An easy-operation aptasensor for simultaneous detection of multiple tumor-associated exosomal proteins based on multicolor fluorescent DNA nanoassemblies.

As a promising liquid biopsy biomarker, exosomes have demonstrated great potential and advantages in the noninvasive tumor diagnosis. However, an accurate and sensitive method for tumors-associated exosomes detection is scarce. Herein, we presented an easy-operation aptasensor which simultaneously detect multiple exosomal proteins by using multicolor fluorescent DNA nanoassemblies (FDNs) and CD63 aptamer-modified magnetic beads (MNPs-AptCD63). In this system, the FDNs were firstly constructed by encapsulating different quantum dots (QDs) into rolling circle amplification (RCA) products that contained different aptamer sequences. Thus, the FDNs could selectively recognize the different exosomal proteins captured by the MNPs-AptCD63, and achieve the multiplex and sensitive detection according to the fluorescence of QDs. Benefiting from the signal amplification capacity and high selectivity of FDNs, this aptasensor not only could detect exosomes as low as 650 particles/µL, but also showed accurate analysis in clinical samples. In addition, we can also achieve point-of-care testing (POCT) due to the simple analysis steps and naked-eye observable fluorescence of QDs under the ultraviolet irradiation. We believe that our aptasensor could provide a promising platform for exosomes-based personalized diagnosis and precise monitoring of human health.

The complete genome sequence of the planctomycetotal bacterium Bremerella sp. P1 with abundant genes involved in polysaccharide degradation.

Isolated from intertidal sediment of the Yellow Sea, China, Bremerella sp. P1 putatively represents a novel species within the genus Bremerella of the family Pirellulaceae in the phylum Planctomycetota. The complete genome of strain P1 comprises a single circular chromosome with a size of 6,955,728 bp and a GC content of 55.26%. The genome contains 5772 protein-coding genes, 80 tRNA and 6 rRNA genes. A total of 147 CAZymes and 128 sulfatases have been identified from the genome of strain P1, indicating that the strain has the capability to degrade a wide range of polysaccharides. Moreover, a gene cluster related to bacterial microcompartments (BMCs) formation containing genes encoding the shell proteins and related enzymes to metabolize fucose or rhamnose is also found in the genome of strain P1. The genome of strain P1 represents the second complete one in the genus Bremerella, expanding the understanding of the physiological and metabolic characteristics, interspecies diversity, and ecological functions of the genus.

YTHDC1/CRM1 Facilitates m6A-Modified circRNA388 Nuclear Export to Induce Coelomocyte Autophagy via the miR-2008/ULK Axis in Apostichopus japonicus.

N 6-methyladenosine (m6A), the most prevalent internal modification in eukaryotic RNA, was able to mediate circular RNA (circRNA) function in many immune processes. Nevertheless, the functional role of m6A-modified circRNAs in innate immunity of invertebrates remained unclear. In this study, we identified m6A-modified circRNA388 from cultured sea cucumber (Apostichopus japonicus) coelomocytes, which was mainly detected in cytoplasm after Vibrio splendidus infection. A knockdown assay indicated that cytoplasm circRNA388 promoted coelomocyte autophagy and decreased the number of intracellular V. splendidus. Mechanistically, the circRNA388 in the cytoplasm directly sponged miR-2008 to block its interaction with Unc-51-like kinase 1 from A. japonicus (AjULK) and further promoted autophagy to resist V. splendidus infection. More importantly, we found that m6A modification was vital to circRNA388 nuclear export with YTH domain-containing protein 1 from A. japonicus (AjYTHDC1) as the reader. AjYTHDC1 facilitated the nuclear export of m6A-modified circRNA388 via interaction with exportin-1 (chromosomal maintenance 1) from A. japonicus (AjCRM1). Knockdown of AjCRM1 could significantly decrease the content of cytoplasm circRNA388. Overall, our results provide the first evidence that nuclear export of m6A-modified circRNA388 is dependent on the novel AjCRM1 to our knowledge, which was further promoted coelomocyte autophagy by miR-2008/AjULK axis to clear intracellular V. splendidus.

Bias-free driven ion assisted photoelectrochemical system for sustainable wastewater treatment.

