A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps.

In deep-sea cold seeps, microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds, differing from photosynthetically driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and 7 metabolomes derived from nine different cold seep areas to investigate their secondary metabolites. Cold seep microbiomes encode diverse and abundant biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling. The BGCs encode diverse antimicrobial compounds that potentially shape community dynamics and various metabolites predicted to influence biogeochemical cycling. BGCs from key players are widely distributed and highly expressed, with their abundance and expression levels varying with sediment depth. Sediment metabolomics reveals unique natural products, highlighting uncharted chemical potential and confirming BGC activity in these sediments. Overall, these results demonstrate that cold seep sediments serve as a reservoir of hidden natural products and sheds light on microbial adaptation in chemosynthetically driven ecosystems.

Genome-based reclassification of Deinococcus saudiensis Hussain et al. 2016 as a later heterotypic synonym of Deinococcus soli Cha et al. 2014.

Deinococcus saudiensis YIM F302T was compared with Deinococcus soli N5T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of D. saudiensis YIM F302T showed high similarity (99.9 %) to that of D. soli N5T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Deinococcus. A draft genomic comparison between the two strains revealed average nucleotide identity values of 96.8-97.9 % and a digital DNA-DNA hybridization estimate of 80.7±1.9 %, strongly indicating that the two strains represented a single species. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we propose D. saudiensis as a later heterotypic synonym of D. soli N5T.

Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments.

BACKGROUND: A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited. RESULTS: Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete ß-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, 13C-labeled acetate was produced in the incubations when 13C-labeled dissolved inorganic carbon was provided. CONCLUSIONS: Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.

In situ diversity of metabolism and carbon use efficiency among soil bacteria.

The central carbon (C) metabolic network harvests energy to power the cell and feed biosynthesis for growth. In pure cultures, bacteria use some but not all of the network's major pathways, such as glycolysis and pentose phosphate and Entner-Doudoroff pathways. However, how these pathways are used in microorganisms in intact soil communities is unknown. Here, we analyzed the incorporation of 13C from glucose isotopomers into phospholipid fatty acids. We showed that groups of Gram-positive and Gram-negative bacteria in an intact agricultural soil used different pathways to metabolize glucose. They also differed in C use efficiency (CUE), the efficiency with which a substrate is used for biosynthesis. Our results provide experimental evidence for diversity among microbes in the organization of their central carbon metabolic network and CUE under in situ conditions. These results have important implications for our understanding of how community composition affects soil C cycling and organic matter formation.

High-Temperature Phase Transition Containing Switchable Dielectric Behavior, Long Fluorescence Lifetime, and Distinct Photoluminescence Changes in a 2D Hybrid CuBr4 Perovskite.

A novel organic-inorganic hybrid perovskite crystal, [ClC6H4(CH2)2NH3]2CuBr4 (1), having experienced an invertible high-temperature phase transition near Tc (the Curie temperature Tc = 355 K), has been successfully synthesized. The phase-transition characteristics for compound 1 are thoroughly revealed by specific heat capacity (Cp), differential thermal analysis, and differential scanning calorimetry tests, possessing 16 K broad thermal hysteresis. Multiple-temperature powder X-ray diffraction analysis further proves the phase-transition behavior of compound 1. Moreover, compound 1 exhibits a significant steplike dielectric response near Tc, revealing that it can be deemed to be a promising dielectric switching material. The variable-temperature fluorescence experiments show distinct photoluminescence (PL) changes of compound 1. Further investigation and calculation disclose that the fluorescence lifetime of compound 1 can reach as long as 55.46 µs, indicating that it can be a potential PL material. All of these researches contribute a substitutable avenue in the design and construction of neoteric phase-transition compounds combining high Curie temperature and PL properties.

[Variation Characteristics and Source Analysis of Carbonaceous Aerosols in Winter in Jiashan].

