Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments

Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.

Beyond Vision: A View from Eye to Alzheimer's Disease and Dementia

With the aging of the global population, the health care burden of Alzheimer's disease (AD) and dementia is considered to increase dramatically in the coming decades. Given the insufficiency of effective interventions for AD and dementia, clinical research on identifying potentially modifiable risk factors and early diagnostic biomarkers becomes a public health priority. Currently, extracerebral manifestations with a large proportion of ocular involvement are usually recognized to precede the symptoms of AD and dementia. Growing epidemiologic evidence also suggests that eye disorders, such as cataracts, age-related macular degeneration, glaucoma, diabetic retinopathy, and so on, are closely associated with and even have a higher incidence of AD and dementia. The eye, as an extension of the central nervous system, therefore has the potential to provide a feasible approach to detecting structural and functional abnormalities of the brain. Numerous new imaging modalities are developed and give novel insights into the detection of several neurodegenerative, vascular, neuropathological, and other ocular abnormalities of AD and dementia in scientific research and clinical application. This review provides an overview of the epidemiologic associations between eye disorders and AD or dementia and summarizes the recent advances in ocular examinations and techniques employed for the detection of AD and dementia. With more brain-and-eye interconnections being identified, the eye is becoming a noninvasive and easily accessible window for the early diagnosis and prevention of AD and dementia.

Characterization and Comparative Genomic Analysis of a Deep-Sea Bacillus Phage Reveal a Novel Genus

As the most abundant biological entities, viruses are the major players in marine ecosystems. However, our knowledge on virus diversity and virus-host interactions in the deep sea remains very limited. In this study, vB_BteM-A9Y, a novel bacteriophage infecting Bacillus tequilensis, was isolated from deep-sea sediments in the South China Sea. vB_BteM-A9Y has a hexametric head and a long, complex contractile tail, which are typical features of myophages. vB_BteM-A9Y initiated host lysis at 60 min post infection with a burst size of 75 PFU/cell. The phage genome comprises 38,634 base pairs and encodes 54 predicted open reading frames (ORFs), of which 27 ORFs can be functionally annotated by homology analysis. Interestingly, abundant ORFs involved in DNA damage repair were identified in the phage genome, suggesting that vB_BteM-A9Y encodes multiple pathways for DNA damage repair, which may help to maintain the stability of the host/phage genome. A BLASTn search of the whole genome sequence of vB_BteM-A9Y against the GenBank revealed no existing homolog. Consistently, a phylogenomic tree and proteome-based phylogenetic tree analysis showed that vB_BteM-A9Y formed a unique branch. Further comparative analysis of genomic nucleotide similarity and ORF homology of vB_BteM-A9Y with its mostly related phages showed that the intergenomic similarity between vB_BteM-A9Y and these phages was 0-33.2%. Collectively, based on the comprehensive morphological, phylogenetic, and comparative genomic analysis, we propose that vB_BteM-A9Y belongs to a novel genus under Caudoviricetes. Therefore, our study will increase our knowledge on deep-sea virus diversity and virus-host interactions, as well as expanding our knowledge on phage taxonomy.

Preparation and Embedding Characterization of Hydroxypropyl-β-cyclodextrin/Menthyl Acetate Microcapsules with Enhanced Stability

OBJECTIVE

Hydroxypropyl-β-cyclodextrin (HP-β-CD)/menthyl acetate (MA) microcapsules were developed to overcome the volatile and unstable defects of MA and improve the ease of use and storage.

METHODS

MA microcapsules were prepared via spray drying using HP-β-CD as the wall material. The embedding rate of MA microcapsules was determined through gas chromatography. The embedding characteristics were studied using phase solubility and nuclear magnetic resonance (NMR). The stability was characterized via differential scanning calorimetry (DSC) and the release and retention rates of MA microcapsules at different temperatures.

RESULTS

The embedding rate of HP-β-CD /MA microcapsules was 96.3%. The Gibbs free energy change, enthalpy change and entropy change of the embedding reaction between HP-β-CD and MA were all less than zero, indicating that the embedding process was a spontaneous exothermic reaction. NMR spectra showed that MA entered the cavity of HP-β-CD through the large opening end and interacted with the inner wall of the small opening end. DSC and the release and retention rates of MA microcapsules at different temperatures showed that the stability of MA was significantly enhanced after being embedded in HP-β-CD.

CONCLUSION

The HP-β-CD/MA microcapsules are able to significantly improve the stability of MA and reduce the volatilization of MA.

The choice of spectral similarity algorithms influences suspected soil sample provenance

Similarity algorithms are commonly used in soil forensic applications to help identify similar samples from an existing reference library as possible source locations of unknown target samples. These algorithms are well-suited to compare soil spectra. However, different similarity algorithms may lead to different clusters of similar samples, and thus different strengths of evidence in forensic investigations. To quantify this, we conducted a study to evaluate the influence of seven similarity algorithms on soil provenance, using as a sample set a soil spectral library consisting of 280 soil profiles from Anhui Province, China. This library includes three spatial scales of datasets: provincial (DS_p), county (DS_c) and field (DS_f). A set of ten samples covering a wide range of spectra variations were selected from the DS_f dataset as the "unknown" samples, with the remaining being used as the reference samples. This study aimed to: (1) evaluate how several commonly-used similarity algorithms, namely Euclidean distance (ED), Mahalanobis distance (MD), Spectral angle mapper (SAM), and Spectral information divergence (SID), as well as variants of several of these measured in standardized principal component space computed from the spectra (ED_PCA, MD_PCA and SAM_PCA), influence the identification of the matched similar samples; (2) determine the overlap in sample selection between different similarity algorithms; (3) propose best practices for similarity algorithms applied to soil forensic analysis using spectroscopy. The use of different similarity algorithms did influence the selection of most similar samples. The similarity algorithms calculated in PC space (ED_PCA, MD_PCA and SAM_PCA) performed slightly better than their counterparts calculated in spectral space. Due to the availability of a detailed spectral library, regardless of the different similarity algorithms used, the matched most similar samples were all located close to the unknowns, mostly within 3 km, with one exception. That is, the varied choices of different similarity algorithms hardly influenced the conclusion of soil provenance in this case. In general, MD_PCA, SAM and ED were the best similarity algorithms overall. However, since there was no single best algorithms for all cases, we recommend the joint use of MD_PCA, SAM and ED as an ensemble. Indications of possible sample provenance from these similarity measured can be useful evidence to complement evidence from other methods in a forensic investigation.

