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DNA storage is a new digital data storage technology based on specific encoding and decoding methods between 0 and 1 binary codes of digital data and A-T-C-G quaternary codes of DNAs, which and is expected to develop into a major data storage form in the future due to its advantages (such as high data density, long storage time, low energy consumption, convenience for carrying, concealed transportation and multiple encryptions). In this review, we mainly summarize the recent research advances of four main encoding and decoding methods of DNA storage technology: direct mapping method between 0 and 1 binary and A-T-C-G quaternary codes in early-stage, fountain code for higher logical storage density, inner and outer codes for random access DNA storage data, and CRISPR mediated in vivo DNA storage method. The first three encoding/decoding methods belong to in vitro DNA storage, representing the mainstream research and application in DNA storage. Their advantages and disadvantages are also reviewed: direct mapping method is easy and efficient, but has high error rate and low logical density; fountain code can achieve higher storage density without random access; inner and outer code has error-correction design to realize random access at the expense of logic density. This review provides important references and improved understanding of DNA storage methods. Development of efficient and accurate DNA storage encoding and decoding methods will play a very important and even decisive role in the transition of DNA storage from the laboratory to practical application, which may fundamentally change the information industry in the future.

Objective We investigated the pathogenesis of a patient with severe acute pancreatitis by comprehensively analysing a rare carbapenem-resistant hypervirulent K1/ST1265 Klebsiella pneumoniae (CR-HvKP) strain. Methods We conducted virulence and multidrug-resistance phenotypic characterization and identified a CR-HvKP strain from the patient. It was subjected to Pacbio sequencing, and subsequent analysis of virulence, resistance genes and mobile genetic elements. Results We described the phenotype and genotype of a rare CR-HvKP strain with an untypeable blaKPC-harboured conjugative plasmid and a pLVPK-like virulent plasmid. Resistance gene analysis showed that the untypeable blaKPC-2-harboured plasmid was formed by IS26-mediated recombination of blaKPC-embedded transposon Tn6500 into pCN061p4 from Escherichia coli. Interestingly, it had an R-M system that might protect plasmid from cleavage. This may facilitate the stabilization of plasmids in bacteria in the event of missing CR-plasmid during transmission. Virulence gene analysis indicated 78 virulence genes on the genome, including 67 on the chromosome (37 in high-pathogenic island) and 11 on the pLVPK-like virulence plasmid (harbouring rmpA/rmpA2). Further phylogenetic analysis revealed that the CR-HvKP evolved from HvKP through acquiring an antimicrobial-resistance plasmid. Conclusion Our research, to our knowledge, first reported a ST1265/K1 CR-HvKP strain with an untypeable blaKPC-harboured plasmid. The trend that HvKP could evolve into CR-HvKP by obtaining stabilized/conjugative blaKPC-carrying plasmids is a considerable threat to public health and should be closely supervised.

Objective: To investigate the RNA profile of synovial fluid (SF) from osteoarthritis (OA) patients and carry out cluster analysis of OA-related genes. Methods: RNA of SF from OA patients was isolated using RNA-specific Trizol. A cDNA library was built and subjected to the second-generation sequencing using HisSeq4000 with a data size of 8G. The sequencing reads were aligned to the UCSC human reference genome (hg38) using Tophat with default parameters. Gene function enrichment was generated using DAVID. Results: The minimum weight 0.096 µg RNA of SF sample was used for sequencing analysis, which produced 66,154,562 clean reads, 91.28% of which were matched to the reference with 2,682 genes identified. Some of the unmatchable reads matched RNAs of bacteria, mainly Pseudomonas. The detected human RNAs in samples fell into different categories of genes, including protein-coding ones, processed and unprocessed pseudogenes, and long noncoding, antisense and miscellaneous RNAs that mediate various biological functions. Interestingly, 80% of the expressed genes belonged to the mitochondrial genome. Conclusion: These results suggest that less than 0.1 µg RNA is sufficient for establishing a cDNA library and deep sequencing, and that the liquid fraction of SF contains a whole RNA repertoire that may reflect a history of previous microorganism infections.

Carbapenemase-producing Klebsiella pneumoniae (cpKP) poses serious threats to public health. Previous studies showed that only ST11/CG258-cpKP successfully disseminated in China, however, the underlying genetic bases are still unknown. We conducted a comprehensive genomic-epidemiology analysis on 420 cpKP isolates from 70 hospitals in 24 Chinese provinces during 2009-2017 based on short-/long-reads sequencing. Three ‘golden’ combinations of host––blaKPC-carrying plasmids (Clade 3.1+3.2—IncFIIpHN7A8, Clade 3.1+3.2—IncFIIpHN7A8:IncR, Clade 3.3—IncFIIpHN7A8:IncpA1763-KPC) endowed cpKP with advantages both in genotypes (strong-correlation/co-evolution) and phenotypes (resistance/growth/competition), thereby facilitating nationwide spread of ST11/CG258-cpKP. Intriguingly, Bayesian skyline illustrated that the three ‘golden’ combinations might directly lead to the strong population expansion during 2007-2008 and subsequent maintenance of the dissemination of ST11/CG258-cpKP after 2008. We tested drug-resistance profiles and proposed combination treatment regimens for CG258/non-CG258 cpKP. Our findings systematically revealed the molecular-epidemiology and genetic-basis for dissemination of Chinese ST11/CG258 cpKP and reminded us to monitor the ‘golden’ combinations of cpKP- plasmid closely.