Organic carbon (OC), elemental carbon (EC), and PM2.5 concentration data obtained from Shanxi Super Station in Jiashan County of Jiaxing City, in the winter of 2018 and 2019, were analyzed to determine the variation and potential source areas of carbonaceous aerosols. The results show that OC concentrations in the winter of 2018 and 2019 were 6.90 µg·m-3 and 5.63 µg·m-3, respectively, while EC concentrations were 2.47 µg·m-3 and 1.57 µg·m-3, respectively. The concentrations of OC and EC in the winter of 2019 were lower than those in the winter of 2018, by approximately 18.4% and 36.4%, respectively. In 2018 and 2019, the concentrations of secondary organic carbon (SOC), calculated using the minimum R-squared (MRS) method, were 1.49 µg·m-3 and 1.97 µg·m-3, respectively, and the concentrations of primary organic carbon (POC) were 5.41 µg·m-3 and 3.66 µg·m-3, respectively. The proportion of POC in OC showed a downward trend, from 96.0% in December 2018 to 64.9% in February 2020, indicating a decrease of 31.1 percentage points. SOC showed an upward trend, increasing by 31.1 percentage points from 4.0% in December 2018 to 35.1% in February 2020. It is worth noting that with the increase in PM2.5 concentration, the concentration of OC and EC increased by 474.7% and 408.2%, respectively, although the proportion of OC in PM2.5 decreased from 18.8% to 12.3%. and the percentage of OC decreased from 5.8% to 3.3%. The contribution of POC to PM2.5 did not fluctuate, and only decreased significantly above 150 µg·m-3, while the contribution of SOC to PM2.5 first decreased and then increased. In Jiaxing, the potential sources of OC and EC were mainly southern Jiangsu, southeastern Anhui, local Jiaxing, and northern Zhejiang. In the winter of the contribution concentrations of OC and EC in the main potential source regions were approximately 2 µg·m-3 and 6 µg·m-3 lower, respectively, than in winter 2018. The range of high values in the potential source regions also decreased in 2019. Before the COVID-19 epidemic, it was affected by both motor vehicle exhaust emissions and coal burning. During the Spring Festival and home isolation, due to traffic control and other reasons, motor vehicle emissions were reduced, which leaving coal burning as the main contributor.

Substrate-dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri.

Dual stable isotope probing has been used to infer rates of microbial biomass production and modes of carbon fixation. In order to validate this approach for assessing archaeal production, the methanogenic archaeon Methanosarcina barkeri was grown either with H2 , acetate or methanol with D2 O and 13 C-dissolved inorganic carbon (DIC). Our results revealed unexpectedly low D incorporation into lipids, with the net fraction of water-derived hydrogen amounting to 0.357 ± 0.042, 0.226 ± 0.003 and 0.393 ± 0.029 for growth on H2 /CO2 , acetate and methanol respectively. The variability in net water H assimilation into lipids during the growth of M. barkeri on different substrates is possibly attributed to different Gibbs free energy yields, such that higher energy yield promoted the exchange of hydrogen between medium water and lipids. Because NADPH likely serves as the portal for H transfer, increased NADPH production and/or turnover associated with high energy yield may explain the apparent differences in net water H assimilation into lipids. The variable DIC and water H incorporation into M. barkeri lipids imply systematic, metabolic patterns of isotope incorporation and suggest that the ratio of 13 C-DIC versus D2 O assimilation in environmental samples may serve as a proxy for microbial energetics in addition to microbial production and carbon assimilation pathways.

Production of a Strain-Measuring Device with an Improved 3D Printer.

A traditional strain measurement sensor needs to be electrified and is susceptible to electromagnetic interference. In order to solve the fluctuations in the analog electrical signal in a traditional strain gauge operation, a new strain measurement method is presented here. It uses a photographic technique to display the strain change by amplifying the change of the pointer displacement of the mechanism. A visual polydimethylsiloxane (PDMS) lens with a focal length of 7.16 mm was added to a smartphone camera to generate a lens group acting as a microscope to capture images. It had an equivalent focal length of 5.74 mm. Acrylonitrile butadiene styrene (ABS) and nylon amplifiers were used to test the influence of different materials on the sensor performance. The production of the amplifiers and PDMS lens is based on improved 3D printing technology. The data obtained were compared with the results from finite element analysis (FEA) to verify their validity. The sensitivity of the ABS amplifier was 36.03 ± 1.34 µÎµ/µm, and the sensitivity of the nylon amplifier was 36.55 ± 0.53 µÎµ/µm.

Endoscopic resection of the pancreatic tail and subsequent wound healing mechanisms in a porcine model.

