Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves.

BACKGROUND: Bivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves. Here, we investigate the hologenome of an extracellular symbiotic thyasirid clam that represents the early stages of symbiosis evolution. RESULTS: We present a hologenome of Conchocele bisecta (Bivalvia: Thyasiridae) collected from deep-sea hydrothermal vents with extracellular symbionts, along with related ultrastructural evidence and expression data. Based on ultrastructural and sequencing evidence, only one dominant Thioglobaceae bacteria was densely aggregated in the large bacterial chambers of C. bisecta, and the bacterial genome shows nutritional complementarity and immune interactions with the host. Overall, gene family expansions may contribute to the symbiosis-related phenotypic variations in different bivalves. For instance, convergent expansions of gaseous substrate transport families in the endosymbiotic bivalves are absent in C. bisecta. Compared to endosymbiotic relatives, the thyasirid genome exhibits large-scale expansion in phagocytosis, which may facilitate symbiont digestion and account for extracellular symbiotic phenotypes. We also reveal that distinct immune system evolution, including expansion in lipopolysaccharide scavenging and contraction of IAP (inhibitor of apoptosis protein), may contribute to the different manners of bacterial virulence resistance in C. bisecta. CONCLUSIONS: Thus, bivalves employ different pathways to adapt to the long-term co-existence with their bacterial symbionts, further highlighting the contribution of stochastic evolution to the independent gain of a symbiotic lifestyle in the lineage.

Dimensional changes in free gingival grafts at implant sites in the reconstructed mandible: a retrospective study.

OBJECTIVE: To evaluate the dimensional changes in free gingival grafts (FGG) at implant sites in mandibular reconstruction patients. METHODS: Patients who received FGG 4 months after implant placement in the reconstructed mandible with no keratinized mucosa (KM) present were invited for re-examination after 36.7 ± 16.8 months (3.06 ± 1.4 years). Immediately after graft extraction (T0), graft width (GW), graft length (GL), graft thickness (GT), graft dimension (GD), and vertical bone height were documented. Re-examination (T1) included clinical examinations (GW, GL, GD, peri-implant probing depths, and modified Sulcus Bleeding Index), radiographic examination (marginal bone level), and medical chart review. RESULTS: Twenty patients and 62 implants (47 in fibula flaps and 15 in iliac flaps) were included. A significant decrease in GW (51.8%), GL (19.2%), and GD (60.2%), were found between T0 and T1 (p < .001). The univariate analysis showed that GW change was not significantly associated with reconstruction technique, baseline GL, baseline GT, baseline GD, implant location, or type of prosthesis. Implant survival rate of 100% was observed at follow-up. CONCLUSIONS: Within the limitations of the study, free gingival grafts at implant sites in the reconstructed mandible undergo dimensional change that result in a reduction of approximately 60% of the original graft dimension. Graft width decreased over 50%. CLINICAL RELEVANCE: FGG is the standard of care intervention for increasing the amount of KM around implants. This study was the first to evaluate the dimensional change in FGG at implant sites in mandibular reconstruction patients after a medium-term follow-up. CLINICAL TRIAL REGISTRATION: Clinical trial registration is not applicable as this study comprehends a retrospective analysis.

Insights into symbiotic interactions from metatranscriptome analysis of deep-sea mussel Gigantidas platifrons under long-term laboratory maintenance.

Symbioses between invertebrates and chemosynthetic bacteria are of fundamental importance in deep-sea ecosystems, but the mechanisms that enable their symbiont associations are still largely undescribed, owing to the culturable difficulties of deep-sea lives. Bathymodiolinae mussels are remarkable in their ability to overcome decompression and can be maintained successfully for an extended period under atmospheric pressure, thus providing a model for investigating the molecular basis of symbiotic interactions. Herein, we conducted metatranscriptome sequencing and gene co-expression network analysis of Gigantidas platifrons under laboratory maintenance with gradual loss of symbionts. The results revealed that one-day short-term maintenance triggered global transcriptional perturbation in symbionts, but little gene expression changes in mussel hosts, which were mainly involved in responses to environmental changes. Long-term maintenance with depleted symbionts induced a metabolic shift in the mussel host. The most notable changes were the suppression of sterol biosynthesis and the complementary activation of terpenoid backbone synthesis in response to the reduction of bacteria-derived terpenoid sources. In addition, we detected the upregulation of host proteasomes responsible for amino acid deprivation caused by symbiont depletion. Additionally, a significant correlation between host microtubule motor activity and symbiont abundance was revealed, suggesting the possible function of microtubule-based intracellular trafficking in the nutritional interaction of symbiosis. Overall, by analyzing the dynamic transcriptomic changes during the loss of symbionts, our study highlights the nutritional importance of symbionts in supplementing terpenoid compounds and essential amino acids and provides insight into the molecular mechanisms and strategies underlying the symbiotic interactions in deep-sea ecosystems.