Photoelectrochemical (PEC) systems have emerged as a prominent renewable energy-based technology for wastewater treatment, offering sustainable advantages such as eliminating dependence on fossil fuels or grid electricity compared to traditional electrochemical treatment methods. However, previous PEC systems often overlook the potential of ions present in wastewater as an alternative to externally applied bias voltage for enhancing carrier separation efficiency. Here we report a bias-free driven ion assisted photoelectrochemical (IAPEC) system by integration of an electron-ion acceptor cathode, which leverages its fast ion-electron coupling capability to significantly enhance the separation of electrons and holes at the photoanode. We demonstrate that Prussian blue analogues (PBAs) can serve as robust and reversible electron-ion acceptors that provide reaction sites for photoelectron coupling cations, thus driving the hole oxidation to produce strong oxidant free radicals at photoanode. Our IAPEC system exhibits superior degradation performance in wastewater containing chloride medium. This indicates that, in addition to the cations (e.g., Na+) accelerating the electron transfer rate, the presence of Cl- ions further enhance efficient and sustainable wastewater treatment. This work highlights the potential of utilizing abundant sodium chloride in seawater as a cost-effective additive for wastewater treatment, offering crucial insights into the use of local materials for effective, low-carbon, and sustainable treatment processes.

Spleen stiffness determined by spleen-dedicated device accurately predicted esophageal varices in cirrhosis patients.

Background: The advantages of spleen stiffness in prediction of high-risk varices (HRV) in cirrhosis patients have been confirmed. Recently, a new device utilizing a 100 Hz probe dedicated to spleen stiffness measurement (SSM) was developed. Objectives: To validate the clinical applicability of SSM@100 Hz in predicting HRV by comparing it with other non-invasive tests (NITs). Design: A prospective cohort study. Methods: A total of 171 cirrhosis patients who underwent esophagogastroduodenoscopy (EGD) examination were included in this study. SSM using a 100 Hz probe and liver stiffness measurement using a 50 Hz probe were performed. Additionally, 22 healthy controls underwent spleen stiffness evaluation using the 100 Hz probe. Results: The failure rates of spleen stiffness examination in patients with cirrhosis and in healthy controls were 2.9% and 4.5%, respectively. The means of SSM values were 56.4 ± 21.6 and 13.8 ± 6.7 kPa in cirrhosis and controls. SSM increased proportionally with the severity of esophageal varices. The area under receiver operating characteristic (ROC) for spleen stiffness in predicting HRV was 0.881 (95% confidence interval 0.829-0.934), with a cutoff value of 43.4 kPa. The accuracy, false negative rate and EGD spare rate were 86.5%, 2.5% and 24.3%, respectively. For HRV prediction, SSM was comparable to expanded Baveno VI and VII and superior to other NITs. As to viral versus non-viral cirrhosis and compensated versus decompensated cirrhosis, the cut-off and performance of SSM were different. Conclusion: SSM@100 Hz demonstrates high accuracy in predicting HRV with a low missed HRV rate. Our findings suggest that SSM@100 Hz can be used independently due to its simplicity and effectiveness. However, further studies are needed to determine appropriate cutoff values based on the cause of cirrhosis and liver function. Trail Registration: ChiCTR2300070270.

SAR92 clade bacteria are potentially important DMSP degraders and sources of climate-active gases in marine environments.

Dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur molecules, which can be catabolized by marine bacteria to release climate-active gases through the cleavage and/or demethylation pathways. The marine SAR92 clade is an abundant oligotrophic group of Gammaproteobacteria in coastal seawater, but their ability to catabolize DMSP is untested. Three SAR92 clade strains isolated from coastal seawater in this study and the SAR92 representative strain HTCC2207 were all shown to catabolize DMSP as a carbon source. All the SAR92 clade strains exhibited DMSP lyase activity producing dimethylsulfide (DMS) and their genomes encoded a ratified DddD DMSP lyase. In contrast, only HTCC2207 and two isolated strains contained the DMSP demethylase dmdA gene and potentially simultaneously demethylated and cleaved DMSP to produce methanethiol (MeSH) and DMS. In SAR92 clade strains with dddD and dmdA, transcription of these genes was inducible by DMSP substrate. Bioinformatic analysis indicated that SAR92 clade bacteria containing and transcribing DddD and DmdA were widely distributed in global oceans, especially in polar regions. This study highlights the SAR92 clade of oligotrophic bacteria as potentially important catabolizers of DMSP and sources of the climate-active gases MeSH and DMS in marine environments, particularly in polar regions.IMPORTANCECatabolism of dimethylsulfoniopropionate (DMSP) by marine bacteria has important impacts on the global sulfur cycle and climate. However, whether and how members of most oligotrophic bacterial groups participate in DMSP metabolism in marine environments remains largely unknown. In this study, by characterizing culturable strains, we have revealed that bacteria of the SAR92 clade, an abundant oligotrophic group of Gammaproteobacteria in coastal seawater, can catabolize DMSP through the DMSP lyase DddD-mediated cleavage pathway and/or the DMSP demethylase DmdA-mediated demethylation pathway to produce climate-active gases dimethylsulfide and methanethiol. Additionally, we found that SAR92 clade bacteria capable of catabolizing DMSP are widely distributed in global oceans. These results indicate that SAR92 clade bacteria are potentially important DMSP degraders and sources of climate-active gases in marine environments that have been overlooked, contributing to a better understanding of the roles and mechanisms of the oligotrophic bacteria in oceanic DMSP degradation.

Spartinivicinus marinus sp. nov., isolated from intertidal sediment.

A Gram-stain-negative, aerobic, flagellated, and long rod-shaped bacterium, designated strain SM1973T, was isolated from an intertidal sediment sample collected from the coast of Qingdao, PR China. Strain SM1973T grew at 15-37 °C and with 0-5.5 % NaCl. It reduced nitrate to nitrite and hydrolysed aesculin but did not hydrolyse casein and gelatin. The strain showed the highest 16S rRNA gene sequence similarity (98.2 %) to the type strain of Spartinivicinus ruber. The phylogenetic trees based on the 16S rRNA genes and single-copy orthologous clusters showed that strain SM1973T clustered with S. ruber, forming a separate lineage within the family Zooshikellaceae. The major cellular fatty acids were summed feature 3 (C16 : 1 ω7с and/or C16 : 1 ω6с) and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The main respiratory quinone was ubiquinone-9. The genomic DNA G+C content of strain SM1973T was 40.4 mol%. Based on the polyphasic evidence presented in this paper, strain SM1973T is considered to represent a novel species within the genus Spartinivicinus, for which the name Spartinivicinus marinus sp. nov. is proposed. The type strain is SM1973T (=MCCC 1K04833T=KCTC 72846T).

N6-methyladenosine helps Apostichopus japonicus resist Vibrio splendidus infection by targeting coelomocyte autophagy via the AjULK-AjYTHDF/AjEEF-1α axis.

N6-Methyladenosine (m6A) modification is one of the most abundant post-transcriptional modifications that can mediate autophagy in various pathological processes. However, the functional role of m6A in autophagy regulation is not well-documented during Vibrio splendidus infection of Apostichopus japonicus. In this study, the inhibition of m6A level by knockdown of methyltransferase-like 3 (AjMETTL3) significantly decreased V. splendidus-induced coelomocyte autophagy and led to an increase in the intracellular V. splendidus burden. In this condition, Unc-51-like kinase 1 (AjULK) displayed the highest differential expression of m6A level. Moreover, knockdown of AjULK can reverse the V. splendidus-mediated autophagy in the condition of AjMETTL3 overexpression. Furthermore, knockdown of AjMETTL3 did not change the AjULK mRNA transcript levels but instead decreased protein levels. Additionally, YTH domain-containing family protein (AjYTHDF) was identified as a reader protein of AjULK and promoted AjULK expression in an m6A-dependent manner. Furthermore, the AjYTHDF-mediated AjULK expression depended on its interaction with translation elongation factor 1-alpha (AjEEF-1α). Altogether, our findings suggest that m6A is involved in resisting V. splendidus infection via facilitating coelomocyte autophagy in AjULK-AjYTHDF/AjEEF-1α-dependent manner, which provides a theoretical basis for disease prevention and therapy in A. japonicus.

circRNA432 enhances the coelomocyte phagocytosis via regulating the miR-2008-ELMO1 axis in Vibrio splendidus-challenged Apostichopus japonicus.

