Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds.

Hu sheep (HS), a breed of sheep carrying the FecB mutation gene, is known for its "year-round estrus and multiple births" and is an ideal model for studying the high fecundity mechanisms of livestock. Through analyzing and comparing the genomic selection features of Hu sheep and other sheep breeds, we identified a series of candidate genes that may play a role in Hu sheep's high fecundity mechanisms. In this study, we conducted whole-genome resequencing on six breeds and screened key mutations significantly correlated with high reproductive traits in sheep. Notably, the CC2D1B gene was selected by the fixation index (FST) and the cross-population composite likelihood ratio (XP-CLR) methods in HS and other five breeds. It was worth noting that the CC2D1B gene in HS was different from that in other sheep breeds, and seven missense mutations have been identified. Furthermore, the linkage disequilibrium (LD) analysis revealed a strong linkage disequilibrium in this specific gene region. Subsequently, by performing different grouping based on FecB genotypes in Hu sheep, genome-wide selective signal analysis screened several genes related to reproduction, such as BMPR1B and PPM1K. Besides, FST analysis identified functional genes related to reproductive traits, including RHEB, HSPA2, PPP1CC, HVCN1, and CCDC63. Additionally, a missense mutation was found in the CCDC63 gene and the haplotype was different between the high reproduction (HR) group and low reproduction (LR) group in HS. In summary, we discovered genetic differentiation among six distinct breeding sheep breeds at the whole genome level. Additionally, we identified a set of genes which were associated with reproductive performance in Hu sheep and visualized how these genes differed in different breeds. These findings laid a theoretical foundation for understanding genetic mechanisms behind high prolific traits in sheep.

Safety and benefit of modified mesohepatectomy in the treatment of bilobar involvement congenital biliary dilatation.

BACKGROUND: The diseased bile duct in bilobar congenital biliary dilatation is extensive and often requires major hepatectomy or liver transplantation associated with a higher risk. We aimed to evaluate the safety and benefit of modified mesohepatectomy, in comparison with trisectionectomy, to treat bilobar congenital biliary dilatation. METHODS: This study included 28 patients with type IV and V bilobar congenital biliary dilatation. An innovative mesohepatectomy comprising the hepatectomy technique beyond the P/U point and bile duct shaping was applied to 14 patients to address the extensively diseased bile duct and difficulty in hepaticojejunostomy. Another 14 patients received trisectionectomy. The perioperative and long-term outcomes of these patients were compared. RESULTS: The ratio of residual liver volume to standard liver volume in the mesohepatectomy group was higher (78.68% vs. 40.90%, p = 0.005), while the resection rate of the liver parenchyma was lower (28.25% vs. 63.97%, p = 0.000), than that in trisectionectomy group. The mesohepatectomy group had a lower severe complication (>Clavein III, 0% vs. 57.70%, p = 0.019) and incidence of posthepatectomy liver failure (7.14% vs. 42.86%, p = 0.038). No significant difference was observed in blood loss and bile leakage (p > 0.05). All the patients in the mesohepatectomy group achieved optimal results in the long-term follow-up. CONCLUSIONS: mesohepatectomy provides an efficient treatment option for bilobar congenital biliary dilatation and can achieve radical resection, retain more liver parenchyma, and reduce the difficulty of hepaticojejunostomy, especially for patients that are not eligible for major hepatectomy and liver transplantation.

Efficacy of radiotherapy in combined treatment of hepatocellular carcinoma patients with portal vein tumor thrombus: a real-world study.

BACKGROUND AND AIMS: Hepatocellular carcinoma (HCC) with portal vein tumor thrombus (PVTT) has an extremely poor prognosis. A previous study proved that low-dose radiotherapy (RT) could prolong the prognosis of HCC patients with PVTT. This study aims to explore the sensitivity of PVTT to RT treatment. METHODS: Patients were selected based on imaging diagnosis of HCC accompanied by PVTT and received combined treatment of radiotherapy, antiangiogenic drugs and immune checkpoint inhibitors, followed by hepatectomy or liver transplantation from January 2019 to August 2022. The efficacy was evaluated by Response Evaluation Criteria in Solid Tumors (RECIST) guidelines and pathological assessment. The sensitivity of tumor cells to the treatment was compared between the primary tumor (PT)and PVTT by analyzing their residual tumor and pathologic complete remission (PCR) incidence. RESULTS: Data from 14 patients were collected in the study. After combined treatment, the size of PVTT decreased more significantly than that of the primary tumor in the imaging study (p < 0.05). The residual cancer was significantly more restrictive than that of primary tumor in paired patients based on pathological measurement (p = 0.008). The PCR incidence of the primary tumor (21.42%) was significantly lower (p = 0.008) than that of PVTT in the pathologic study (78.57%). CONCLUSION: PVTT is more sensitive to radiotherapy treatment than the primary tumor in patients with HCC. This combination therapy might be an effective option as a downstaging therapy for patients with HCC with PVTT.