Aequorivita iocasae sp. nov., a halophilic bacterium isolated from sediment collected at a cold seep field in the South China Sea.

A moderately halophilic bacterium, designated strain KX20305T, was isolated from sediment collected from a cold seep field in the South China Sea. Cells of strain KX20305T were Gram-stain-negative, rod-shaped, non-motile, facultatively anaerobic, oxidase- and catalase-positive, and grew optimally at 25-30 °C, pH 6.0-8.0 and with 3-6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KX20305T grouped with members of the genus Aequorivita, including Aequorivita aquimaris D-24T (98.3 % sequence similarity), Aequorivita vladivostokensis KMM 3516T (98.1 %) and Aequorivita echinoideorum CC-CZW007T (97.5 %). Genome sequencing of strain KX20305T revealed a genome size of 3.35 Mb and a DNA G+C content of 38.71 mol%. Genomic average nucleotide identity (orthoANI) values of strain KX20305T with A. aquimaris D-24T, A. vladivostokensis KMM 3516T and A. echinoideorum JCM 30378T were 83.8, 81.7 and 75.4 %, respectively, while in silico DNA-DNA hybridization (GGDC) values for strain KX20305T with these strains were 27.2, 25.0 and 19.6 %, respectively. The major fatty acids of strain KX20305T were iso-C15 : 0, iso-C17 : 0 3-OH and 10-methyl C16 : 0/iso-C17 : 1 ω9c. The predominant respiratory quinone was menaquinone-6 (MK-6). The polar lipids mainly comprised phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. Based on comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain KX20305T represents a novel species of the genus Aequorivita, for which the name Aequorivita iocasae sp. nov. is proposed. The type strain is KX20305T (=KCTC 82699T=MCCC 1K06238T=JCM 34635T).

A glimpse of deep-sea adaptation in chemosynthetic holobionts: Depressurization causes DNA fragmentation and cell death of methanotrophic endosymbionts rather than their deep-sea Bathymodiolinae host.

Bathymodiolinae mussels are typical species in deep-sea cold seeps and hydrothermal vents and an ideal model for investigating chemosynthetic symbiosis and the influence of high hydrostatic pressure on deep-sea organisms. Herein, the potential influence of depressurization on DNA fragmentation and cell death in Bathymodiolinae hosts and their methanotrophic symbionts were surveyed using isobaric and unpressurized samples. As a hallmark of cell death, massive DNA fragmentation was observed in methanotrophic symbionts from unpressurized Bathymodiolinae while several endonucleases and restriction enzymes were upregulated. Additionally, genes involved in DNA repair, glucose/methane metabolism as well as two-component regulatory system were also differentially expressed in depressurized symbionts. DNA fragmentation and programmed cell death, however, were rarely detected in the host bacteriocytes owing to the orchestrated upregulation of inhibitor of apoptosis genes and downregulation of caspase genes. Meanwhile, diverse host immune recognition receptors were promoted during depressurization, probably enabling the regain of symbionts. When the holobionts were subjected to a prolonged acclimation at atmospheric pressure, alternations in both the DNA fragmentation and the expression atlas of aforesaid genes were continuously observed in symbionts, demonstrating the persistent influence of depressurization. Contrarily, the host cells demonstrated certain tolerance against depressurization stress as expression level of some immune-related genes returned to the basal level in isobaric samples. Altogether, the present study illustrates the distinct stress responses of Bathymodiolinae hosts and their methanotrophic symbionts against depressurization, which could provide further insight into the deep-sea adaptation of Bathymodiolinae holobionts while highlighting the necessity of using isobaric sampling methods in deep-sea research.