The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment

BACKGROUND

Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in deep-sea hydrothermal vents, cold seeps, and organic falls. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to endemic environment. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, remain to be investigated.

RESULT

We assembled a draft genome of R. piscesae collected at the Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis showed that vent-dwelling tubeworms with a higher growth rate had smaller genome sizes than seep-dwelling tubeworms that grew much slower. A strong positive correlation between repeat content and genome size but not intron size and the number of protein-coding genes was identified in these deep-sea tubeworm species. Evolutionary analysis revealed that Ridgeia pachyptila and R. piscesae, the two tubeworm species that are endemic to hydrothermal vents of the eastern Pacific, started to diverge between 28.5 and 35 million years ago. Four genes involved in cell proliferation were found to be subject to positive selection in the genome of R. piscesae.

CONCLUSION

Ridgeia pachyptila and R. piscesae started to diverge after the formation of the Gorda/Juan de Fuca/Explorer ridge systems and the East Pacific Rise. The high growth rates of vent-dwelling tubeworms might be derived from their small genome sizes. Cell proliferation is important for regulating the growth rate in R. piscesae.

The efficacy and safety of pulsed-field ablation in para-Hisian paroxysmal supraventricular tachycardia: first-in-human pilot trial

Funding Acknowledgements

Type of funding sources: Public Institution(s). Main funding source(s): National Key Research and Development Program of China

Background

Para-Hisian paroxysmal supraventricular tachycardia (PSVT) is associated with a higher risk of atrioventricular block due to proximity of the His bundle during catheter ablation. Pulsed-field ablation (PFA) with high tissue selectivity may be a promising technique for catheter ablation in patients with para-Hisian PSVT.

Purpose

This study aimed to evaluate the efficacy and safety of PFA for para-Hisian PSVT.

Methods

This investigator-initiated, single-center, single-arm, prospective study was the first in-human pilot phase to evaluate the efficacy and safety of a novel PFA system in patients with PSVT. Patients diagnosed with para-Hisian PSVT via electrophysiological examination were included and treated with PFA. The primary outcome was the ability to achieve acute ablation success. The secondary outcome was ablation success and safety after 3 months.

Results

A total of seven patients with a mean age of 49.4±13.1 years were included and underwent PFA. Acute ablation success was achieved in all seven patients. The skin-to-skin procedure time was 135.0±17.7 minutes, fluoroscopy time was 4.3±1.6 minutes, and the number of PFA applications was 7±1.6. No adverse events occurred in any patient during the ablation or during the 3-month follow-up.

Conclusion

PFA had favorable efficacy and safety in para-Hisian PSVT patients and can help minimize the risk of inadvertent atrioventricular block during ablation. PFA may be a favorable treatment choice for patients with para-Hisian PSVT.

Agarose-Degrading Characteristics of a Deep-Sea Bacterium Vibrio Natriegens WPAGA4 and Its Cold-Adapted GH50 Agarase Aga3420

Up until now, the characterizations of GH50 agarases from Vibrio species have rarely been reported compared to GH16 agarases. In this study, a deep-sea strain, WPAGA4, was isolated and identified as Vibrio natriegens due to the maximum similarity of its 16S rRNA gene sequence, the values of its average nucleotide identity, and through digital DNA-DNA hybridization. Two circular chromosomes in V. natriegens WPAGA4 were assembled. A total of 4561 coding genes, 37 rRNA, 131 tRNA, and 59 other non-coding RNA genes were predicted in the genome of V. natriegens WPAGA4. An agarase gene belonging to the GH50 family was annotated in the genome sequence and expressed in E. coli cells. The optimum temperature and pH of the recombinant Aga3420 (rAga3420) were 40 °C and 7.0, respectively. Neoagarobiose (NA2) was the only product during the degradation process of agarose by rAga3420. rAga3420 had a favorable stability following incubation at 10-30 °C for 50 min. The Km, Vmax, and kcat values of rAga3420 were 2.8 mg/mL, 78.1 U/mg, and 376.9 s-1, respectively. rAga3420 displayed cold-adapted properties as 59.7% and 41.2% of the relative activity remained at 10 3 °C and 0 °C, respectively. This property ensured V. natriegens WPAGA4 could degrade and metabolize the agarose in cold deep-sea environments and enables rAga3420 to be an appropriate industrial enzyme for NA2 production, with industrial potential in medical and cosmetic fields.

Predicting survival and immune microenvironment in colorectal cancer: a STAT signaling-related signature

BACKGROUND

Despite research advances, studies on predictive models of colorectal cancer (CRC) remain scarce and none have evaluated signal transducer and activator of transcription (STAT) signaling.

AIM

To develop an effective prognostic signature for and evaluate its association with immune microenvironment.

DESIGN

Comprehensive analysis based on The Cancer Genome Atlas and Gene Expression Omnibus databases with experimental validation.

METHODS

Gene expression and clinical profiles of CRC patients were extracted from the databases. Differentially expressed genes with prognostic values were used to construct a signature. Immune cell infiltration and composition were further evaluated by TIMER, single-sample gene set enrichment and CIBERSORT analyses. The impact of the hub gene Caveolin-1 (CAV1) on cell proliferation, apoptosis, senescence and tumor angiogenesis was experimentally validated.

RESULTS

The five-gene-based STAT signaling-related prognostic signature was significantly associated with CRC survival, and the nomogram was with improved prognostic efficacy than the conventional TNM stage. The STAT signaling-related signature was correlated with tumor immune microenvironment. CAV1 was further identified as the hub gene within the signature. CAV1 inhibits the proliferation and induces the apoptosis as well as senescence of CRC cells. In addition, the tumor angiogenesis of CRC can be suppressed by CAV1 overexpression.

