Comparative study on mitogenomes of green tide algae.

Since 2007, the annual green tide disaster in the Yellow Sea has brought serious economic losses to China. There is no research on the genetic similarities of four constituent species of green tide algae at the genomic level. We previously determined the mitochondrial genomes of Ulva prolifera, Ulva linza and Ulva flexuosa. In the present work, the mitochondrial genome of another green tide (Ulva compressa) was sequenced and analyzed. With the length of 62,311 bp, it contained 29 encoding genes, 26 tRNAs and 10 open reading frames. By comparing these four mitochondrial genomes, we found that U. compressa was quite different from the other three types of Ulva species. However, there were similarities between U. prolifera and U. linza in the number, distribution and homology of open reading frames, evolutionary and codon variation of tRNA, evolutionary relationship and selection pressure of coding genes. Repetitive sequence analysis of simple sequence repeats, tandem repeat and forward repeats further supposed that they have evolved from the same origin. In addition, we directly analyzed gene homologies and translocation of four green tide algae by Mauve alignment. There were gene order rearrangements among them. With fast-evolving genomes, these four green algal mitochondria have both conservatism and variation, thus opening another window for the understanding of origin and evolution of Ulva.

Analysis of the potential of marine bioblue carbon storage and their regional contributions in Shanghai marine areas.

Shanghai's extensive coastline and offshore marine areas feature diverse ecosystems. This study aimed to determine the current status, spatial distribution, and total capacity of marine carbon storage in Shanghai. Surveys were conducted on oyster reefs, phytoplankton, and fish populations from August to November 2022, with samples collected to quantify biomass and carbon content. The carbon storage of oyster reefs, phytoplankton, and fish was found to be 2.045 × 105 tC, 5113.19 kgC, and 56.6014 tC, respectively. The spatial distributions exhibited significant heterogeneity, influenced by substrate type, nutrient concentrations, and fishing activities. The total marine carbon storage capacity in Shanghai's offshore waters was estimated at 2.045 × 105 tC, highlighting a pathway for achieving regional carbon neutrality goals. This study enriches baseline data, elucidates carbon sequestration functions and spatial patterns, and provides scientific support for marine ecological protection and blue carbon resource utilization. Future research should investigate spatiotemporal variation mechanisms and potential regulation pathways.

Outlook on the Security and Potential Improvements of CRISPR-Cas9.

Gene editing technology is regarded as a good news to save patients with genetic diseases because of its significant function of specifically changing genetic information. From zinc-finger proteins to transcription activator-like effector protein nucleases gene editing tools are constantly updated. At the same time, scientists are constantly developing a variety of new gene editing therapy strategies, in order to promote gene editing therapy from various aspects and realize the maturity of the technology as soon as possible. In 2016, CRISPR-Cas9-mediated CAR-T therapy was the first to enter the clinical trial stage, indicating that the use of CRISPR-Cas system as the blade of the genetic lancet to save patients is officially on the schedule. The first challenge to achieve this exciting goal is to improve the security of the technology. This review will introduce the gene security issues faced by the CRISPR system as a clinical treatment tool, the current safer delivery methods and the newly developed CRISPR editing tools with higher precision. Many reviews summarize the means of improving the security of gene editing therapy and the comprehensive delivery method, while few articles focus on the threat of gene editing to the genomic security of the treatment target. Therefore, this review focuses on the risks brought by gene editing therapy to the patient genome, which provides a broader perspective for exploring and improving the security of gene editing therapy from two aspects of delivery system and CRISPR editing tools.

Activated abscisic acid pathway and C4 pathway, inhibited cell cycle progression, responses of Ulva prolifera to short term high temperature elucidated by multi-omics.

The annual outbreak of green tides since 2007 has destroyed coastal waters' ecological environment and caused substantial economic losses. Ulva prolifera, known as the dominant species of green tides, is influenced by temperatures. Omics-based technology was used to analyze U. prolifera under 12 h of treatment at 30 °C in the work. High temperature has the following advantages, e.g., activating the abscisic acid signaling pathway, improving the heat tolerance of U. prolifera, up-regulating metabolites such as glycolipids, glyceroyl, and glutamic acid to maintain the stability and fluidity of cells, and reducing the stimulatory effect of external stress on cells. The key genes and proteins of the tricarboxylic acid cycle, glycolysis, and pentose phosphorylation pathways were inhibited; however, the key enzyme pyruvate phospho-dikinase of the C4 pathway was up-regulated. The C4 pathway was activated in U. prolifera in response to high-temperature stress and may play a key role in photosynthesis. Besides, U. prolifera metabolizing amino acids was active. High temperature inhibited genes and proteins related to DNA replication and cell cycle in the transcriptome and proteome as well as the growth and reproduction of U. prolifera.

Molecular Response of Ulva prolifera to Short-Term High Light Stress Revealed by a Multi-Omics Approach.