The value of ultrasonography combined with clinical features for predicting carotid imaging progression of Takayasu's arteritis: a prospective cohort study.

OBJECTIVES: To identify valuable ultrasonography findings combined with clinical markers for predicting carotid progression of Takayasu's arteritis (TAK) on imaging during a 1-year follow-up period. METHODS: From May 2016 to June 2019, 77 Chinese TAK patients with carotid artery involvement were enrolled in the present study. The patients' clinical characteristics and serological test and carotid ultrasonography results were recorded at baseline and each visit. Carotid progression was evaluated by ultrasonography every 3 months during the 1-year follow-up. Baseline clinical characteristics and ultrasonography results for predicting progression on imaging were identified. RESULTS: Sixteen (20.8%) patients presented with carotid progression on imaging during the 1-year follow-up period. The patients in the progressive group were younger (23.4±3.7 vs. 32.3±9.8 years, p<0.01) than those in the non-progressive group. At baseline, the vessel wall was thicker in the progressive group than in the non-progressive group (2.4±0.8 vs. 1.9±0.5 mm, p=0.041). Furthermore, the proportion of patients with refractory disease (87.5% vs. 16.4%, p<0.01) was higher in the progressive group than in the non-progressive group. Patients with a thickened carotid wall (≥1.9 mm), refractory disease, and younger age (≤30 years) might be at a high risk of carotid progression on imaging (75%, AUC: 0.93, sensitivity: 75%, specificity: 93.4%). CONCLUSIONS: Younger patients with early vascular structural changes at baseline as well as refractory disease seemed more likely to show carotid progression on imaging.

microRNAs facilitate comprehensive responses of Bathymodiolinae mussel against symbiotic and nonsymbiotic bacteria stimulation.

Bathymodiolinae mussels are dominant species in cold seeps and hydrothermal vents and could harbor endosymbionts in gill bacteriocytes. However, mechanisms underlying the symbiosis have remained largely undisclosed for years. In the present study, the global expression pattern of immune-related genes and miRNAs were surveyed in Gigantidas platifrons during bacterial challenges using enriched symbiotic methane oxidation bacteria MOBs or nonsymbiotic Vibrio. As a result, multiple pattern recognition receptors were found differentially expressed at 12 h and 24 h post bacteria challenges and distinctly clustered between stimulations. Dozens of immune effectors along with signal transducers were also modulated simultaneously during MOB or Vibrio challenge. A total of 459 miRNAs were identified in the gill while some were differentially expressed post MOB or nonsymbiotic bacteria challenge. A variety of immune-related genes were annotated as target genes of aforesaid differentially expressed miRNAs. As a result, biological processes including the immune recognition, lysosome activity and bacteria engulfment were suggested to be dynamically modulated by miRNAs in either symbiotic or nonsymbiotic bacteria challenge. It was suggested that G. platifrons mussels could maintain a robust immune response against invading pathogens while establishing symbiosis with chemosynthetic bacteria with the orchestra of immune-related genes and miRNAs.

Endosymbionts of Metazoans Dwelling in the PACManus Hydrothermal Vent: Diversity and Potential Adaptive Features Revealed by Genome Analysis.