Circular RNAs (circRNAs) are a kind of extensive and diverse covalently closed circular endogenous RNA, which exert crucial functions in immune regulation in mammals. However, the functions and mechanisms of circRNAs in invertebrates are largely unclarified. In our previous work, 261 differentially expressed circRNAs including circRNA432 (circ432) were identified from skin ulcer syndrome (SUS) diseased sea cucumber Apostichopus japonicus by RNA-seq. To better address the functional role of sea cucumber circRNAs, circ432 was first found to be significantly induced by Vibrio splendidus challenge and LPS exposure in this study. Knock-down circ432 could depress the V. splendidus-induced coelomocytes phagocytosis. Moreover, circ432 is validated to serve as the sponge of miR-2008, a differential expressed miRNA in SUS-diseased sea cucumbers, by Argonaute 2-RNA immunoprecipitation (AGO2-RIP) assay, luciferase reporter assay and RNA fluorescence in situ hybridization (FISH) in vitro. Engulfment and cell motility protein 1 (AjELMO1) is further demonstrated to be the target of miR-2008, and silencing AjELMO1 inhibits the V. splendidus-induced coelomocytes phagocytosis, and this phenomenon could be further suppressed by supplementing with miR-2008 mimics, suggesting that circ432 might regulate coelomocytes phagocytosis via miR-2008-AjELMO1 axis. We further confirm that the depressed coelomocytes' phagocytosis by circ432 silencing is consistent with the decreased abundance of AjELMO1, and could be recovered by miR-2008 inhibitors transfection. All our results provide the evidence that circ432 is involved in regulating pathogen-induced coelomocyte phagocytosis via sponge miR-2008 and promotes the abundance of AjELMO1. These findings will enrich the regulatory mechanism of phagocytosis in echinoderm and provide theoretical data for SUS disease prevention and control in sea cucumbers.

MATE transporter GFD1 cooperates with sugar transporters, mediates carbohydrate partitioning and controls grain-filling duration, grain size and number in rice.

More than half of the world's food is provided by cereals, as humans obtain >60% of daily calories from grains. Producing more carbohydrates is always the final target of crop cultivation. The carbohydrate partitioning pathway directly affects grain yield, but the molecular mechanisms and biological functions are poorly understood, including rice (Oryza sativa L.), one of the most important food sources. Here, we reported a prolonged grain filling duration mutant 1 (gfd1), exhibiting a long grain-filling duration, less grain number per panicle and bigger grain size without changing grain weight. Map-based cloning and molecular biological analyses revealed that GFD1 encoded a MATE transporter and expressed high in vascular tissues of the stem, spikelet hulls and rachilla, but low in the leaf, controlling carbohydrate partitioning in the stem and grain but not in the leaf. GFD1 protein was partially localized on the plasma membrane and in the Golgi apparatus, and was finally verified to interact with two sugar transporters, OsSWEET4 and OsSUT2. Genetic analyses showed that GFD1 might control grain-filling duration through OsSWEET4, adjust grain size with OsSUT2 and synergistically modulate grain number per panicle with both OsSUT2 and OsSWEET4. Together, our work proved that the three transporters, which are all initially classified in the major facilitator superfamily family, could control starch storage in both the primary sink (grain) and temporary sink (stem), and affect carbohydrate partitioning in the whole plant through physical interaction, giving a new vision of sugar transporter interactome and providing a tool for rice yield improvement.

Corrigendum: CircRNA75 and CircRNA72 Function as the Sponge of MicroRNA-200 to Suppress Coelomocyte Apoptosis Via Targeting Tollip in Apostichopus japonicus.

[This corrects the article DOI: 10.3389/fimmu.2021.770055.].

Effect of High-Voltage Electrostatic Field Heating on the Oxidative Stability of Duck Oils Containing Diacylglycerol.