Quantitative determination of rhamnolipid using HPLC-UV through carboxyl labeling.

Rhamnolipid, as a low-toxic, biodegradable and environmentally friendly biosurfactant, has broad application prospects in many industries. However, the quantitative determination of rhamnolipid is still a challenging task. Here, a new sensitive method for the quantitative analysis of rhamnolipid based on a simple derivatization reaction was developed. In this study, 3-[3'-(l-rhamnopyranosyloxy) decanoyloxy] decanoic acid (Rha-C10-C10) and 3-[3'-(2'-O-α-l-rhamnopyranosyloxy) decanoyloxy] decanoic acid (Rha-Rha-C10-C10) were utilized as the representative rhamnolipids. Liquid chromatography-mass spectrometry and high-performance liquid chromatography-ultra violet results showed that these two compounds were successfully labeled with 1 N1-(4-nitrophenyl)-1,2-ethylenediamine. There was an excellent linear relationship between rhamnolipid concentration and peak area of labeled rhamnolipid. The detection limits of the Rha-C10-C10 and Rha-Rha-C10-C10 were 0.018 mg/L (36 nmol/L) and 0.014 mg/L (22 nmol/L), respectively. The established amidation method was suitable for the accurate analysis of rhamnolipids in the biotechnological process. The method had good reproducibility with the relative standard deviation of 0.96% and 0.79%, respectively, and sufficient accuracy with a recovery of 96%-100%. This method was applied to quantitative analysis of 10 rhamnolipid homologs metabolized by Pseudomonas aeruginosa LJ-8. The single labeling method was used for the quantitative analysis of multiple components, which provided an effective method for the quality evaluation of other glycolipids with carboxyl groups.

Genetic engineering of the branched-chain fatty acid biosynthesis pathway to enhance surfactin production from Bacillus subtilis.

Surfactin, which is composed of a ß-hydroxy fatty acid chain and a peptide ring, has drawn considerable attention due to its potential applications in the biomedicine, bioremediation, and petroleum industries. However, the low yield of surfactin from wild strains still restricts its industrial applications. In this study, eight genes relevant to the fatty acid biosynthesis pathway were targeted to enhance surfactin production, and high surfactin-yielding strains with potential industrial applications were obtained. When ldeHA and acc were co-overexpressed, the surfactin yield of recombinant strains TDS8 and TPS8 increased to 1.55- and 1.19-fold of their parental strains, respectively, again proving that the conversion of acetyl-coenzyme A (CoA) to malonyl-CoA is the rate-limiting step in fatty acid biosynthesis. Furthermore, changes in surfactin isoforms of recombinant strain TPS8 suggest that the fatty acid precursor synthesis pathway can be modified to improve the proportion of different isoforms. In addition, the deletion of lpdV, which is responsible for the conversion of α-ketoacyl-CoA precursors, resulted in a sharp decrease in surfactin production, further demonstrating the importance of branched-chain fatty acid biosynthesis in surfactin production. This work will facilitate the design and construction of more efficiently engineered strains for surfactin production and further extend industrial applications.

Molecular dynamics simulation studies of 1,3-dimethyl imidazolium nitrate ionic liquid with water.