Deep-sea hydrothermal vent communities are dominated by invertebrates, namely, bathymodiolin mussels, siboglinid tubeworms, and provannid snails. Symbiosis is considered key to successful colonization by these sedentary species in such extreme environments. In the PACManus vent fields, snails, tubeworms, and mussels each colonized a niche with distinct geochemical characteristics. To better understand the metabolic potentials and genomic features contributing to host-environment adaptation, we compared the genomes of the symbionts of Bathymodiolus manusensis, Arcovestia ivanovi, and Alviniconcha boucheti sampled at PACManus, and we discuss their environmentally adaptive features. We found that B. manusensis and A. ivanovi are colonized by Gammaproteobacteria from distinct clades, whereas endosymbionts of B. manusensis feature high intraspecific heterogeneity with differing metabolic potentials. A. boucheti harbored three novel Epsilonproteobacteria symbionts, suggesting potential species-level diversity of snail symbionts. Genome comparisons revealed that the relative abundance of gene families related to low-pH homeostasis, metal resistance, oxidative stress resistance, environmental sensing/responses, and chemotaxis and motility was the highest in A. ivanovi's symbiont, followed by symbionts of the vent-mouth-dwelling snail A. boucheti, and was relatively low in the symbiont of the vent-periphery-dwelling mussel B. manusensis, which is consistent with their environmental adaptations and host-symbiont interactions. Gene families classified as encoding host interaction/attachment, virulence factors/toxins, and eukaryotic-like proteins were most abundant in symbionts of mussels and least abundant in those of snails, indicating that these symbionts may differ in their host colonization strategies. Comparison of Epsilonproteobacteria symbionts to nonsymbionts demonstrated that the expanded gene families in symbionts were related to vitamin B12 synthesis, toxin-antitoxin systems, methylation, and lipopolysaccharide biosynthesis, suggesting that these are vital to symbiont establishment and development in EpsilonproteobacteriaIMPORTANCE Deep-sea hydrothermal vents are dominated by several invertebrate species. The establishment of symbiosis has long been thought to be the key to successful colonization by these sedentary species in such harsh environments. However, the relationships between symbiotic bacteria and their hosts and their role in environmental adaptations generally remain unclear. In this paper, we show that the distribution of three host species showed characteristic niche partitioning in the Manus Basin, giving us the opportunity to understand how they adapt to their particular habitats. This study also revealed three novel genomes of symbionts from the snails of A. boucheti Combined with a data set on other ectosymbiont and free-living bacteria, genome comparisons for the snail endosymbionts pointed to several genetic traits that may have contributed to the lifestyle shift of Epsilonproteobacteria into the epithelial cells. These findings could increase our understanding of invertebrate-endosymbiont relationships in deep-sea ecosystems.

Salinimonas iocasae sp. nov., a halophilic bacterium isolated from a polychaete tube in a hydrothermal field.

A moderately halophilic bacterium, designated strain KX18D6T, was isolated from the tube of the polychaete Paralvinella hessleri collected from a hydrothermal field located in the Okinawa Trough. Strain KX18D6T was Gram-stain-negative, rod-shaped, facultatively anaerobic, motile, oxidase- and catalase-positive, and grew optimally at 30-35 °C, pH 7.0 and in the presence of 3-5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KX18D6T grouped with the members of the genus Salinimonas, including Salinimonas chungwhensis BH030046T (97.7 % sequence similarity), Salinimonas lutimaris DPSR-4T (97.2 %) and Salinimonas sediminis N102T (96.4 %). Genome sequencing of strain KX18D6T revealed a genome size of 4.16 Mb and a DNA G+C content of 47.3 mol%. Genomic average nucleotide identity (orthoANI) values of strain KX18D6T with S. chungwhensis DSM 16280T, S. lutimaris KCTC 23464T and S. sediminis N102T were 76.2, 73.1 and 73.2 %, respectively, while the in silico DNA-DNA hybridization (GGDC) values for strain KX18D6T with these strains were 25.3, 17.7 and 18.0 %, respectively. The major fatty acids were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The predominant respiratory quinone was ubiquinone 8, and the predominant polar lipids were phosphatidylethanolamine and phosphatidylglycerol. On the basis of comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain KX18D6T (=KCTC 72464T=MCCC 1K03884T) is clearly distinguishable from the type strains of species of the genus Salinimonas and is considered to represent a novel species of the genus Salinimonas, for which the name Salinimonas iocasae sp. nov. is proposed.

Nitrincola iocasae sp. nov., a bacterium isolated from sediment collected at a cold seep field in the South China Sea.

A novel bacterium, designated strain KXZD1103T, was isolated from sediment collected at a cold seep field of the Formosa Ridge in the South China Sea. Cells were Gram-stain-negative, facultatively anaerobic, motile, oxidase- and catalase-positive, and grew optimally at 28 °C, pH 6.0-pH 7.0 and in the presence of 1-3 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 0. The major respiratory ubiquinone was Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Analysis of 16S rRNA gene sequences revealed that strain KXZD1103T grouped with members of the genus Nitrincola, with Nitrincola lacisaponensis 4CAT (98.1 % sequence similarity) and Nitrincola schmidtii R4-8T (97.7 %) as its closest neighbours. Genome sequencing revealed a genome size of 4.17 Mb and a DNA G+C content of 50.1 %. Genomic average nucleotide identity values for strain KXZD1103T with the type strains within the genus Nitrincola ranged from 71.0 to 75.7 %, while the in silico DNA-DNA hybridization values for strain KXZD1103T with these strains ranged from 16.1 to 21.6 %. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses, strain KXZD1103T is considered to represent a novel species of the genus Nitrincola, for which the name Nitrincola iocasae sp. nov. is proposed. The type strain is KXZD1103T (=KCTC 72678T=MCCC 1K04283T).