High-voltage electrostatic field (HVEF) as an emerging green technology is just at the beginning of its use in meat products and by-products processing. In this study, we employed duck oil to produce duck-oil-based diacylglycerol (DAG), termed DDAG. Three different DDAG volume concentrations (0, 20%, and 100%) of hybrid duck oils, named 0%DDAG, 20%DDAG, and 100%DDAG, respectively, were used to investigate their thermal oxidation stability in high-voltage electrostatic field heating and ordinary heating at 180 ± 1 ℃. The results show that the content of saturated fatty acids and trans fatty acids of the three kinds of duck oils increased (p < 0.05), while that of polyunsaturated fatty acids decreased (p < 0.05) from 0 h to 8 h. After heating for 8 h, the low-field nuclear magnetic resonance showed that the transverse relaxation time (T21) of the three oils decreased (p < 0.05), while the peak area ratio (S21) was increased significantly (p < 0.05). The above results indicate that more oxidation products were generated with heating time. The peroxide value, the content of saturated fatty acids, and the S21 increased with more DAG in the duck oil, which suggested that the oxidation stability was likely negatively correlated with the DAG content. Moreover, the peroxide value, the content of saturated fatty acids and trans fatty acids, and the S21 of the three concentrations of duck oils were higher (p < 0.05) under ordinary heating than HVEF heating. It was concluded that HVEF could restrain the speed of the thermal oxidation reaction occurring in the duck oil heating and be applied in heating conditions.

Src kinase mediates coelomocytes phagocytosis via interacting with focal adhesion kinase in Vibrio splendidus challenged Apostichopus japonicus.

Immune cells have many efficient ways to participate in the host immunity, including phagocytosis, which is an important pathway to eliminate pathogens. Only ß-integrin-mediated phagocytosis pathways have been confirmed in Apostichopus japonicus. The Src family kinases (SFKs), a class of non-receptor tyrosine kinases plays an important role in the regulation of phagocytic signals in invertebrates. However, the SFK-mediated phagocytic mechanism is largely unknown in A. japonicus. In this study, a novel SFK homologue (AjSrc) with a conservative SH3 domain, an SH2 domain, and a tyrosine kinase domain was identified from A. japonicus. Both gene and protein expression of AjSrc and phosphorylation levels increased under Vibrio splendidus challenged, reaching the highest level at 24 h. Knock-down of AjSrc could depress coelomocytes' phagocytosis by 25% compared to the control group. To better understand the mechanism of AjSrc-mediated phagocytosis, focal adhesion kinase (FAK) was identified by a Co-immunoprecipitation experiment to be verified as an interactive protein of AjSrc. The phagocytosis rates of coelomocytes were decreased by 33% and 37% in AjFAK and AjSrc + AjFAK interference groups compared with the control group, respectively. Furthermore, the phosphorylation level of AjFAK was increased and reached the maximum level at 24 h post V. splendidus infection, as the same as that of AjSrc. Our results suggested that AjSrc could mediate V. splendidus-induced coelomocytes' phagocytosis via interacting with AjFAK and co-phosphorylation. This study enriched the mechanism of phagocytosis in echinoderm and provided the new theoretical foundation for disease control of sea cucumber.

CircRNA75 and CircRNA72 Function as the Sponge of MicroRNA-200 to Suppress Coelomocyte Apoptosis Via Targeting Tollip in Apostichopus japonicus.

Circular RNAs (circRNAs) act as essential regulators in many biological processes, especially in mammalian immune response. Nonetheless, the functions and mechanisms of circRNAs in the invertebrate immune system are largely unclarified. In our previous work, 261 differentially expressed circRNAs potentially related to the development of Apostichopus japonicus skin ulceration syndrome (SUS), which is a major problem restricting the sea cucumber breeding industry, were identified by genome-wide screening. In this study, via miRanda analysis, both circRNA75 and circrRNA72 were shown to share the miR-200 binding site, a key microRNA in the SUS. The two circRNAs were verified to be increased significantly in LPS-exposed primary coelomocytes, similar to the results of circRNA-seq in sea cucumber under Vibrio splendidus-challenged conditions. A dual-luciferase assay indicated that both circRNA75 and circRNA72 could bind miR-200 in vivo, in which circRNA75 had four binding sites of miR-200 and only one for circRNA72. Furthermore, we found that miR-200 could bind the 3'-UTR of Toll interacting protein (Tollip) to negatively mediate the expression of Tollip. Silencing Tollip increased primary coelomocyte apoptosis. Consistently, inference of circRNA75 and circRNA72 could also downregulate Tollip expression, thereby increasing the apoptosis of primary coelomocytes, which could be blocked by miR-200 inhibitor treatment. Moreover, the rate of si-circRNA75-downregulated Tollip expression was higher than that of si-circRNA72 under an equivalent amount. CircRNA75 and circRNA72 suppressed coelomocyte apoptosis by sponging miR-200 to promote Tollip expression. The ability of circRNA to adsorb miRNA might be positively related to the number of binding sites for miRNA.