The fundamental understanding of intermolecular interactions of ionic liquids (ILs) with water is essential in predicting IL-water thermodynamic properties. In this study, intermolecular or noncovalent interactions were studied for 1,3-dimethyl imidazolium [DMIM]+ cation and nitrate [NO3]- anion with water, employing quantum mechanics and molecular dynamics simulations. Molecular dynamics simulations were performed using a revised multipolar polarizable force field. The effect of water on ionic liquids was evaluated in terms of thermodynamic and dynamic properties. Thermodynamic properties included liquid densities ρ, excess molar volumes ΔVE, and liquid structures gr. Dynamic properties included self-diffusion coefficients D of mixture constituents as a function of water concentration. The density of ionic liquid-water mixtures monotonically decrease with increasing concentration of water. A negative excess volume was obtained for low and high water concentrations, demonstrating strong intermolecular interactions of water with ionic liquid components. Liquid structures of ionic liquid-water mixtures revealed a tendency for anions to interact with cations at shorter intermolecular distances when the water concentration is increased. Diffusion rates were found to increase for all mixture components with increase in the fraction of water. A significant change in the diffusion rate was found at ∼0.3 weight fraction of water. However, the water self-diffusion coefficient was dominant at all concentrations. The ratio of water/anion and anion/cation self-diffusion coefficients was found to decrease linearly with increasing concentration of water molecules.

Discovery of the non-cosmopolitan lineages in Candidatus Thermoprofundales.

The recently proposed order Candidatus Thermoprofundales, currently containing only one family-level lineage Marine Benthic Group-D (MBG-D), is distributed in global subsurface ecosystems and ecologically important, but its diversity, evolution and metabolism remain largely unknown. Here we described two novel family-level specialized lineages in Ca. Thermoprofundales, JdFR-43 and HyVt, which are restricted to specific biotopes (primarily in marine hydrothermal vents and occasionally in oil reservoirs and hot springs) in contrast to the cosmopolitan lineage MBG-D. The comparative genomics revealed that the specialized lineages have streamlined genomes, higher GC contents, enriched genes associated with nucleotide biosynthesis, ribosome biogenesis and DNA repair and additional thermostable aminopeptidases, enabling them to adapt to high-temperature habitats such as marine hydrothermal vents, deep subsurface oil reservoirs and hot springs. On the contrary, the unique metabolic traits of the cosmopolitan MBG-D, motility, glycolysis, butanoate metabolism, secondary metabolites production and additional genes for specific peptides and carbohydrates degradation potentially enhance its response to environmental change. Substrate preference is found for most MAGs across all lineages with the ability to utilize both polysaccharides (chitin and starch) and proteinaceous substances, whereas JdFR-43 members from oil reservoirs can only utilize proteins. These results expand the diversity of Ca. Thermoprofundales significantly and further improve our understandings of the adaptations of Ca. Thermoprofundales to various environments.

An Efficient LiDAR Point Cloud Map Coding Scheme Based on Segmentation and Frame-Inserting Network.

In this article, we present an efficient coding scheme for LiDAR point cloud maps. As a point cloud map consists of numerous single scans spliced together, by recording the time stamp and quaternion matrix of each scan during map building, we cast the point cloud map compression into the point cloud sequence compression problem. The coding architecture includes two techniques: intra-coding and inter-coding. For intra-frames, a segmentation-based intra-prediction technique is developed. For inter-frames, an interpolation-based inter-frame coding network is explored to remove temporal redundancy by generating virtual point clouds based on the decoded frames. We only need to code the difference between the original LiDAR data and the intra/inter-predicted point cloud data. The point cloud map can be reconstructed according to the decoded point cloud sequence and quaternion matrices. Experiments on the KITTI dataset show that the proposed coding scheme can largely eliminate the temporal and spatial redundancies. The point cloud map can be encoded to 1/24 of its original size with 2 mm-level precision. Our algorithm also obtains better coding performance compared with the octree and Google Draco algorithms.

Depth-Keeping Control for a Deep-Sea Self-Holding Intelligent Buoy System Based on Inversion Time Constraint Stability Strategy Optimization.

Based on the nonlinear disturbance observer (NDO), the inversion time-constraint stability strategy (ITCS) is designed to make the deep-sea self-holding intelligent buoy (DSIB) system hovered at an appointed depth within a specified time limit. However, it is very challenging to determine the optimal parameters of an ITCS depth controller. Firstly, a genetic algorithm based on quantum theory (QGA) is proposed to obtain the optimal parameter combination by using the individual expression form of quantum bit and the adjustment strategy of quantum rotary gate. To improve the speed and accuracy of global search in the QGA optimization process, taking the number of odd and even evolutions as the best combination point of the genetic and chaos particle swarm algorithm (GACPSO), an ITCS depth controller based on GACPSO strategy is proposed. Besides, the simulations and hardware-in-the-loop system experiments are conducted to examine the effectiveness and feasibility of the proposed QGA-ITCS and GACPSO-ITCS depth controller. The results show that the proposed GACPSO-ITCS depth controller provides higher stability with smaller steady-state error and less settling time in the depth-control process. The research of the proposed method can provide a stable operation condition for the marine sensors carried by the DSIB.