Gill symbionts of the cold-seep mussel Bathymodiolus platifrons: Composition, environmental dependency and immune control.

Deep-sea Bathymodiolus mussels depend on the organic carbon supplied by symbionts inside their gills. In this study, optimized methods of quantitative real-time PCR and fluorescence in situ hybridization targeted to both mRNA and 16S rRNA were used to investigate the gill symbionts of the cold-seep mussel Bathymodiolus platifrons, including species composition, environmental dependency and immune control by the host. Our results showed that methanotrophs were the major symbiotic bacteria in the gills of B. platifrons, while thiotrophs were scarce. In the mussels freshly collected from the deep sea, methanotrophs were housed in bacteriocytes in a unique circular pattern, and a lysosome-related gene (VAMP) encoding a vesicle-associated membrane protein was expressed at a high level and presented exactly where the methanotrophs occurred. After the mussels were reared for three months in aquaria without methane supply, the abundance of methanotrophs decreased significantly and their circle-shaped distribution pattern disappeared; in addition, the expression of VAMP decreased significantly. These results suggest that the symbiosis between B. platifrons and methanotrophs is influenced by the environment and that the lysosomal system plays an important immune role in controlling the abundance of endosymbionts in host. This study provides a reliable method for investigating symbionts in deep-sea mussels and enriches the knowledge about symbionts in B. platifrons.

An LRR-domain containing protein identified in Bathymodiolus platifrons serves as intracellular recognition receptor for the endosymbiotic methane-oxidation bacteria.

As domain species in seep and vent ecosystem, Bathymodioline mussels has been regarded as a model organism in investigating deep sea chemosymbiosis. However, mechanisms underlying their symbiosis with chemosynthetic bacteria, especially how the host recognizes symbionts, have remained largely unsolved. In the present study, a modified pull-down assay was conducted using enriched symbiotic methane-oxidation bacteria as bait and gill proteins of Bathymodiolus platifrons as a target to isolate pattern recognition receptors involved in the immune recognition of symbionts. As a result, a total of 47 proteins including BpLRR-1 were identified from the pull-down assay. It was found that complete cDNA sequence of BpLRR-1 contained an open reading frame of 1479 bp and could encode a protein of 492 amino acid residues with no signal peptide or transmembrane region but eight LRR motif and two EFh motif. The binding patterns of BpLRR-1 against microbial associated molecular patterns were subsequently investigated by surface plasmon resonance analysis and LPS pull-down assay. Consequently, BpLRR-1 was found with high binding affinity with LPS and suggested as a key molecule in recognizing symbionts. Besides, transcripts of BpLRR-1 were found decreased significantly during symbiont depletion assay yet increased rigorously during symbionts or nonsymbiotic Vibrio alginolyticus challenge, further demonstrating its participation in the chemosynthetic symbiosis. Collectively, these results suggest that BpLRR-1 could serve as an intracellular recognition receptor for the endosymbionts, providing new hints for understanding the immune recognition in symbiosis of B. platifrons.

Efficacy Evaluation of Hyaluronic Acid Gel for the Restoration of Gingival Interdental Papilla Defects.

PURPOSE: This clinical study aimed to evaluate the long-term efficacy of reconstruction of the gingival interdental papilla via injection of hyaluronic acid gel. MATERIALS AND METHODS: Eight female participants with Class I or II gingival papilla loss in anterior sites were included in this study. The gingival biotype was evaluated previously. Hyaluronic acid gel was injected into the base of the deficient papilla, which was repeated twice at 3 and 6 weeks after the initial injection. The height of the gingival papilla and the area of papilla loss were examined on clinical photographs before treatment and 3, 6, and 12 months after treatment. The data were tested for a normal distribution and analyzed by the Wilcoxon signed rank test. P < .05 was considered significant. RESULTS: The height of the gingival papilla increased 0.311, 0.45, and 0.4 mm from baseline at 3, 6, and 12 months, respectively, after treatment (P < .05), whereas the area of the black triangle was reduced by 0.31, 0.41, and 0.36 mm2 at the same time points (P < .05). In addition, patients with a thick gingival biotype showed a better effect of treatment on the increase in the height of the gingival papilla and decrease in the area of the black triangle. CONCLUSIONS: Our study verified a remarkable effect of hyaluronic acid gel injection in restoring the deficient gingival papilla of the natural teeth, especially in patients with a thick gingival biotype.