Cyclophilin A mediates coelomocyte apoptosis via the NF-κB/Bcl-2 signaling pathway in Apostichopus japonicus.

As a multifunctional protein, cyclophilin A (CypA) plays an important role in cell apoptosis. In our previous work, we found that CypA from Apostichopus japonicus (AjCypA), as a cofactor, could modulate nuclear translocation of NF-κB. However, the immune function of AjCypA is largely unknown. In the present study, we found that siRNA-mediated AjCypA knockdown in vivo significantly increased the coelomocyte apoptosis rate. In addition, the expression of B-cell lymphoma-2 (AjBcl-2, an anti-apoptosis gene) was synchronously downregulated. To better understand the connection between AjCypA and AjBcl-2 expression, we cloned the promoter of AjBcl-2 via genomic walking, which spanned 1870 bp and contained four potential binding sites of NF-κB. Dual-luciferase reporter assay revealed that the full-length sequence and all truncated fragments exhibited high transcriptional activity. Moreover, 1 µg/mL LPS exposure significantly increased the luciferase activity of P1 (-1870/+57) by 2.31-fold and 3.15-fold at 12 and 24 h, respectively. Furthermore, the four potential NF-κB binding sites and pCMV-Flag2C-AjNF-κB co-transfection assay demonstrated that NF-κB could regulate the expression of AjBcl-2 via the NF-κB binding sites of AjBcl-2 promoter. All results supported that AjCypA mediates coelomocyte apoptosis via NF-κB/AjBcl-2 signaling pathway in A. japonicus.

A cyclophilin A (CypA) from Apostichopus japonicus modulates NF-κB translocation as a cofactor.

As a ubiquitously expressed protein, cyclophilin A (CypA) is involved in a variety of pathological process, including immune suppression, inflammation, cell apoptosis, viral infection and stress response. However, the functional roles of CypA were largely unknown in economic marine animals. In this report, a novel CypA gene from sea cucumber Apostichopus japonicus (designated as AjCypA) was cloned and its function roles in immune responses were explored. The full-length cDNA of AjCypA was 1297 bp containing an open reading frame of 489 bp encoding a putative protein of 162 amino acids (aa). A conserved cyclophilin-like domain (CLD) with PPIase signature was located from 5 to 155 aa sequences in AjCypA, in which five necessary aa residues was totally conserved. In healthy sea cucumbers, AjCypA was expressed in all detected tissues, with highly expressed in muscles and weakly expressed in coelomocytes. AjCypA transcripts was significantly induced 8.08-fold and 5.65-fold in coelomocytes when sea cucumbers challenged with Vibrio splendidus in vivo and LPS in vitro, respectively. The expression pattern is similar with the expression of AjRel in the same condition. Moreover, GST pull-down and immunofluorescence analysis both revealed that AjCypA might be interacted with AjRel. Furthermore, AjCypA knockdown not only inhibited the expression of inflammation cytokines, but also suppressed the translocation of AjRel in nucleus induced by LPS. Taken together, our results suggested that AjCypA play key roles in V. splendidus mediated immune responses via suppressing the nuclear translocation of AjRel activity in sea cucumber.

GRA78 encoding a putative S-sulfocysteine synthase is involved in chloroplast development at the early seedling stage of rice.