CONCLUSIONS

The STAT signaling-related signature effectively predicts the prognosis and regulates tumor immune microenvironment in CRC. Our study underscores the role of STAT regulator, CAV1, as an important tumor suppressor in CRC carcinogenesis. Modulating STAT and its regulators could be a promising strategy for CRC in clinical practice.

[Clinical analysis of chronic eosinophilic pneumonia in 9 cases]

Objective: To investigate the clinical features, treatment and prognosis of chronic eosinophilic pneumonia. Methods: Nine patients with chronic eosinophilic pneumonia diagnosed in Shandong Provincial Qianfoshan Hospital from January 2014 to December 2020 were enrolled and followed up. The data of clinically proven chronic eosinophilic pneumonia were reviewed. Results: The 9 cases included one male and eight females, aged from 16 to 71 years (median 47 years). Among them, 5 cases were complicated with asthma, 1 case was complicated with allergic rhinitis, and 1 case had an allergic history of pollen. All the patients had cough, expectoration, chest tightness and wheezing, and a few had fatigue (3/9), fever (1/9) and chest pain (1/9). Single or multiple patchy high-density shadows (9/9), mediastinal lymphadenopathy (7/9), air bronchogram (2/9), and reticular shadow (1/9) were observed in chest CT. Peripheral eosinophils (EOS) and serum total IgE increased to varying degrees in the 9 patients. Meanwhile, the bronchoscopy of 5 cases showed elevated percentage of eosinophils in alveolar lavage fluid, and the lung biopsy of remaining 4 cases showed EOS infiltration in lung alveolar and interstitium. After receiving glucocorticoid therapy for 0.5 to 1 month, the clinical symptoms of all 9 patients had been improved and lung lesions on CT scans had been obviously absorbed. Four cases relapsed during follow-up. Conclusions: For patients especially women who have a history of allergy, elevated blood eosinophils and serum total IgE with pulmonary high-density shadow or consolidation, chronic eosinophilic pneumonia should be considered, and bronchoscopy or percutaneous lung biopsy is indicated for a definite diagnosis. Glucocorticoid therapy is effective, but the rate of recurrence is high.

Expression and Characterization of a Novel Cold-Adapted and Stable β-Agarase Gene agaW1540 from the Deep-Sea Bacterium Shewanella sp. WPAGA9

The neoagaro-oligosaccharides, degraded from agarose by agarases, are important natural substances with many bioactivities. In this study, a novel agarase gene, agaW1540, from the genome of a deep-sea bacterium Shewanella sp. WPAGA9, was expressed, and the recombinant AgaW1540 (rAgaW1540) displayed the maximum activity under the optimal pH and temperature of 7.0 and 35 °C, respectively. rAgaW1540 retained 85.4% of its maximum activity at 0 °C and retained more than 92% of its maximum activity at the temperature range of 20-40 °C and the pH range of 4.0-9.0, respectively, indicating its extensive working temperature and pH values. The activity of rAgaW1540 was dramatically suppressed by Cu²⁺ and Zn²⁺, whereas Fe²⁺ displayed an intensification of enzymatic activity. The K_m and V_max of rAgaW1540 for agarose degradation were 15.7 mg/mL and 23.4 U/mg, respectively. rAgaW1540 retained 94.7%, 97.9%, and 42.4% of its maximum activity after incubation at 20 °C, 25 °C, and 30 °C for 60 min, respectively. Thin-layer chromatography and ion chromatography analyses verified that rAgaW1540 is an endo-acting β-agarase that degrades agarose into neoagarotetraose and neoagarohexaose as the main products. The wide variety of working conditions and stable activity at room temperatures make rAgaW1540an appropriate bio-tool for further industrial production of neoagaro-oligosaccharides.

Vibrio ziniensis sp. nov., isolated from mangrove sediments

A novel Gram-staining-negative, catalase- and oxidase-positive, facultatively anaerobic and rod-shaped motile bacterial strain, designated as ZWAL4003^T, was isolated from mangrove sediments of the Zini Mangrove Forest, Zhangzhou City, PR China. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that ZWAL4003^T was grouped into a separated branch with Vibrio plantisponsor MSSRF60^T (97.38% nucleotide sequence identity) and Vibrio diazotrophicus NBRC 103148^T (97.27%). The major cellular fatty acids were C_{14 : 0} (12.6%), C_{16 : 0} (17.6%), and summed feature 3 (C_{16 : 1}ω6c /C_{16 : 1} ω7c, 45.6%). Its genome had a length of 4650556 bp with 42.8% DNA G+C content, and contained genes involved in the biosynthesis of bacteriocin, β-lactone, resorcinol, N-acyl amino acid, and arylpolyene. The in silico DNA-DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between ZWAL4003^T and V. plantisponsor LMG 24470^T were clearly below the thresholds used for the delineation of a novel species. The morphological and chemotaxonomic characteristics and the genotypic data of ZWAL4003^T indicated that it represented a novel species of the genus Vibrio. Its proposed name is Vibrio ziniensis sp. nov., and the type strain is ZWAL4003^T (=KCTC 72971^T=MCCC 1A17474^T).

The degradation activities for three seaweed polysaccharides of Shewanella sp. WPAGA9 isolated from deep-sea sediments

Seaweed oligosaccharides possess great bioactivities. However, different microbial strains are required to degrade multiple polysaccharides due to their limited biodegradability, thereby increasing the cost and complexity of production. Shewanella sp. WPAGA9 was isolated from deep-sea sediments in this study. According to the genomic and biochemical analyses, the extracellular fermentation broth of WPAGA9 had versatile degradation abilities for three typical seaweed polysaccharides including agar, carrageenan, and alginate. The maximum enzyme activities of the extracellular fermentation broth of WPAGA9 were 71.63, 76.4, and 735.13 U/ml for the degradation of agar, alginate, and carrageenan, respectively. Moreover, multiple seaweed oligosaccharides can be produced by the extracellular fermentation broth of WPAGA9 under similar optimum conditions. Therefore, WPAGA9 can simultaneously degrade three types of seaweed polysaccharides under similar conditions, thereby greatly reducing the production cost of seaweed oligosaccharides. This finding indicates that Shewanella sp. WPAGA9 is an ideal biochemical tool for producing multiple active seaweed oligosaccharides at low costs and is also an important participant in the carbon cycle process of the deep-sea environment.