Insights into deep-sea adaptations and host-symbiont interactions: A comparative transcriptome study on Bathymodiolus mussels and their coastal relatives.

Mussels (Bivalve: Mytilidae) have adapted to various habitats, from fresh water to the deep sea. To understand their adaptive characteristics in different habitats, particularly in the bathymodiolin mussels in deep-sea chemosynthetic ecosystems, we conducted a comparative transcriptomic analysis between deep-sea bathymodiolin mussels and their shallow-water relatives. A number of gene families related to stress responses were shared across all mussels, without specific or significantly expanded families in deep-sea species, indicating that all mussels are capable of adapting to diverse harsh environments, but that different members of the same gene family may be preferentially utilized by different species. One of the most extraordinary trait of bathymodiolin mussels is their endosymbiosis. Lineage-specific and positively selected TLRs and highly expressed C1QDC proteins were identified in the gills of the bathymodiolins, suggesting their possible functions in symbiont recognition. However, pattern recognition receptors of the bathymodiolins were globally reduced, facilitating the invasion and maintenance of the symbionts obtained by either endocytosis or phagocytosis. Additionally, various transporters were positively selected or more highly expressed in the deep-sea mussels, indicating a means by which necessary materials could be provided for the symbionts. Key genes supporting lysosomal activity were also positively selected or more highly expressed in the deep-sea mussels, suggesting that nutrition fixed by the symbionts can be absorbed in a "farming" way wherein the symbionts are digested by lysosomes. Regulation of key physiological processes including lysosome activity, apoptosis and immune reactions is needed to maintain a stable host-symbiont relationship, but the mechanisms are still unclear.

[Computer-assisted quantitative analysis of contrast-enhanced ultrasonography in Takayasu arteritis carotid artery lesions].

Takayasu arteritis (TA) is a chronic nonspecific inflammation that commonly occurs in the aorta and its main branches. Most patients with TA are lack of clinical manifestations, leading to misdiagnosis. When the TA is correctly diagnosed, the patients may already have stenosis or occlusion in the involved arteries, resulting in arterial ischemia and hypoxia symptoms, and in severe cases it will be life-threatening. Contrast-enhanced ultrasonography (CEUS) is an emerging method for assessing TA, but the assessment relies heavily on experiences of radiologists performing manual and qualitative analyses, so the diagnostic results are often not accurate. To overcome this limitation, this paper presents a computer-assisted quantitative analysis of TA carotid artery lesions based on CEUS. First, the TA lesion was outlined on the carotid wall, and one homogeneous rectangle and one polygon were selected as two reference regions in the carotid lumen. The temporal and spatial features of the lesion region and the reference regions were then calculated. Furthermore, the difference and ratio of the features between the lesion and the reference regions were computed as new features (to eliminate interference factors). Finally, the correlation was analyzed between the CEUS features and inflammation biomarkers consisting of erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP). The data in this paper were collected from 34 TA patients in Zhongshan Hospital undergoing CEUS examination with a total of thirty-seven carotid lesions, where two patients were with two lesions before and after treatment and one patient was with left and right bilateral lesions. Among these patients, 13 were untreated primary patients with a total of 14 lesions, where one patient was with bilateral lesions. The results showed that for all patients, the neovascularization area ratio in the 1/3 inner region of a lesion (ARi 1/3) achieved a correlation coefficient ( r) of 0.56 ( P=0.001) with CRP, and for the primary patients, the neovascularization area ratio in the 1/2 inner region of a lesion (ARi 1/2) had an r-value of 0.76 ( P=0.001) with CRP. This study indicates that the proposed computer-assisted method can objectively and semi-automatically extract quantitative features from CEUS images, so as to reduce the effect on diagnosis due to subjective experiences of the radiologists, and thus it is expected to be used for clinical diagnosis and severity evaluation of TA carotid lesions.