The main algal species of Ulva prolifera green tide in the coastal areas of China are four species, but after reaching the coast of Qingdao, U. prolifera becomes the dominant species, where the light intensity is one of the most important influencing factors. In order to explore the effects of short-term high light stress on the internal molecular level of cells and its coping mechanism, the transcriptome, proteome, metabolome, and lipid data of U. prolifera were collected. The algae were cultivated in high light environment conditions (400 µmol·m−2·s−1) for 12 h and measured, and the data with greater relative difference (p < 0.05) were selected, then analyzed with the KEGG pathway. The results showed that the high light stress inhibited the assimilation of U. prolifera, destroyed the cell structure, and arrested its growth and development. Cells entered the emergency defense state, the TCA cycle was weakened, and the energy consumption processes such as DNA activation, RNA transcription, protein synthesis and degradation, and lipid alienation were inhibited. A gradual increase in the proportion of the C4 pathway was recorded. This study showed that U. prolifera can reduce the reactive oxygen species produced by high light stress, inhibit respiration, and reduce the generation of NADPH. At the same time, the C3 pathway began to change to the C4 pathway which consumed more energy. Moreover, this research provides the basis for the study of algae coping with high light stress.

Purification, crystallization and preliminary X-ray analysis of phycocyanin and phycoerythrin from Porphyra yezoensis Ueda.

Porphyra yezoensis is one of the most important and widely cultured seaweeds in China. Phycobiliproteins exhibit excellent spectroscopic properties and play versatile roles in the biomedical, food, cosmetics and chemical synthetic dye industries. Here, the purification and crystallization of phycoerythrin and phycocyanin, two phycobiliproteins extracted from P. yezoensis, are described. Using a novel protocol including co-precipitation with ammonium sulfate and hydroxyapatite column chromatography, both phycobiliproteins were produced on a large scale with improved quality and yield compared with those previously reported. Native PAGE analysis indicated that phycoerythrin and phycocyanin exist as (αß)(3) heterohexamers in solution. The crystals of phycoerythrin diffracted to 2.07 Å resolution and belonged to space group R3. The unit-cell parameters referred to hexagonal axes are a = b = 187.7, c = 59.7 Å, with nine (αß)(2) heterotetramers per unit cell. The crystals of phycocyanin diffracted to 2.70 Å resolution in space group P2(1). Matthews coefficient analysis shows that 10-19 (αß) heterodimers of phycocyanin in the asymmetric unit would be reasonable. A self-rotation function calculation clarified this ambiguity and indicated that 12 (αß) heterodimers of phycocyanin are assembled in the asymmetric unit.

Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea.

Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.

Anti-complementary activity of a degraded sulfated heterogalactan from red alga Pyropia haitanensis.

A sulfated galactan LP-G2 was isolated and purified from red alga, Pyropia haitanensis. It was a branched polysaccharide with average molecular weight about 8381 Da, composed of Gal, Glc, GalA and Ara. The structure of LP-G2 was determined using IR and NMR spectroscopy. It was composed of →4)-ß-d-galactose→4)-α-l-galactose-6- sulfate segments, with ß-d-Glc and α-d-galactose unit substituted at the 6-position of α-l-galactose. Functional analysis showed that LP-G2 inhibited complement activation on both the classic and alternative pathways with CH50 value of 3.08 ± 0.25 mg/mL and AP50 value of 2.23 ± 0.20 mg/mL, respectively. Preliminary mechanism studies by using complement component depleted-sera indicated that LP-G2 selectively interacts with C1q, C2, C4 and C9. The results suggested that LP-G2 could be of potential benefits in treatment of the complement associated diseases.

Secondary Metabolites of Antarctic Fungi Antagonistic to Aquatic Pathogenic Bacteria.

Polar microbial derived antibiotics have potential as alternatives to traditional antibiotics in treating fish against pathogenic bacteria. In this paper, 23 strains of polar fungi were fermented to detect bacteriostatic products on three aquatic pathogenic bacteria, subsequently the active fungus was identified. It was indicated that secondary metabolites of 23 strains weredistinct; of these, the extract of strain B-7 (belonging to Bjerkandera according to molecular identification) demonstrated a strong antibacterial activity to Streptococcus agalactiae, Vibrio anguillarum and Aeromonas hydrophila ATCC7966 by Kirby-Bauerpaper strip method. During one fermentation cycle, the pH curve of the fermentation liquor became lowest (4.0) on the 4th day and rose back to 7.6 finally after 5 days, The residual sugar curve was decreased before stablising on the 6th day. It is presumed that a large amount of alkaline secondary metabolites might have been produced during fermentation. This study focuses on antagonism between aquatic pathogenic bacteria and fermentation metabolites from Antarctic fungi for the first time, which may provide data on research of antibiotics against aquatic pathogenic bacteria.

Complete chloroplast genome of green tide algae Ulva flexuosa (Ulvophyceae, Chlorophyta) with comparative analysis.