Characterization of Bacillus phage Gxv1, a novel lytic Salasvirus phage isolated from deep-sea seamount sediments

Seamounts are hotspots for marine life, but to date, no bacteriophages have been reported. Here, a novel Bacillus podophage (named as Bacillus phage Gxv1) was isolated from deep-sea seamount sediments of the western Pacific Ocean (~ 5790 m). Phage Gxv1 has a hexameric head ~ 42-53 nm in diameter and a short tail of ~ 30 nm long, which is a typical feature of the Podoviridae family. One-step curve analysis showed that Gxv1 is a lytic phage that can initiate host lysis within 3.5 h post-infection, and has a relatively large burst size. The 21,781-bp genome contains 34 predicted genes, and the G + C content of phage Gxv1 is 39.69%. Whole-genome comparison of phage Gxv1 with known bacteriophages, using BlastN analysis against the IMG/VR database, revealed that phage Gxv1 is closely related to Bacillus phage phi29 that infects Bacillus subtilis, and their genome-wide similarity is 93.62%. Phylogenetic analysis based on DNA polymerase showed that phage Gxv1 belongs to the Salasvirus genus. Multiple genome alignment showed that phage Gxv1 shares a high level of sequence similarity and common gene order with Bacillus phage phi29. However, some sequences are unique to phage Gxv1, and this region contains genes encoding DNA packing protein, DNA replication protein, and unknown protein. These sequences exhibit low sequence similarity to known bacteriophages, highlighting an unknown origin of these sequences. This study will help improve our understanding of the Salasvirus genus and phage diversity in deep-sea seamounts.

Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

The elevated NH₃-N and NO₂-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

Forensic soil source identification: comparing matching by color, vis-NIR spectroscopy and easily-measured physio-chemical properties

This study evaluates to what degree soil samples associated in characteristic space are also close in geographical space, i.e., the possible location from which an unknown sample was obtained in a forensic investigation. The study compares similarity computed from Munsell colors, RGB colors, and full visible-near infrared (vis-NIR) spectra by the spectral angle mapper with similarity based on six easily-measured physio-chemical properties. The reference area is Anhui Province, China with three scales of datasets: provincial, county, and field. Ten diverse "unknown" samples were selected by the Kennard-Stone algorithm from the field-scale dataset and their matches in characteristic space from the several datasets were found by the different methods. The geographic distances of the matches to the "unknowns" were used to evaluate the source identification ability. When a detailed library with local samples is present, a limited set of physio-chemical properties achieved higher geographic accuracy than the color and spectral methods. However, with a regional library the spectral and color methods are superior. Distances in RGB space reveal finer differences than exact matching in Munsell space, but whole-spectra matching outperforms both, because of the rich information influenced by more soil properties than influencing color. We recommend the use of soil vis-NIR spectra as a priority indicator for forensic soil analysis because of its success in this study and its ability to work non-destructively on small quantities of soil.

Amelioration of Androgenetic Alopecia by Algal Oligosaccharides Prepared by Deep-Sea Bacterium Biodegradation

Androgenetic alopecia (AGA) is a dihydrotestosterone (DHT)-mediated hair loss disorder characterized by shortened anagen hair cycle. Oligosaccharides derived from seaweeds possess diverse biological functions. However, little is known about their effects on AGA. In this study, algal oligosaccharide (AOS) was characterized for its mitigation effects on key features involved in AGA pathogenesis, such as DHT- mediated cellular signaling and shortened anagen hair cycle. AOS with varying degrees of polymerization (DP), namely, AOS (DP2), AOS (DP4-6), and AOS (DP8-12), were prepared by agar biodegradation with Flammeovirga pacifica WPAGA1, an agarolytic bacterium isolated from deep-sea sediments. In vitro results showed that AOS with varying DPs significantly ameliorated the DHT-induced alterations of regulatory factors in human hair follicle dermal papilla cells in a dose- and DP-dependent manner, as revealed by the normalization of several hair-growth-stimulating or inhibitory factors. In vivo studies showed that AOS (DP2) extended the anagen phase and thereby delayed catagen progression in mice. Furthermore, AOS (DP2) stimulated dorsal hair growth in mice by increasing hair length, density, and thickness. Therefore, our findings indicated that AOS antagonized key factors involved in AGA pathogenesis, suggesting the potential application of AOS in the prevention and the treatment of AGA.

Production of Neoagaro-Oligosaccharides With Various Degrees of Polymerization by Using a Truncated Marine Agarase

Bioactivities, such as freshness maintenance, whitening, and prebiotics, of marine neoagaro-oligosaccharides (NAOS) with 4-12 degrees of polymerization (DPs) have been proven. However, NAOS produced by most marine β-agarases always possess low DPs (≤6) and limited categories; thus, a strategy that can efficiently produce NAOS especially with various DPs ≥8 must be developed. In this study, 60 amino acid residues with no functional annotation result were removed from the C-terminal of agarase AgaM1, and truncated recombinant AgaM1 (trAgaM1) was found to have the ability to produce NAOS with various DPs (4-12) under certain conditions. The catalytic efficiency and stability of trAgaM1 were obviously lower than the wild type (rAgaM1), which probably endowed trAgaM1 with the ability to produce NAOS with various DPs. The optimum conditions for various NAOS production included mixing 1% agarose (w/v) with 10.26 U/ml trAgaM1 and incubating the mixture at 50°C in deionized water for 100 min. This strategy produced neoagarotetraose (NA4), neoagarohexaose (NA6), neoagarooctaose (NA8), neoagarodecaose (NA10), and neoagarododecaose (NA12) at final concentrations of 0.15, 1.53, 1.53, 3.02, and 3.02 g/L, respectively. The NAOS served as end-products of the reaction. The conditions for trAgaM1 expression in a shake flask and 5 L fermentation tank were optimized, and the yields of trAgaM1 increased by 56- and 842-fold compared with those before optimization, respectively. This study provides numerous substrate sources for production and activity tests of NAOS with high DPs and offers a foundation for large-scale production of NAOS with various DPs at a low cost.