A Novel System for the Measurement of an Evaporation Duct Using the Magnetic Coupling Principle for Power Feeding and Data Transmission.

Since the evaporation duct height (EDH) only covers the antenna height of most shipborne microwave radars, mastering the EDH in advance has great significance in achieving long-range target detection. In this paper, a set of hydrological and meteorological sensors based on the gradient meteorological instrument (GMI) were built to monitor the evaporation duct of the South China Sea (SCS). However, the monitoring needed to be interrupted during the battery replacement of the sensor, which could result in the loss of some important data collection. On the basis of the inductively coupled power transfer (ICPT) technology, the resonance principle was used to compensate the inductive reactance on the closed steel ring (CSR), and the energy stored in the super capacitor was introduced for data collection and return. A novel measuring system for the detection of an evaporation duct was proposed. To avoid iterative calculation by setting the initial value of the current evaporation duct models in large-scale and multi time evaporation duct prediction and diagnosis, on the basis of the non-iterative air-sea flux (NAF) model, the EDH was obtained by introducing the K theoretical flux observation method into the atmospheric refractive index equation. Finally, preliminary experimental results are presented for the detection of evaporation duct to demonstrate the feasibility and effectiveness of the proposed system. The communication accuracy rate of the proposed system was 99.7%. The system transmission power reached 22.8 W. The research results of the NAF model adaptability showed that the mean value of the EDH was 8.7 m, which was lower than the mean EDH of the SCS. The EDH calculated by the NAF model in the unstable air-sea stratification state was slightly lower than that calculated by the NPS model. The diagnosis of the EDH by the NAF model was similar to that of the NPS model, but the calculation stability of the NAF model was better.

Preoperative Remnant Liver Function Evaluation Using a Routine Clinical Dynamic Gd-EOB-DTPA-Enhanced MRI Protocol in Patients with Hepatocellular Carcinoma.

BACKGROUND: To investigate the clinical feasibility of preoperative routine clinical dynamic Gd-EOB-DTPA-enhanced MRI alone to predict post-hepatectomy liver failure (PHLF) in patients with hepatocellular carcinoma (HCC). METHODS: 116 patients with HCC who underwent liver resection in Southwest Hospital from 2014 through 2017 were selected in this retrospective cohort study. The remnant function (RF) of the liver RFUR and RFRE15 were calculated by the sum of the uptake rate (UR) or relative enhancement at 15 min (RE15) from dynamic Gd-EOB-DTPA-enhanced MR images in the remnant liver regions, and standardized by standard liver volume (SLV) to generate sRFUR (standardized RFUR) and sRFRE15 (standardized RFRE15). Student's t test or Mann-Whitney U test, logistic regression, and ROC analyses were used to test the associations of preoperative RFUR, sRFUR, RFRE15, sRFRE15, the remnant liver volume (RLV)/SLV, ICG retention rate at 15 min (ICG R15) and sRFICG-K [ICG clearance rate (ICG-K) × RLV/SLV] with PHLF. RESULTS: 28 patients were found to have PHLF, who showed lower RFUR, sRFUR, RFRE15, sRFRE15, RLV/SLV, sRFICG-K, and higher ICG R15 than patients without PHLF (p < 0.001 for all). After adjusting for clinical parameters, RFUR (p = 0.001), sRFUR (p = 0.001), RFRE15 (p = 0.002), or sRFRE15 (p = 0.003) was found to be independently significant indicator in multivariable logistic regression, respectively. RFUR (0.882) and sRFUR (0.882) had larger AUCs than RLV/SLV (0.731, p = 0.008; p = 0.005), ICG R15 (0.765, p = 0.039; p = 0.044) and sRFICG-K (0.767, p = 0.031; p = 0.023). RFRE15 (0.845) and sRFRE15 (0.839) had larger AUCs than RLV/SLV (0.731, p = 0.027; p = 0.025). CONCLUSIONS: The remnant liver function parameters preoperatively estimated from a routine clinical dynamic Gd-EOB-DTPA-enhanced MRI protocol can predict PHLF in patients with HCC, and may be better predictors than conventional methods.