Role of Doppler Sonography in Early Detection of Splenic Steal Syndrome.

OBJECTIVES: To retrospectively investigate the role of Doppler sonography in the early detection of splenic steal syndrome. METHODS: Fifty cases of splenic steal syndrome after orthotopic liver transplantation were identified. A control group was matched to the splenic steal syndrome group. Information was collected about the clinical presentation, liver enzyme levels, Doppler sonographic results, and follow-up after patients underwent splenic artery embolization. RESULTS: A persistent hepatic arterial diastolic reversal waveform was observed in 25 patients with splenic steal syndrome versus 0 control patients. The mean hepatic arterial resistive index (RI) values ± SD were 0.95 ± 0.09 in patients with splenic steal syndrome and 0.80 ± 0.10 in control patients (P < .0001). One week after orthotopic liver transplantation, the area under the receiver operating characteristic curve for the RI was 0.884 (95% confidence interval, 0.793-0.975; P = .001) for splenic steal syndrome diagnosis. After splenic artery embolization, there was normalization of the reversal waveform, with an average RI of 0.77 ± 0.11 (P < .0001). CONCLUSIONS: Dynamic changes in the hepatic arterial waveform and RI are keys to detecting splenic steal syndrome with Doppler sonography.

Insights into prokaryotic communities and their potential functions in biogeochemical cycles in cold seep.

Microorganisms are significant drivers of organic matter mineralization and are essential in marine biogeochemical cycles. However, the variations and influencing factors in prokaryotic communities from cold-seep sediments to the water column and the specific role of these microorganisms in biogeochemical cycles in the water column above cold seep remain unclear. Here, we investigated prokaryotic communities and their roles in nitrogen/sulfur cycling processes and conducted in situ dissolved organic matter (DOM) enrichment experiments to explore the effects of diverse sources of DOM on prokaryotic communities. Field investigations showed that the prokaryotic communities in the near-bottom water were more similar to those in the deep layer of the euphotic zone (44.60%) and at a depth of 400 m (50.89%) than those in the sediment (18.00%). DOM enrichment experiments revealed that adding dissolved organic nitrogen (DON) and phosphorus DOP caused a notable increase in the relative abundances of Rhodobacterales and Vibrionales, respectively. A remarkable increase was observed in the relative abundance of Alteromonadales and Pseudomonadales after the addition of dissolved organic sulfur (DOS). The metagenomic results revealed that Proteobacteria served as the keystone taxa in mediating the biogeochemical cycles of nitrogen, phosphorus, and sulfur in the Haima cold seep. This study highlights the responses of prokaryotes to DOM with different components and the microbially driven elemental cycles in cold seeps, providing a foundational reference for further studies on material energy metabolism and the coupled cycling of essential elements mediated by deep-sea microorganisms. IMPORTANCE: Deep-sea cold seeps are among the most productive ecosystems, sustaining unique fauna and microbial communities through the release of methane and other hydrocarbons. Our study revealed that the influence of seepage fluid on the prokaryotic community in the water column is surprisingly limited, which challenges conventional views regarding the impact of seepage fluids. In addition, we identified that different DOM compositions play a crucial role in shaping the prokaryotic community composition, providing new insights into the factors driving microbial diversity in cold seeps. Furthermore, the study highlighted Proteobacteria as key and multifaceted drivers of biogeochemical cycles in cold seeps, emphasizing their significant contribution to complex interactions and processes. These findings offer a fresh perspective on the dynamics of cold-seep environments and their microbial communities, advancing our understanding of the biogeochemical functions in deep-sea environments.

Transcriptomic responses to shifts in light and nitrogen in two congeneric diatom species.