Identification and Characterization of a Novel Thermostable and Salt-Tolerant β-1,3 Xylanase from Flammeovirga pacifica Strain WPAGA1

β-1,3 xylanase is an important enzyme in the biorefinery process for some algae. The discovery and characterization of new β-1,3 xylanase is a hot research topic. In this paper, a novel β-1,3 xylanase (Xyl88) is revealed from the annotated genome of Flammeovirga pacifica strain WPAGA1. Bioinformatic analysis shows that Xyl88 belongs to the glycoside hydrolase 26 (GH26) with a suspected CBM (carbohydrate-binding module) sequence. The activity of rXyl88 is 75% of the highest enzyme activity (1.5 mol/L NaCl) in 3 mol/L NaCl buffer, which suggests good salt tolerance of rXy188. The optimum reaction temperature in the buffer without NaCl and with 1.5 mol/L NaCl is 45 °C and 55 °C, respectively. Notably, the catalytic efficiency of rXyl88 (k_cat/K_m) is approximately 20 higher than that of the thermophilic β-1,3 xylanase that has the highest catalytic efficiency. Xyl88 in this study becomes the most efficient enzyme ever found, and it is also the first reported moderately thermophilic and salt-tolerant β-1,3 xylanase. Results of molecular dynamics simulation further prove the excellent thermal stability of Xyl88. Moreover, according to the predicted 3D structure of the Xyl88, the surface of the enzyme is distributed with more negative charges, which is related to its salt tolerance, and significantly more hydrogen bonds and Van der Waals force between the intramolecular residues, which is related to its thermal stability.

miR-143-3p inhibits proliferation and invasion of hepatocellular carcinoma cells by regulating its target gene FGF1

PURPOSE

To explore FGF1 and miR-143-3p expression in hepatocellular carcinoma (HCC) cells and its related mechanisms.

METHODS

Eighty-two HCC patients treated at our hospital from January 2018 to January 2019 were enrolled as Group A, while further 80 healthy people undergoing physical examinations during the same time period were enrolled as Group B. HCC cells and normal human liver cells were purchased, with HepG2 and SMMC-7721 cells transfected with pcDNA3.1-FGF1, si-FGF1, NC, miR-143-3p-inhibitor and miR-143-3p-mimics. FGF1 and miR-143-3p expression was detected by qRT-PCR. The expression of N-cadherin, vimentin, Snail, Slug, E-cadherin and γ-catenin was detected by Western Blotting (WB). Cell proliferation was detected by MTT assay. Cell invasion was detected by Transwell. Cell apoptosis was detected by flow cytometry (FCM).

RESULTS

FGF1 was highly expressed but miR-143-3p was poorly expressed in HCC cells. Areas under the curves (AUCs) of the two indicators were > 0.8. The indicators were correlated with the age, gender, tumor invasion, degree of differentiation, tumor location and TNM staging of the patients. Silencing FGF1 and overexpressing miR-143-3p could promote cell apoptosis, inhibit cell growth, cell epithelial-mesenchymal transition (EMT) and the expression of N-cadherin, vimentin, Snail and Slug, and increase the expression of E-cadherin and γ-catenin. Dual luciferase reporter gene assay (DLRGA) confirmed that FGF1 and miR-143-3p had a targeted relationship. The rescue experiment showed that the proliferation, invasion and apoptosis of HepG2 and SMMC-7721 cells in the miR-143-3p-mimics+pcDNA3.1-FGF1 and miR-143-3p-inhibitor+Si-FGF1 groups were not different from those in the miR-NC group.

CONCLUSION

Inhibiting FGF1 can upregulate miR-143-3p-mediated Hedgehog signaling pathway, and affect cells' EMT, proliferation and invasion, so FGF1 is expected to become a potential therapeutic target for HCC.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

CT metal artifact reduction algorithms: Toward a framework for objective performance assessment

Purpose

Although several metal artifact reduction (MAR) algorithms for computed tomography (CT) scanning are commercially available, no quantitative, rigorous, and reproducible method exists for assessing their performance. The lack of assessment methods poses a challenge to regulators, consumers, and industry. We explored a phantom‐based framework for assessing an important aspect of MAR performance: how applying MAR in the presence of metal affects model observer performance at a low‐contrast detectability (LCD) task This work is, to our knowledge, the first model observer–based framework for the evaluation of MAR algorithms in the published literature.

Methods

We designed a numerical head phantom with metal implants. In order to incorporate an element of randomness, the phantom included a rotatable inset with an inhomogeneous background. We generated simulated projection data for the phantom. We applied two variants of a simple MAR algorithm, sinogram inpainting, to the projection data, that we reconstructed using filtered backprojection. To assess how MAR affected observer performance, we examined the detectability of a signal at the center of a region of interest (ROI) by a channelized Hotelling observer (CHO). As a figure of merit, we used the area under the ROC curve (AUC).

Results

We used simulation to test our framework on two variants of the MAR technique of sinogram inpainting. We found that our method was able to resolve the difference in two different MAR algorithms’ effect on LCD task performance, as well as the difference in task performances when MAR was applied, vs not.

Conclusion

We laid out a phantom‐based framework for objective assessment of how MAR impacts low‐contrast detectability, that we tested on two MAR algorithms. Our results demonstrate the importance of testing MAR performance over a range of object and imaging parameters, since applying MAR does not always improve the quality of an image for a given diagnostic task. Our framework is an initial step toward developing a more comprehensive objective assessment method for MAR, which would require developing additional phantoms and methods specific to various clinical applications of MAR, and increasing study efficiency.

Possible scenario of forming a catalyst layer for proton exchange membrane fuel cells

Ionomer in the catalyst layer provides an ion transport channel which is essential for many electrochemical devices. As the ionomer and electrochemical catalyst are packed together in the catalyst layer, it is difficult to have a clear image of the ionomer distribution in the catalyst layer and how the ionomer is in contact with Pt or carbon. A highly dispersed catalyst was deposited on the TEM SiN grid directly using the same (ultrasonic spray) or a similar way as the catalyst was deposited on the membrane. By analyzing the distribution of various elements (C, F, S, Pt etc.), we found that the ionomer may coexist in the catalyst layer in three ways: ionomer covered Pt particles due to the relatively strong interaction between Pt and the ionomer; ionomer covered C particles; packed free ionomer in between the aggregated catalyst particles. The results show that the ionomer is prone to covering the surface of Pt particles as further evidenced by the accelerated degradation test (ADT).