Synthesis and mass spectra of rearrangement bio-signature metabolites of anaerobic alkane degradation via fumarate addition.

Metabolite profiling in anaerobic alkane biodegradation plays an important role in revealing activation mechanisms. Apart from alkylsuccinates, which are considered to be the usual biomarkers via fumarate addition, the downstream metabolites of C-skeleton rearrangement can also be regarded as biomarkers. However, it is difficult to detect intermediate metabolites in both environmental samples and enrichment cultures, resulting in lacking direct evidence to prove the occurrence of fumarate addition pathway. In this work, a synthetic method of rearrangement metabolites was established. Four compounds, namely, propylmalonic acid, 2-(2-methylbutyl)malonic acid, 2-(2-methylpentyl)malonic acid and 2-(2-methyloctyl)malonic acid, were synthesized and determined by four derivatization approaches. Besides, their mass spectra were obtained. Four characteristic ions were observed at m/z 133 + 14n, 160 + 28n, 173 + 28n and [M - (45 + 14n)]+ (n = 0 and 2 for ethyl and n-butyl esters, respectively). For methyl esterification, mass spectral features were m/z 132, 145 and [M - 31]+, while for silylation, fragments were m/z 73, 147, 217, 248, 261 and [M - 15]+. These data provide basis on identification of potential rearrangement metabolites in anaerobic alkane biodegradation via fumarate addition.

Anaerobic Degradation of Paraffins by Thermophilic Actinobacteria under Methanogenic Conditions.

Microbial anaerobic alkane degradation is a key process in subsurface oil reservoirs and anoxic environments contaminated with petroleum, with a major impact on global carbon cycling. However, the thermophiles capable of water-insoluble paraffins (>C17) degradation under methanogenic conditions has remained understudied. Here, we established thermophilic (55 °C) n-paraffins-degrading (C21-C30) cultures from an oil reservoir. After over 900 days of incubation, the even-numbered n-paraffins were biodegraded to methane. The bacterial communities are dominated by a novel class-level lineage of actinobacteria, 'Candidatus Syntraliphaticia'. These 'Ca. Syntraliphaticia'-like metagenome-assembled genomes (MAGs) encode a complete alkylsuccinate synthases (ASS) gene operon, as well as hydrogenases and formate dehydrogenase, and several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. Metatranscriptomic analysis suggests that n-paraffins are activated via fumarate addition reaction, and oxidized into carbon dioxide, hydrogen/formate and acetate by 'Ca. Syntraliphaticia', that could be further converted to methane by the abundant hydrogenotrophic and acetoclastic methanogens. We also found a divergent methyl-CoM reductase-like complex (MCR) and a canonical MCR in two MAGs representing 'Ca. Methanosuratus' (within candidate phylum Verstraetearchaeota), indicating the capability of methane and short-chain alkane metabolism in the oil reservoir. Ultimately, this result offers new insights into the degradability and the mechanisms of n-paraffins under methanogenic conditions at high temperatures.

Carbide Formation in Refractory Mo15Nb20Re15Ta30W20 Alloy under a Combined High-Pressure and High-Temperature Condition.

In this work, the formation of carbide with the concertation of carbon at 0.1 at.% in refractory high-entropy alloy (RHEA) Mo15Nb20Re15Ta30W20 was studied under both ambient and high-pressure high-temperature conditions. The x-ray diffraction of dilute carbon (C)-doped RHEA under ambient pressure showed that the phases and lattice constant of RHEA were not influenced by the addition of 0.1 at.% C. In contrast, C-doped RHEA showed unexpected phase formation and transformation under combined high-pressure and high-temperature conditions by resistively employing the heated diamond anvil cell (DAC) technique. The new FCC_L12 phase appeared at 6 GPa and 809 °C and preserved the ambient temperature and pressure. High-pressure and high-temperature promoted the formation of carbides Ta3C and Nb3C, which are stable and may further improve the mechanical performance of the dilute C-doped alloy Mo15Nb20Re15Ta30W20.