BACKGROUND: Laparoscopic resection of the pancreatic body and tail is the predominant methodology to remove lesions in these locations; its safety and surgical planning are relatively mature, but it remains a complex and high-precision surgical operation, requiring abundant experience and skills in laparoscopic surgery, with a 10% rate of complications. AIM: To verify the feasibility and safety, as well as to examine the complications of endoscopic pancreatectomy and healing mechanisms of pancreatic wounds after endoscopic resection. METHODS: Transgastric endoscopic resections of varying sizes of pancreases were performed in 15 healthy Bama miniature pigs. The technical success rate, the incidence of serious complications, and the survival of the animals were studied. The healing of the wounds was evaluated by sacrificing the animals at various time points. Finally, the expression of transforming growth factor-ß1 and Smad3/Smad7 in the surgical site was examined by immunohistochemistry to explore the role of these factors in wound healing of the pancreas. RESULTS: Partial and total resections were successfully performed in two groups of animals, respectively. The technical success rate and the survival rate of the pigs were both 100%. We obtained 12 pancreatic tissue samples by endoscopic resection. The pancreatic wounds were closed with metal clips in one group and the wounds healed well by forming scars. There was a small amount of pancreatic leakage in the other group, but it can be fully encapsulated. The level of transforming growth factor-ß1 (TGF-ß1) in the wounds increased during the inflammatory and fibrous hyperplasia phases, and decreased in the scar phase. The expression of Smad3 paralleled that of TGF-ß1, while the expression of Smad7 had an inverse relationship with the expression of TGF-ß1. CONCLUSION: Purely transgastric endoscopic resection of the pancreas is a safe, effective, and feasible procedure, but the incidence of pancreatic leakage in total pancreatic tail resection is high. The expression of TGF-ß1 and Smad3/Samd7 is related to the progression of pancreatic wound healing.

CO2 conversion to methane and biomass in obligate methylotrophic methanogens in marine sediments.

Methyl substrates are important compounds for methanogenesis in marine sediments but diversity and carbon utilization by methylotrophic methanogenic archaea have not been clarified. Here, we demonstrate that RNA-stable isotope probing (SIP) requires 13C-labeled bicarbonate as co-substrate for identification of methylotrophic methanogens in sediment samples of the Helgoland mud area, North Sea. Using lipid-SIP, we found that methylotrophic methanogens incorporate 60-86% of dissolved inorganic carbon (DIC) into lipids, and thus considerably more than what can be predicted from known metabolic pathways (~40% contribution). In slurry experiments amended with the marine methylotroph Methanococcoides methylutens, up to 12% of methane was produced from CO2, indicating that CO2-dependent methanogenesis is an alternative methanogenic pathway and suggesting that obligate methylotrophic methanogens grow in fact mixotrophically on methyl compounds and DIC. Although methane formation from methanol is the primary pathway of methanogenesis, the observed high DIC incorporation into lipids is likely linked to CO2-dependent methanogenesis, which was triggered when methane production rates were low. Since methylotrophic methanogenesis rates are much lower in marine sediments than under optimal conditions in pure culture, CO2 conversion to methane is an important but previously overlooked methanogenic process in sediments for methylotrophic methanogens.

Growth of sedimentary Bathyarchaeota on lignin as an energy source.

Members of the archaeal phylum Bathyarchaeota are among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth of Bathyarchaeota in the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth of Bathyarchaeota subgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth of Bathyarchaeota Meanwhile, putative bathyarchaeotal tetraether lipids incorporated 13C from 13C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth's most abundant biopolymers in anoxic marine sediment.

Acellular dermal matrix for esophageal stricture prevention after endoscopic submucosal dissection in a porcine model.

BACKGROUND AND AIMS: Endoscopic submucosal dissection (ESD) is considered an effective treatment for early esophageal cancer and precancerous lesions. Esophageal stenosis is closely associated with quasi-circumferential ESD. We examined whether post-ESD esophageal stricture can be prevented by grafting an acellular dermal matrix (ADM) membrane. METHODS: Fourteen Bama miniature pigs were randomly divided into an ADM group (n = 7) and a control group (n = 7). Semicircumferential ESD was performed at the distal esophagus in all animals, and in the ADM group an ADM patch graft was placed at the resection site and secured innovatively with metal clips. Animals in the control group underwent ESD only. Endoscopy was performed at 3 days, 1 week, 2 weeks, and 4 weeks post-ESD, and fluoroscopy was performed at 4 weeks for assessment of the degree of stenosis, after which the remodeled esophageal tissues were excised for histologic analysis. RESULTS: No animals in the ADM group developed clinically significant esophageal stenosis, whereas 42.8% (3/7) in the control group did. The degree of stenosis was severe in the control group (39.8% vs 17.2%, respectively; P = .01). Animals in the ADM group had less feeding difficulty and lost less weight (-.9 kg vs -4.1 kg, respectively; P = .007). Histologically, complete mucosal epithelium, slight local inflammation, and organized collagenous fibers were observed in the ADM group. CONCLUSIONS: ADM patch graft appears, after short-term observation, to be a potentially useful new treatment strategy for prevention of esophageal stricture after ESD. A metal clip fixation technique is effective for endoscopic graft attachment.