Ionomer in the catalyst layer provides an ion transport channel which is essential for many electrochemical devices.

Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review

The deep sea, which is defined as sea water below a depth of 1000 m, is one of the largest biomes on the Earth, and is recognised as an extreme environment due to its range of challenging physical parameters, such as pressure, salinity, temperature, chemicals and metals (such as hydrogen sulphide, copper and arsenic). For surviving in such extreme conditions, deep-sea extremophilic microorganisms employ a variety of adaptive strategies, such as the production of extremozymes, which exhibit outstanding thermal or cold adaptability, salt tolerance and/or pressure tolerance. Owing to their great stability, deep-sea extremozymes have numerous potential applications in a wide range of industries, such as the agricultural, food, chemical, pharmaceutical and biotechnological sectors. This enormous economic potential combined with recent advances in sampling and molecular and omics technologies has led to the emergence of research regarding deep-sea extremozymes and their primary applications in recent decades. In the present review, we introduced recent advances in research regarding deep-sea extremophiles and the enzymes they produce and discussed their potential industrial applications, with special emphasis on thermophilic, psychrophilic, halophilic and piezophilic enzymes.

Relationship between Hashimoto's thyroiditis and papillary thyroid carcinoma in children and adolescents

OBJECTIVE

We investigated the relationship between Hashimoto's thyroiditis (HT) and papillary thyroid carcinoma (PTC) in children and adolescents.

PATIENTS AND METHODS

We carried out a retrospective study of thyroidectomies performed from 2004 to 2017 at The First People's Hospital and the Tumor Hospital of Yunnan Province (Kunming, China). The occurrence and features of PTC and benign thyroid disease (BTD) in children and adolescents (age ≤ 20 years) were compared.

RESULTS

We evaluated 258 consecutive thyroidectomies. Among children and adolescents with PTC, 23 cases were histopathologically confirmed as HT. Mean tumor diameter was smaller in children and adolescents with PTC than in those with BTD. Thyroid-stimulating hormone (TSH) level was abnormally elevated in a greater proportion of children and adolescents with PTC as compared to those with BTD or youths with PTC. The proportion of thyroglobulin antibody (TGAb)- and thyroid peroxidase antibody (TpoAb)-positive children and adolescents was higher in the PTC than in the BTD group. Among children and adolescents with PTC, 23 had HT as compared to two in the BTD group. The proportion of children/adolescents with abnormally elevated TSH levels was higher for the PTC combined with HT group than for the PTC without HT group. A multivariate conditional logistic regression analysis showed that elevated TGAb was an independent risk factor for PTC in children and adolescents.

CONCLUSIONS

HT is associated with an increased occurrence of PTC in children and adolescents.

Effects of Marichromatium gracile YL28 on the nitrogen management in the aquaculture pond water

Nitrogen pollution in aquaculture needs the efficient and cost-effective in-situ technology. This study aims to apply Marichromatium gracile YL28 to in-situ bioremediation and test its ability to maintain the nitrogen balance in aquaculture. In laboratory aquaculture system, approximately 99.96% of nitrite (1 mg/L) was removed within 7 d through denitrification coupled with assimilatory nitrate reduction. Ammonium (3.5 mg/L) of 95.6% was directly assimilated by YL28 within 7 d. Moreover, in zero exchange water from shrimp (Penaeus vannamei) aquaculture field trials (20 days), YL28 significantly reduced the ammonium accumulation (0.6 mg/L) and 99.3% of nitrite (1.25 mg/L). Toxicological studies with the Institute of Cancer Research (ICR) mice and Oryzias melastigma indicated that M. gracile YL28 can be safely applied in aquatic ecosystems. All results demonstrate that strain YL28 has high promise for future applications of removing inorganic nitrogen and maintaining the nitrogen balance from in-situ aquaculture.

A Novel Strategy for Efficient Agaro-Oligosaccharide Production Based on the Enzymatic Degradation of Crude Agarose in Flammeovirga pacifica WPAGA1

To avoid conflict between biofuel and food resource production, marine macroalgae (main algal polysaccharides) have been suggested as potent feedstock for biofuel production. Flammeovirga pacifica WPAGA1, a typical marine polysaccharide-degrading bacterium, can utilize crude agarose as the sole carbon source. Transcriptomic analysis was performed to further investigate the metabolic pathway of environmental-friendly utilization of crude agarose in F. pacifica WPAGA1. All these enzymes were overexpressed in Escherichia coli BL21(DE3), and the purified enzymes were characterized in vitro. As a result, the pathway of crude agarose which is desulfurized and hydrolyzed by enzymes to produce fermentable sugar is clear. Interestingly, sole neoagarobiose (~450 mg/L) was produced from crude agarose as a feedstock using engineered E. coli BL21(DE3). This study firstly reveals the metabolic pathway of crude agarose in strain WPAGA1 and establishes a novel and environmental-friendly strategy for neoagarobiose production using crude agarose as cost-effective and non-food-based feedstock.

[Experience of revision cochlear implantation]

Objective:To analyse the characteristics of the revision cochlear implantation （RCI）patients，the cause of the cochlear malfunction，and the choice of RCI operative approach. Method:A total of 39 patients with RCI were enrolled in this study. The cochlear use time, cause of failure and reoperation procedure are recorded and analyzed retrospectively. Result:There were 39 patients accepted cochlear reoperation，the ages ranges from 1 to 28，average age was 7.8 years, median age was 5 years old. The cochlear use time ranges from 1 month to 7 years，average was 2.2 years, median time was 1 year. Thirty-seven patients underwent RCI,30 cases right side and 7 cases left side. The reason of RCI contains device failure (28 cases)，infection (5 cases)，incorrect electrode implantation (3 cases)，facial nerve stimulation (2 cases)，and electrode prolapse (1 case).The choice of RCI procedure was dependent on the first operation procedure,contains facial nerve recess approach (35 cases) and mastoid approach (2 cases).Contralateral implantation was performed in 5 cases, the rest were ipsilateral. Conclusion:RCI has a variety causes and the common reason is trauma and device failure，the RCI should be completed as early as possible to avoid the ossified cochlear and hearing or speech stagnation，the electrode implantation through previous approach is the best method.