Methanogenic Degradation of Long n-Alkanes Requires Fumarate-Dependent Activation.

Methanogenic degradation of n-alkanes is prevalent in n-alkane-impacted anoxic oil reservoirs and oil-polluted sites. However, little is known about the initial activation mechanism of the substrate, especially n-alkanes with a chain length above C16 Here, a methanogenic C16 to C20n-alkane-degrading enrichment culture was established from production water of a low-temperature oil reservoir. At the end of the incubation (364 days), C16 to C20 (1-methylalkyl)succinates were detected in the n-alkane-amended enrichment culture, suggesting that fumarate addition had occurred in the degradation process. This evidence is supported further by the positive amplification of the assA gene encoding the alpha subunit of alkylsuccinate synthase. A phylogenetic analysis shows these assA amplicons to be affiliated with Smithella and Desulfatibacillum clades. Together with the high abundance of these clades in the bacterial community, these two species are postulated to be the key players in the degradation of C16 to C20n-alkanes in the present study. Our results provide evidence that long n-alkanes are activated via a fumarate addition mechanism under methanogenic conditions.IMPORTANCE Methanogenic hydrocarbon degradation is the major process for oil degradation in subsurface oil reservoirs and is blamed for the formation of heavy oil and oil sands. Addition of n-alkanes to fumarate yielding alkyl-substituted succinates is a well-characterized anaerobic activation mechanism for hydrocarbons and is the most common activation mechanism in the anaerobic biodegradation of n-alkanes with chain lengths less than C16 However, the activation mechanism involved in the methanogenic biodegradation of n-alkanes longer than C16 is still uncertain. In this study, we analyzed a methanogenic enrichment culture amended with a mixture of C16 to C20n-alkanes. These n-alkanes can be activated via fumarate addition by mixed cultures containing Smithella and Desulfatibacillum species under methanogenic conditions. These observations provide a fundamental understanding of long-n-alkane metabolism under methanogenic conditions and have important applications for the remediation of oil-contaminated sites and for energy recovery from oil reservoirs.

Methanogenic degradation of branched alkanes in enrichment cultures of production water from a high-temperature petroleum reservoir.

Branched alkanes are important constituents of crude oil and are usually regarded as resistant to microbial degradation, resulting in little knowledge of biochemical processes involved in anaerobic branched alkanes biodegradation. Here, we initiated an incubation study by amendment of iso-C9 (2-methyl, 3-methyl, and 4-methyloctane) as substrates for methanogenic degradation in production water from a high-temperature petroleum reservoir. Over an incubation period of 367 days, significant methanogenesis was observed in samples amended with these branched alkanes. The strong methanogenic activity only observed in iso-C9 amendments suggested the presence of microbial transformation from iso-alkanes into methane. GC-MS-based examination of the original production water identified an intermediate tentatively to be iso-C9-like alkylsuccinate, but was not detected in the enrichment cultures, combined with the successful amplification of assA functional gene in inoculating samples, revealing the ability of anaerobic biodegradation of iso-C9 via fumarate addition pathway. Microorganisms affiliated with members of the Firmicutes, Synergistetes, and methanogens of genus Methanothermobacter spp. were highly enriched in samples amended with iso-C9. The co-occurrence of known syntrophic acetate oxidizers Thermoacetogenium spp. and Methanothermobacter spp. (known hydrogenotrophic methanogens) indicates a potential syntrophic acetate oxidation associated with the methanogenic biodegradation of iso-C9. These results provide some useful information on the potential biodegradation of branched alkanes via methanogenesis and also suggest that branched alkanes are likely activated via fumarate addition in high-temperature petroleum reservoirs.

Anaerobic biodegradation of partially hydrolyzed polyacrylamide in long-term methanogenic enrichment cultures from production water of oil reservoirs.