Cysteine functions not only as an amino acid in proteins but also as a precursor for a large number of essential biomolecules. Cysteine is synthesized via the incorporation of sulfide to O-acetylserine under the catalysis of O-acetylserine(thiol)lyase (OASTL). In dicotyledonous Arabidopsis, nine OASTL genes have been reported. However, in their null mutants, only the mutant of CS26 encoding S-sulfocysteine synthase showed the visible phenotypic changes, displaying significantly small plants and pale-green leaves under long-day condition but not short-day condition. Up to now, no OASTL gene or mutant has been identified in monocotyledon. In this study, we isolated a green-revertible albino mutant gra78 in rice (Oryza sativa). Its albino phenotype at the early seedling stage was sensitive to temperature but independent of photoperiod. Map-based cloning revealed that candidate gene LOC_Os01g59920 of GRA78 encodes a putative S-sulfocysteine synthase showing significant similarity with Arabidopsis CS26. Complementation experiment confirmed that mutation in LOC_Os01g59920 accounted for the mutant phenotype of gra78. GRA78 is constitutively expressed in all tissues and its encoded protein is targeted to the chloroplast. In addition, qRT-PCR suggested that expression levels of four OASTL homolog genes and five photosynthetic genes were remarkably down-regulated.

Petroleum hydrocarbon persistence following the Deepwater Horizon oil spill as a function of shoreline energy.

An important aspect of oil spill science is understanding how the compounds within spilled oil, especially toxic components, change with weathering. In this study we follow the evolution of petroleum hydrocarbons, including n-alkanes, polycyclic aromatic hydrocarbons (PAHs) and alkylated PAHs, on a Louisiana beach and salt marsh for three years following the Deepwater Horizon spill. Relative to source oil, we report overall depletion of low molecular weight n-alkanes and PAHs in all locations with time. The magnitude of depletion, however, depends on the sampling location, whereby sites with highest wave energy have highest compound depletion. Oiled sediment from an enclosed bay shows high enrichment of high molecular weight PAHs relative to 17α(H),21ß(H)-hopane, suggesting the contribution from sources other than the Deepwater Horizon spill, such as fossil fuel burning. This insight into hydrocarbon persistence as a function of hydrography and hydrocarbon source can inform policy and response for future spills.

Potential Environmental Factors Affecting Oil-Degrading Bacterial Populations in Deep and Surface Waters of the Northern Gulf of Mexico.

Understanding bacterial community dynamics as a result of an oil spill is important for predicting the fate of oil released to the environment and developing bioremediation strategies in the Gulf of Mexico. In this study, we aimed to elucidate the roles of temperature, water chemistry (nutrients), and initial bacterial community in selecting oil degraders through a series of incubation experiments. Surface (2 m) and bottom (1537 m) waters, collected near the Deepwater Horizon site, were amended with 200 ppm light Louisiana sweet crude oil and bacterial inoculums from surface or bottom water, and incubated at 4 or 24°C for 50 days. Bacterial community and residual oil were analyzed by pyrosequencing and gas chromatography-mass spectrometry (GC-MS), respectively. The results showed that temperature played a key role in selecting oil-degrading bacteria. Incubation at 4°C favored the development of Cycloclasticus, Pseudoalteromonas, Sulfitobacter, and Reinekea, while 24°C incubations enhanced Oleibacter, Thalassobius, Phaeobacter, and Roseobacter. Water chemistry and the initial community also had potential roles in the development of hydrocarbon-degrading bacterial communities. Pseudoalteromonas, Oleibacter, and Winogradskyella developed well in the nutrient-enriched bottom water, while Reinekea and Thalassobius were favored by low-nutrient surface water. We revealed that the combination of 4°C, crude oil and bottom inoculum was a key factor for the growth of Cycloclasticus, while the combination of surface inoculum and bottom water chemistry was important for the growth of Pseudoalteromonas. Moreover, regardless of the source of inoculum, bottom water at 24°C was a favorable condition for Oleibacter. Redundancy analysis further showed that temperature and initial community explained 57 and 19% of the variation observed, while oil and water chemistry contributed 14 and 10%, respectively. Overall, this study revealed the relative roles of temperature, water chemistry, and initial bacterial community in selecting oil degraders and regulating their evolution in the northern Gulf of Mexico.