One-Step Process for Environment-Friendly Preparation of Agar Oligosaccharides From Gracilaria lemaneiformis by the Action of Flammeovirga sp. OC4

Oligosaccharides extracted from agar Gracilaria lemaneiformis (G. lemaneiformis) have stronger physiological activities and a higher value than agar itself, but the pollution caused by the extraction process greatly restricts the sustainable use of agar. In this study, four bacterial strains with a high ability to degrade G. lemaneiformis were isolated from seawater by in situ enrichment in the deep sea. Among them, Flammeovirga sp. OC4, identified by morphological observation and its 16S rRNA sequencing (98.07% similarity to type strain JL-4 of Flammeovirga aprica), was selected. The optimum temperature and pH of crude enzyme produced by Flammeovirga sp. OC4 were 50°C and 8, respectively. More than 60% of the maximum enzyme activity remained after storage at pH 5.0-10.0 for 60 min. Both Mn²⁺ and Ba²⁺ could enhance the enzyme activity. A "one-step process" for preparation of oligosaccharides from G. lemaneiformis was established using Flammeovirga sp. OC4. After optimization of the Plackett-Burman (PB) design and response surface methodology (RSM), the yield of oligosaccharides was increased by 36.1% from 2.71 to 3.09 g L^-1 in a 250-mL fermenter with optimized parameters: 30 g L^-1 G. lemaneiformis powder, 4.84 g L^-1 (NH4)₂SO₄, 44.8-mL working medium volume at 36.7°C, and a shaking speed of 200 × g for 42 h. The extracted oligosaccharides were identified by thin layer chromatography (TLC) and ion chromatography, which consisted of neoagarobiose, agarotriose, neoagarotetraose, agaropentaose, and neoagarohexaose. These results provided an alternative approach for environment-friendly and sustainable utilization of algae.

Diversities and potential biogeochemical impacts of mangrove soil viruses

BACKGROUND

Mangroves are ecologically and economically important forests of the tropics. As one of the most carbon-rich biomes, mangroves account for 11% of the total input of terrestrial carbon into oceans. Although viruses are considered to significantly influence local and global biogeochemical cycles, little information is available regarding the community structure, genetic diversity and ecological roles of viruses in mangrove ecosystems.

METHODS

Here, we utilised viral metagenomics sequencing and virome-specific bioinformatics tools to study viral communities in six mangrove soil samples collected from different mangrove habitats in Southern China.

RESULTS

Mangrove soil viruses were found to be largely uncharacterised. Phylogenetic analyses of the major viral groups demonstrated extensive diversity and previously unknown viral clades and suggested that global mangrove viral communities possibly comprise evolutionarily close genotypes. Comparative analysis of viral genotypes revealed that mangrove soil viromes are mainly affected by marine waters, with less influence coming from freshwaters. Notably, we identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from mangrove viruses, most of which participate in biolysis of complex polysaccharides, which are abundant in mangrove soils and organism debris. Host prediction results showed that viral CAZyme genes are diverse and probably widespread in mangrove soil phages infecting diverse bacteria of different phyla.

CONCLUSIONS

Our results showed that mangrove viruses are diverse and probably directly manipulate carbon cycling by participating in biomass recycling of complex polysaccharides, providing the knowledge essential in revealing the ecological roles of viruses in mangrove ecosystems.

Extracellular expression of agarase rAgaM1 in Bacillus subtilis and its ability for neoagaro-oligosaccharide production

An agarase gene (agaM1) was cloned, expressed and characterized by using Escherichia coli as host strain, revealing the outstanding properties of recombinant AgaM1 (rAgaM1) in agarose degradation and neoagaro-oligosaccharides (NAs) production in our previous work. In current study, agaM1 was extracellularly expressed in Bacillus subtilis, and we aim to assess the ability of the supernatant of recombinant B. subtilis fermentation broth containing rAgaM1 to degrade agarose without protein purification, which would save the cost of purification and avoid the activity loss during purification. The pH and temperature optima for the supernatant were 7.0 and 50 °C, respectively. The supernatant containing rAgaM1 has outstanding stability against 40 °C and 50 °C. Besides, we detailedly studied the possible influence factors of rAgaM1 expression in the supernatant, including pH, temperature, isopropyl β-D-thiogalactoside (IPTG) concentration, initial optical density at a wavelength of 600 nm (OD₆₀₀ ), and induction time, and the optimum conditions for rAgaM1 expression by B. subtilis were confirmed. Moreover, the supernatant was able to produce NAs by using the Gracilaria lemaneiformis, whose cells were broken by autoclaving, as substrate, and a total of 1.41 µmol ml^-1 of NA, including neoagarotetraose and neoagarohexaose, was produced after degradation for 48 h. This ability could save the cost of substrates in NA production, although the method requires a further study. Our results reveal that the NAs with great potential in food and pharmaceutical industries could be inexpensive to make by the supernatant containing rAgaM1 of B. subtilis fermentation broth in the foreseeable future.

In vitro and in vivo studies of the ALS-FTLD protein CHCHD10 reveal novel mitochondrial topology and protein interactions

Mutations in coiled-coil-helix-coiled-coil-helix-domain containing 10 (CHCHD10), a mitochondrial twin CX9C protein whose function is still unknown, cause myopathy, motor neuron disease, frontotemporal dementia, and Parkinson's disease. Here, we investigate CHCHD10 topology and its protein interactome, as well as the effects of CHCHD10 depletion or expression of disease-associated mutations in wild-type cells. We find that CHCHD10 associates with membranes in the mitochondrial intermembrane space, where it interacts with a closely related protein, CHCHD2. Furthermore, both CHCHD10 and CHCHD2 interact with p32/GC1QR, a protein with various intra and extra-mitochondrial functions. CHCHD10 and CHCHD2 have short half-lives, suggesting regulatory rather than structural functions. Cell lines with CHCHD10 knockdown do not display bioenergetic defects, but, unexpectedly, accumulate excessive intramitochondrial iron. In mice, CHCHD10 is expressed in many tissues, most abundantly in heart, skeletal muscle, liver, and in specific CNS regions, notably the dopaminergic neurons of the substantia nigra and spinal cord neurons, which is consistent with the pathology associated with CHCHD10 mutations. Homozygote CHCHD10 knockout mice are viable, have no gross phenotypes, no bioenergetic defects or ultrastructural mitochondrial abnormalities in brain, heart or skeletal muscle, indicating that functional redundancy or compensatory mechanisms for CHCHD10 loss occur in vivo. Instead, cells expressing S59L or R15L mutant versions of CHCHD10, but not WT, have impaired mitochondrial energy metabolism. Taken together, the evidence obtained from our in vitro and in vivo studies suggest that CHCHD10 mutants cause disease through a gain of toxic function mechanism, rather than a loss of function.