Introduction Increasing evidence shows that gut microbiota dysbiosis may play important roles in the occurrence and progression of Parkinson's disease (PD), but the findings are inconsistent. Besides, the effect of family environment on gut microbiota dysbiosis remains unclear. Methods We characterized the gut microbial compositions of 63 PD patients, 63 healthy spouses (HS) and 74 healthy people (HP) using 16S rRNA sequencing. Clinical phenotypes and microbial composition were analyzed comprehensively. Results There were markedly different microbial compositions among PD, HS and HP samples by alpha/beta diversity. We also found differential microbial compositions among Hoehn & Yahr stage/disease duration. Eight inflammation-associated microbial genera shared a continuously increase trend with increased Hoehn & Yahr stage and disease duration, indicating characteristic bacteria associated with deterioration in PD. Additionally, seven bacterial markers were identified for accurately differentiating PD patients from the controls (area under the curve [AUC]: 0.856). Conclusions Our study shows altered gut microbiota in PD patients. Importantly, inflammation-associated microbial genera may play roles in PD progression. Differential microbial compositions in HS and HP samples demonstrate that the gut microbiota are also affected by family environment. Disease-associated metagenomics studies should consider the family environmental factor. Our research provides an important reference and improves the understanding of gut microbiota in PD patients.

Here, we report a multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-HvKP) strain of sequence type 23 (ST23) with a rare hybrid plasmid harboring virulence genes and blaCTX-M-24, and we analyze the genetic basis for relationship between genotypes and MDR-hypervirulence phenotypes. Further analysis indicates that the hybrid plasmid is formed by IS903D-mediated intermolecular transposition of the blaCTX-M-24 gene into the virulence plasmid., Here, we report a multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-HvKP) strain of sequence type 23 (ST23) with a rare hybrid plasmid harboring virulence genes and blaCTX-M-24, and we analyze the genetic basis for relationship between genotypes and MDR-hypervirulence phenotypes. Further analysis indicates that the hybrid plasmid is formed by IS903D-mediated intermolecular transposition of the blaCTX-M-24 gene into the virulence plasmid. The emergence of MDR-HvKP strains, especially those carrying drug-resistant virulent plasmids, poses unprecedented threats/challenges to public health. This is a dangerous trend and should be closely monitored.

In this paper, we contribute to investigate the problem that providing service for High Speed Railway (HSR) in multiple-input multiple-output non-orthogonal multiple access (MIMO-NOMA) system to increase HSR rate. A novel system model is proposed to serve both HSR and local users. Coordinated Regularized Zero Forcing (CRZF) precoding is applied to deal with inter-cluster and inter-cell interference with considering the effect of Doppler Shift of HSR and the feedback delay of the Channel State Information (CSI). The proof of the performance of proposed model can outperform conventional MIMO-NOMA and MIMO-OMA is provided. At last, simulation is performed to demonstrate the correctness of the theory.

Two Artemia culture experiments were conducted in a zero water exchange system at salinity 80 g L−1. In Experiment I, different carbon sources including molasses, glucose, sucrose and corn flour were given to supplement suboptimal feeding with the microalgae Dunaliella viridis, whereas the control was fed only D. viridis. In Experiment II, molasses was supplemented to the culture medium, as well as the bacteria Alkalibacterium sp. or the archaea Halobacterium sp., isolated from the brine in the local saltponds. The control groups were fed only with D. viridis or with D. viridis and molasses. Our study shows that in laboratory culture biofloc development can be stimulated under hypersaline conditions. Supplementation of carbon sources, bacteria and archaea benefited biofloc development, water quality in terms of nitrogen load and enhanced Artemia production. Denaturing gradient gel electrophoresis analysis on the bioflocs also indicates an increased biodiversity and richness of the microbial community in the culture medium. These results need to be confirmed for large scale Artemia pond production, in which case, we recommend molasses as carbon source.

In this paper, we propose a hybrid decode-forward & amplify-forward relaying with opportunistic layered multicast (HDAF-OLM) scheme for a cellular system with multiple relays and multiple users. The scheme integrates hybrid decode-forward and amplify-forward with non-orthogonal multiple access transmission (HDAF-NOMA) scheme and layered multicast transmission into one strategy. Besides, a novel multicast partitioning analysis combined with this scheme is studied and we obtain the maximum transmission rates of a basic multicast stream (BMS) and an enhanced multicast stream (EMS) for fixed number of selected users. Simulation results show that the proposed multicast partitioning method in the HDAF-OLM scheme can achieve larger maximum transmission rates, larger system average throughput and lower delay as compared to conventional multicast scheme. Meanwhile, the HDAF-OLM scheme can also achieve larger total system capacity than traditional scheme.