The increasing usage of partially hydrolyzed polyacrylamide (HPAM) in oilfields as a flooding agent to enhance oil recovery at so large quantities is an ecological hazard to the subsurface ecosystem due to persistence and inertness. Biodegradation of HPAM is a potentially promising strategy for dealing with this problem among many other methods available. To understand the responsible microorganisms and mechanism of HPAM biodegradation under anaerobic conditions, an enrichment culture from production waters of oil reservoirs were established with HPAM as the sole source of carbon and nitrogen incubated for over 328 days, and analyzed using both molecular microbiology and chemical characterization methods. Gel permeation chromatography, High-pressure liquid chromatography and Fourier-transformed infrared spectroscopy results indicated that, after 328 days of anaerobic incubation, some of the amide groups on HPAM were removed and released as ammonia/ammonium and carboxylic groups, while the carbon backbone of HPAM was converted to smaller polymeric fragments, including oligomers and various fatty acids. Based on these results, the biochemical process of anaerobic biodegradation of HPAM was proposed. The phylogenetic analysis of 16S rRNA gene sequences retrieved from the enrichments showed that Proteobacteria and Planctomycetes were the dominant bacteria in the culture with HPAM as the source of carbon and nitrogen, respectively. For archaea, Methanofollis was more abundant in the anaerobic enrichment. These results are helpful for understanding the process of HPAM biodegradation and provide significant insights to the fate of HPAM in subsurface environment and for possible bioremediation.

Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir.

Acetate is a key intermediate in anaerobic crude oil biodegradation and also a precursor for methanogenesis in petroleum reservoirs. The impact of iron oxides, viz. ß-FeOOH (akaganéite) and magnetite (Fe3O4), on the methanogenic acetate metabolism in production water of a high-temperature petroleum reservoir was investigated. Methane production was observed in all the treatments amended with acetate. In the microcosms amended with acetate solely about 30% of the acetate utilized was converted to methane, whereas methane production was stimulated in the presence of magnetite (Fe3O4) resulting in a 48.34% conversion to methane. Methane production in acetate-amended, ß-FeOOH (akaganéite)-supplemented microcosms was much faster and acetate consumption was greatly improved compared to the other conditions in which the stoichiometric expected amounts of methane were not produced. Microbial community analysis showed that Thermacetogenium spp. (known syntrophic acetate oxidizers) and hydrogenotrophic methanogens closely related to Methanothermobacter spp. were enriched in acetate and acetate/magnetite (Fe3O4) microcosms suggesting that methanogenic acetate metabolism was through hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers. The acetate/ß-FeOOH (akaganéite) microcosms, however, differed by the dominance of archaea closely related to the acetoclastic Methanosaeta thermophila. These observations suggest that supplementation of ß-FeOOH (akaganéite) accelerated the production of methane further, driven the alteration of the methanogenic community, and changed the pathway of acetate methanogenesis from hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers to acetoclastic.

Detecting grain rotation at the nanoscale.

It is well-believed that below a certain particle size, grain boundary-mediated plastic deformation (e.g., grain rotation, grain boundary sliding and diffusion) substitutes for conventional dislocation nucleation and motion as the dominant deformation mechanism. However, in situ probing of grain boundary processes of ultrafine nanocrystals during plastic deformation has not been feasible, precluding the direct exploration of the nanomechanics. Here we present the in situ texturing observation of bulk-sized platinum in a nickel pressure medium of various particle sizes from 500 nm down to 3 nm. Surprisingly, the texture strength of the same-sized platinum drops rapidly with decreasing grain size of the nickel medium, indicating that more active grain rotation occurs in the smaller nickel nanocrystals. Insight into these processes provides a better understanding of the plastic deformation of nanomaterials in a few-nanometer length scale.

Propionate metabolism and diversity of relevant functional genes by in silico analysis and detection in subsurface petroleum reservoirs.

Propionate is a common metabolic intermediate occurring in environmental samples including petroleum reservoirs. Available microbial genomes were obtained from the NCBI database and analyzed in silico by hmmscan to check three metabolic pathways of propionate production in petroleum reservoir systems. The succinate pathway was the dominant one while the other two (lactate and 1,2-propanediol pathways) contributed less to the formation of propionate according to the Hidden Markov Model calculation. The mmdA gene encoding methylmalonyl-CoA decarboxylase was used as a biomarker gene to detect the diversity of microbes involved in the propionate formation in Jiangsu oil reservoirs. The mmdA gene clone library showed that microbes affiliated within the genus of Archaeoglobus, Thermococcus, Anaerobaculum, as well as more than ten other genera were the potential microorganisms involved in the production of propionate. Meanwhile, as the biomarker genes involved in the other two propionate-producing pathways, the functional genes of lcdA and pduP were tested with PCR amplification, but no positive results were observed in Jiangsu oil reservoirs.