Metagenomics Investigation of Agarlytic Genes and Genomes in Mangrove Sediments in China: A Potential Repertory for Carbohydrate-Active Enzymes

Monosaccharides and oligosaccharides produced by agarose degradation exhibit potential in the fields of bioenergy, medicine, and cosmetics. Mangrove sediments (MGSs) provide a special environment to enrich enzymes for agarose degradation. However, representative investigations of the agarlytic genes in MGSs have been rarely reported. In this study, agarlytic genes in MGSs were researched in detail from the aspects of diversity, abundance, activity, and location through deep metagenomics sequencing. Functional genes in MGSs were usually incomplete but were shown as results, which could cause virtually high number of results in previous studies because multiple fragmented sequences could originate from the same genes. In our work, only complete and nonredundant (CNR) genes were analyzed to avoid virtually high amount of the results. The number of CNR agarlytic genes in our datasets was significantly higher than that in the datasets of previous studies. Twenty-one recombinant agarases with agarose-degrading activity were detected using heterologous expression based on numerous complete open-reading frames, which are rarely obtained in metagenomics sequencing of samples with complex microbial communities, such as MGSs. Aga2, which had the highest crude enzyme activity among the 21 recombinant agarases, was further purified and subjected to enzymatic characterization. With its high agarose-degrading activity, resistance to temperature changes and chemical agents, Aga2 could be a suitable option for industrial production. The agarase ratio with signal peptides to that without signal peptides in our MGS datasets was lower than that of other reported agarases. Six draft genomes, namely, Clusters 1-6, were recovered from the datasets. The taxonomic annotation of these genomes revealed that Clusters 1, 3, 5, and 6 were annotated as Desulfuromonas sp., Treponema sp., Ignavibacteriales spp., and Polyangiaceae spp., respectively. Meanwhile, Clusters 2 and 4 were potential new species. All these genomes were first reported and found to have abilities of degrading various important polysaccharides. The metabolic pathway of agarose in Cluster 4 was also speculated. Our results showed the capacity and activity of agarases in the MGS microbiome, and MGSs exert potential as a repertory for mining not only agarlytic genes but also almost all genes of the carbohydrate-active enzyme family.

Proposal of nine novel species of the Bacillus cereus group

Nine novel Gram-stain-positive bacteria were investigated by a polyphasic taxonomic approach. Based on the analysis of 16S rRNA gene sequences, these strains belonged to the Bacillus cereus group, sharing over 97 % similarity with the known species of this group, and less than 95 % similarity with other species of the genus Bacillus. Multilocus sequence typing analysis showed that they formed nine robust and well-separated branches from the known species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the nine strains were, respectively, below the 70 and 96 % threshold values for species definition, and between each strain and the known type strains of this group were also below the two threshold values. On the basis of the phenotypic and phylogenetic data, along with low dDDH and ANI values among these strains, these bacteria are assigned to the following nine novel species of the B. cereus group: Bacillus paranthracis sp. nov., type strain Mn5T (=MCCC 1A00395T=KCTC 33714T=LMG 28873T); Bacillus pacificus sp. nov., type strain EB422T (=MCCC 1A06182T=KCTC 33858T); Bacillus tropicus sp. nov., type strain N24T (=MCCC 1A01406T=KCTC 33711T=LMG 28874T); Bacillus albus sp. nov., type strain N35-10-2T (=MCCC 1A02146T=KCTC 33710T=LMG 28875T); Bacillus mobilis sp. nov., type strain 0711P9-1T (=MCCC 1A05942T=KCTC 33717T=LMG 28877T); Bacillus luti sp. nov., type strain TD41T (=MCCC 1A00359T=KCTC 33716T=LMG 28872T); Bacillus proteolyticus sp. nov., type strain TD42T (=MCCC 1A00365T=KCTC 33715T=LMG 28870T); Bacillus nitratireducens sp. nov., type strain 4049T (=MCCC 1A00732T=KCTC 33713T=LMG 28871T); and Bacillus paramycoides sp. nov., type strain NH24A2T (=MCCC 1A04098T=KCTC 33709T=LMG 28876T).

Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1

Flammeovirga pacifica strain WPAGA1 is a Gram-negative, polysaccharide-degrading bacterium isolated from the marine sediment of the West Pacific Ocean. This strain is a cosmopolitan marine bacterium that uses complex polysaccharides as exclusive source of carbon and energy and plays a key role in the marine carbon cycle. Genome sequence analysis of strain WPAGA1 revealed that the assembled fine genome contains 6,610,326 bp with 32.89% G+C content, 5036 open reading frames (ORFs) and abundant genomic elements. Amongst these ORFs, 1022 genes encoding carbohydrate enzymes were found in the F. pacifica WPAGA1 genome. In addition, abundant putative enzymes involved in degrading polysaccharide were found. These enzymes include amylase, xylosidase, cellulase, alginate lyase, pectate lyase, rhamnogalacturonan lyase, chitinase, carrageenase, heparinase and fucosidase. To further investigate the use of these polysaccharides in strain WPAGA1, a schematic of various polysaccharide-degrading metabolic pathways were deduced from the genome sequence. This study showed that strain WPAGA1 may serve as a potential candidate for research of glycometabolism and have potential biotechnological and industrial applications and play key roles in the marine carbon cycle.