Poly-beta-hydroxybutyrate (PHB) is microbial carbon and energy storage polymer, which can be degraded into water-soluble beta-hydroxybutyric acid in the gastrointestinal tract of aquatic animals. A 60-day culture experiment was performed using Chinese mitten crab, Eriocheir sinensis (Milne-Edwards) juveniles with an average initial body weight of 0.74 +/- 0.06 g which were fed a diet supplemented with 0%, 0.5%, 1%, 3% or 5% PHB. A PHB dietary supplementation of 1% and 3% significantly improved the body weight gain, moulting frequency and concomitantly reduced 2nd-3rd moulting intervals of the crabs (P < 0.05). The dietary PHB level positively related to hepatopan-creatic pepsin, trypsin and lipase activity (P < 0.05). Increasing the dietary PHB also improved total superoxide dismutase activity, but reduced alkaline phosphatase and acid phosphatase activity in the serum of hemolymph (P < 0.05). A 16S rRNA gene analysis by denaturing gradient gel electrophoresis indicated that PHB supplementation led to a significantly higher range-weighted richness, diversity and evenness of the gut bacterial community when dosed at 3% in the feed. The beneficial effects of PHB are discussed in terms of immune defense, metabolism and gut microbiota of the crabs.

Litopenaeus vannamei (Boone, 1931) postlarvae with average initial body weight of 0.089 g were reared in 75-litre PVC tanks for 40 days at salinities of 30 and 60 g l−1. The shrimps were fed compound feed containing protein levels of 35, 40, 45 and 50%, respectively. Salinity had a remarkable effect on growth and survival of L. vannamei juveniles. Higher survival rate and lower growth were observed at 60 g l−1 salinity. Dietary protein level affected the survival and growth of juveniles at both salinities, increased with dietary protein levels in the range of 35 to 45%, but decreased slightly with 50% dietary protein. Broken line analysis showed that the estimated optimal dietary protein levels at salinities of 30 and 60 g l−1 were 45.93 and 46.74%, respectively. Higher salinity resulted in an increased moisture content, ash and crude protein content in the shrimp muscle tissue. The amino acid contents in the shrimp muscle tissue were generally higher at 60 g l−1 salinity and increased dietary protein level led to higher protein content, except with 50% dietary protein. At salinity 60 g l−1, the soluble protein content and activities of glutamic oxalacetic transferase (GOT) and glutamic pyruvic transaminase (GPT) in shrimp muscle tissue were higher, while catalase (CAT) activities were lower. Farming of L. vannamei at a marginal culture salinity (60 g l−1) is feasible though the shrimps were likely exposed to stressful conditions. Reduced growth rate at higher salinity may be attributed to the higher total ammonium (TAN) concentration in the culture medium and extra energy consumption for osmoregulation at hypersaline conditions.

Crop growth models have been applied successfully in forecasting crop yield at a local scale, while satellite remote sensing has the advantage of retrieving regional crop parameters. The new assimilation method of integrating the crop growth model with remote sensing has presented great potential in regional crop yield assessment. In this study, the Moderate Resolution Imaging Spectrometer (MODIS) leaf area index (LAI) data product was assimilated into the World Food Studies (WOFOST) crop growth model. Using the Extended Fourier Amplitude Sensitivity Test (EFAST) global sensitivity analysis approach, several local and regional crop parameters were identified to be recalibrated. The Shuffled Complex Evolution (SCE) optimization algorithm was used to estimate the emergence date, initial biomass and initial available soil water by minimizing the differences between the corrected MODIS-LAI and simulated LAI. Results indicated that the accuracy of water-limited crop yield was improved significantly after the assimilation. The root mean square error (RMSE) reduced from 983 kg/ha to 474 kg/ha and 667 kg/ha respectively in two different optimization schemes.

Part 1: Simulation, Optimization, Monitoring and Control Technology; International audience; Regional crop yield prediction is a vital component of national food security assessment. Data assimilation method which combines crop growth model and remotely sensed data has been proven the most potential method in regional crop production estimation. This paper takes Hengshui district as study area, WOFOST as crop model, MODIS-LAI as observation data to test and verify the efficiency of EnKF assimilation method. The results show that the precision of crop yield estimation are obviously improved with EnKF assimilation, in the WOFOST potential level the R2 improved from 0.10 to 0.38 and RMSE was reduced from 2480 kg/ha to 880kg/ha. Our study indicates that EnKF assimilation method has great potential in regional crop production forecasting.

MODIS data is of significant for the classification of regional forest cover due to its high temporal resolution and high spectral resolution. Forest cover is an important parameter for forest ecosystem. The objective of this preliminary study is to mapping forest cover from multi-temporal MODIS data with decision tree. The classification forest samples were selected from four global land cover datasets with specific rules. The selected samples were used to generate rules of the decision tree for the classification of forest cover. The study results show that multi-temporal remote sensing data with decision tree method have great potential to improve the regional forest cover mapping.