Light and nitrogen availability are basic requirements for photosynthesis. Changing in light intensity and nitrogen concentration may require adaptive physiological and life process changes in phytoplankton cells. Our previous study demonstrated that two Thalassiosira species exhibited, respectively, distinctive physiological responses to light and nitrogen stresses. Transcriptomic analyses were employed to investigate the mechanisms behind the different physiological responses observed in two diatom species of the genus Thalassiosira. The results indicate that the congeneric species are different in their cellular responses to the same shifting light and nitrogen conditions. When conditions changed to high light with low nitrate (HLLN), the large-celled T. punctigera was photodamaged. Thus, the photosynthesis pathway and carbon fixation related genes were significantly down-regulated. In contrast, the small-celled T. pseudonana sacrificed cellular processes, especially amino acid metabolisms, to overcome the photodamage. When changing to high light with high nitrate (HLHN) conditions, the additional nitrogen appeared to compensate for the photodamage in the large-celled T. punctigera, with the tricarboxylic acid cycle (TCA cycle) and carbon fixation significantly boosted. Consequently, the growth rate of T. punctigera increased, which suggest that the larger-celled species is adapted for forming post-storm algal blooms. The impact of high light stress on the small-celled T. pseudonana was not mitigated by elevated nitrate levels, and photodamage persisted.

Positive selection in cilia-related genes may facilitate deep-sea adaptation of Thermocollonia jamsteci.

Deep-sea hydrothermal vents are characterized by high hydrostatic pressure, hypoxia, darkness and toxic substances. However, how organisms adapt to such extreme marine ecosystems remain poorly understood. We hypothesize that adaptive evolution plays an essential role in generating novelty for evolutionary adaptation to the deep-sea environment because adaptive evolution has been found to be critical for species origin and evolution. In this project, the chromosome-level genome of the deep-sea hydrothermal vent gastropod T. jamsteci was constructed for the first time to examine molecular mechanisms of its adaptation to the deep-sea environment. The genome size was large (2.54 Gb), ranking at the top of all species in the Vetigastropoda subclass, driven primarily by the bursts of transposable elements (TEs). The transposition of TEs may also trigger chromosomal changes including both inter-chromosomal fusions and intra-chromosomal activities involving chromosome inversions, rearrangements and fusions, as revealed by comparing the genomes of T. jamsteci and its closely related shallow-sea species Gibbula magus. Innovative changes including the expansion of the ABC transporter gene family that may facilitate detoxification, duplication of genes related to endocytosis, immunity, apoptosis, and anti-apoptotic domains that may help T. jamsteci fight against microbial pathogens, were identified. Furthermore, comparative analysis identified positive selection signals in a large number of genes including the hypoxia up-regulated protein 1, which is a chaperone that may promote adaptation of the T. jamsteci to hypoxic deepsea environments, hox2, Rx2, Pax6 and cilia-related genes BBS1, BBS2, BBS9 and RFX4. Notably, because of the critical importance of cilia and IFT in development, positive selection in cilia-related genes may play a critical role in facilitating T. jamsteci to adapt to the high-pressure deep-sea ecosystem. Results from this study thus revealed important molecular clues that may facilitate further research on the adaptation of molluscs to deep-sea hydrothermal vents.

Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent.

Heimdallarchaeia is a class of the Asgardarchaeota, are the most probable candidates for the archaeal protoeukaryote ancestor that have been identified to date. However, little is known about their life habits regardless of their ubiquitous distribution in diverse habitats, which is especially true for Heimdallarchaeia from deep-sea environments. In this study, we obtained 13 metagenome-assembled genomes (MAGs) of Heimdallarchaeia from the deep-sea cold seep and hydrothermal vent. These MAGs belonged to orders o_Heimdallarchaeales and o_JABLTI01, and most of them (9 MAGs) come from the family f_Heimdallarchaeaceae according to genome taxonomy database (GTDB). These are enriched for common eukaryote-specific signatures. Our results show that these Heimdallarchaeia have the metabolic potential to reduce sulfate (assimilatory) and nitrate (dissimilatory) to sulfide and ammonia, respectively, suggesting a previously unappreciated role in biogeochemical cycling. Furthermore, we find that they could perform both TCA and rTCA pathways coupled with pyruvate metabolism for energy conservation, fix CO2 and generate organic compounds through an atypical Wood-Ljungdahl pathway. In addition, many genes closely associated with bacteriochlorophyll and carotenoid biosynthesis, and oxygen-dependent metabolic pathways are identified in these Heimdallarchaeia MAGs, suggesting a potential light-utilization by pigments and microoxic lifestyle. Taken together, our results indicate that Heimdallarchaeia possess a mixotrophic lifestyle, which may give them more flexibility to adapt to the harsh deep-sea conditions.