Ulva flexuosa, one kind of green tide algae, has outbroken in the Yellow Sea of China during the past ten years. In the present study, we sequenced the chloroplast genome of U. flexuosa followed by annotation and comparative analysis. It indicated that the chloroplast genomes had high conservation among Ulva spp., and high rearrangement outside them. Though U. flexuosa was closer to U. linza than U. fasciata in phylogenetic tree, the average Ka/Ks between U. flexuosa and U. linza assessed by 67 protein-coding genes was higher than those between U. flexuosa and other species in Ulva spp., due to the variation of psbZ, psbM and ycf20. Our results laid the foundation for the future studies on the evolution of chloroplast genomes of Ulva, as well as the molecular identification of U. flexuosa varieties.

Complete mitochondrial genome of Ulva linza, one of the causal species of green macroalgal blooms in Yellow Sea, China.

Ulva linza, a green macroalgae, is one of the causal species of the world's largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U.linza (GenBank accession no. KU189740). The genome consists of circular chromosomes of 70 858 bp and encodes a total of 28 protein-coding genes including eight rps genes, three rpl genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. linza clustered into Ulvophyceae clade and had close genetic relationship with algae Ulva prolifera.

Complete mitochondrial genome of Ulva prolifera, the dominant species of green macroalgal blooms in Yellow Sea, China.

Ulva prolifera (U. prolifera), a green macroalgae, is widely known as the dominant species of the world's largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U. prolifera (GenBank accession number: KU161104). The genome consists of circular chromosomes of 61 962 bp and encodes a total of 26 protein-coding genes include nine ribosomal protein genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. prolifera clustered into Ulvo phyceae clade and had close genetic relationship with algae Ulva fasciata.

Inhibition of hydrogen peroxide induced injuring on human skin fibroblast by Ulva prolifera polysaccharide.

Ulva prolifera can protect human skin fibroblast from being injured by hydrogen peroxide. This work studied the composition of Ulva prolifera polysaccharide and identified its physicochemical properties. The results showed that the cell proliferation of 0.5mg/mL crude polysaccharide was 154.4% of that in negative control group. Moreover, ROS detection indices, including DCFH-DA, GSH-PX, MDA and CAT, indicated that crude polysaccharide could improve cellular ability to scavenge free radical and decrease the injury on human skin fibroblast by hydrogen peroxide. In purified polysaccharide, the activity of fraction P1-1 was the highest, with 174.6% of that in negative control group. The average molecular weight of P1-1 was 137kD with 18.0% of sulfate content. This work showed the inhibition of hydrogen peroxide induced injuries on human skin fibroblast by Ulva prolifera polysaccharide, which may further evaluate the application of U. prolifera on cosmetics.

[Scale-up preparation of phycoerythrin from Porphyra haitanensis].

We developed large-scale preparation of phycoerythrin from Porphyra haitanensis, a main economic red algae in China. Firstly, P. haitanensis thallus was broken by using "swelling and smash" method. Then times of grads ammonium sulfate precipitation applied to the crude extraction were compared. Desalted solution was further purified with one-step chromatography using hydroxyapatite and properties on spectrum and molecular weight were identified finally. The results indicated that after four times of ammonium sulfate precipitation (15%, 50%, 10% and 40%), the absorption spectrum purity of P. haitanensis achieved 0.9 (A564/A280), and 507.82 mg phycoerythrin (A564/A280 > 3.2) was obtained from 7 kg fresh algae after further hydroxyapatite chromatography. This research provides a potential way for preparation of phycoerythrin in large sclae.

[Photodynamic effect of two kinds of phycobiliproteins on human liver cancer cell line SMMC-7721 in vitro].

We studied the effect of photodynamic therapy with phycobiliproteins on human liver cancer cells in vitro. With 3-(4, 5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay (MTT assay), we used two phycobiliproteins, R-phycoerythrin (R-PE) and C-phycocyanin (C-PC) prepared from Porphyra yezoensis, to determine the killing rates and apoptosis rates of human liver cancer cells (SMMC-7721) mediated by laser. When the concentration of R-PE was 120 mg/L, the survival rate of human liver cancer cells was 27% after treated by Argon laser with 100 J/cm2 doses, while the survival rate in the control group (without adding R-PE) was 65%. When the C-PC concentration was 120 mg/L, the survival cell rate was 47% after treated by He-Ne laser with 35 J/cm2 dose, while the survival rate in the control group (without adding C-PC) was 70%. After handled only with these two kinds of phycobiliproteins for 72 h, the growth of cancer cells presented significant inhibition. The maximal inhibition rates reached up to 31% with R-PE (120 mg/L concentration) and 27% with C-PC (250 mg/L concentration) respectively. After irradiated by laser for 8 h, the maximal cell apoptosis rates were 31.54% with R-PE and 32.54% with C-PC, respectively. It indicated that R-PE and C-PC extracted from Porphyra yezoensis could develop to new photosensitizers for cancer photodynamic therapy.