tRNA composition, the P. affinis mitogenome differs significantly from that of P. lancifolius. Phylogenetic analysis shows P. affinis mitogenome in a branch sister to P. lancifolius, indicating a close relationship with other Halymeniales species.

Complete mitochondrial genome of scorpionfish Scorpaena neglecta (Actinopterygii).

Scorpaena neglecta (Temminck and Schlegel, 1843) is a marine fish, in the family Scorpaenidae, order Scorpaeniformes, class Actinopterygii of the phylum Chordata. The first species of Scorpaena with a complete mitochondrial genome is described in the present study. The circular mitochondrial genome of S. neglecta has 17,202 bp with 54.75% A + T content and encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA). The phylogenetic tree indicates S. neglecta clustered into one branch and is closely related to other Scorpaenidae species. The mitochondrial genome structure and gene content of S. neglecta will support the study of evolution and phylogenetic relationships among Scorpaenidae species.