High response speed microfluidic ice valves with enhanced thermal conductivity and a movable refrigeration source.

Due to their ease of fabrication, facile use and low cost, ice valves have great potential for use in microfluidic platforms. For this to be possible, a rapid response speed is key and hence there is still much scope for improvement in current ice valve technology. Therefore, in this study, an ice valve with enhanced thermal conductivity and a movable refrigeration source has been developed. An embedded aluminium cylinder is used to dramatically enhance the heat conduction performance of the microfluidic platform and a movable thermoelectric unit eliminates the thermal inertia, resulting in a faster cooling process. The proposed ice valve achieves very short closing times (0.37 s at 10 µL/min) and also operates at high flow rates (1150 µL/min). Furthermore, the response time of the valve decreased by a factor of 8 when compared to current state of the art technology.

Diagnosis of lymphoma by endoscopic ultrasound-assisted transendoscopic direct retroperitoneal lymph node biopsy: A case report (with video).

Since its introduction in the early 1990s, endoscopic ultrasound-assisted fine-needle aspiration (EUS-FNA) has been used for sampling of extraintestinal mass lesions and peri-intestinal lymphadenopathy. Although EUS-FNA is highly accurate, lymphomas can be challenging to diagnose using EUS-FNA. We present the case of a 60-year-old male who had experienced upper abdominal discomfort for 1 month. Computerized tomography (CT) examination revealed multiple soft-tissue shadows located above the pancreatic body. The biggest shadow had a cross-sectional area of 7.7 cm × 7.2 cm. Positron emission tomography-CT (PET-CT) imaging showed increased uptake of (18)F-FDG by these soft-tissue shadows. To investigate further, EUS was performed and it revealed the presence of multiple hypoechoic round lymph nodes. During the procedure, EUS-FNA was performed, but only a few dyskaryotic cells were observed by cytological evaluation. EUS-assisted retroperitoneoscopy and lymph node biopsy were performed to obtain more tissue for immunohistochemical analysis and subclassification of lymphoma. Finally, the patient was diagnosed with non-Hodgkin lymphoma, germinal center B-cell-like diffuse large B-cell lymphoma by this technique. EUS-assisted transendoscopic retroperitoneal lymph node biopsy is an alternative procedure for the diagnosis of lymphomas.

Spatial and temporal variability of polycyclic aromatic hydrocarbons in sediments from yellow river-dominated margin.

Polycyclic aromatic hydrocarbons (PAHs) were analyzed for surface sediments and a sediment core from the Yellow River-dominated margin. The concentration of 16 USEPA priority PAHs in surface sediments ranged from 5.6 to 175.4 ng g(-1) dry weight sediment (dws) with a mean of 49.1 ng g(-1) dws. From 1930 to 2011, the distribution of PAHs (37.2 to 210.6 ng g(-1) dws) was consistent with the socioeconomic development of China. The PAHs' concentration peaked in 1964 and 1986, corresponding to the rapid economic growth in China (1958-1965) and the initiation of the "Reform and Open" policy in 1978, respectively. The applications of molecular diagnostic ratios and principal component analysis suggest that PAHs are predominantly produced by the coal and biomass combustion, whereas the contribution of petroleum combustions slightly increased after the 1970s, synchronous with an increasing usage of oil and gas in China.

[Value of auto-fluorescence spectrum combined with tumor markers in diagnosis of lung cancer].

To improve the diagnostic efficiency of cancer, serum fluorescence spectrum combined with tumor marker groups was proved more powerful, especially when used with mathematical evaluation model, that is, artificial neural network (ANN) modeling. ANN modeling is very suitable for the discrimination of lung cancer. ANN has evident superiority in solving nonlinear, multi-parameter and uncertain complicated problems. In the present paper, serum fluorescence spectrum was applied to study the difference among normal, benign and malignant groups and develop the relevant method of determination. On the other hand, combined with tumor markers, CEA, NSE, SCC-Ag, CYFRA21-1 and p16 methylation, artificial neural network and Fisher linear discriminatory analysis were used to develop the prediction models of diagnosis of lung cancer, and compared by ROC. It was shown that the result of the fluorescence spectrum combined with tumor markers based on ANN model is superior to that of the fluorescence spectrum ANN model. The performance of ANN model is superior to that of Fisher linear discriminatory analysis.