Whole genome sequencing of the halophilic Halomonas qaidamensis XH36, a novel species strain with high ectoine production

Here, we report the whole genome of a novel halophilic Halomonas species strain XH36 with high ectoine production potential. The genome was 3,818,310 bp in size with a GC content of 51.97%, and contained 3533 genes, 61 tRNAs and 18 rRNAs. The phylogenetic analysis using the 16s rRNA genes, the UBCGs and the TYGS database indicated that XH36 belongs to a novel Halomonas species, which we named as Halomonas qaidamensis. Osmoadaptation related genes including Na(+) and K(+) transport and compatible solute accumulation were both present in the XH36 genome, the latter of which mainly contained ectoine, 5-hydroxyectoine and betaine. HPLC validation studies showed that H. qaidamensis XH36 accumulated ectoine to cope with salt stress, and the content of ectoine could be as high as 315 mg/g CDW under 3 mol/l NaCl. Our results show that XH36 is a new promising industrial strain for ectoine production, and the genomic analysis will guide us to better understand its salt-induced osmoadaptation mechanisms, and provide theoretical references for future application research of ectoine.

Moisture Distribution and Structural Properties of Frozen Cooked Noodles with NaCl and Kansui

The effects of NaCl (1-3%) and kansui (0.5-1.5%) on the quality of frozen cooked noodles (FCNs) were investigated, which provided a reference for alleviating the quality deterioration of FCNs. Textural testing illustrated that the optimal tensile properties were observed in 2% NaCl (N-2) and the maximum hardness and chewiness were reached at 1% kansui (K-1). Compared to NaCl, the water absorption and cooking loss of recooked FCNs increased significantly with increasing kansui levels (p < 0.05). Rheological results confirmed NaCl and kansui improved the resistance to deformation and recovery ability of thawed dough; K-1 especially had the highest dough strength. SEM showed N-2 induced a more elongated fibrous protein network that contributed to the extensibility, while excessive levels of kansui formed a deformed membrane-like gluten network that increased the solid loss. Moisture analysis revealed that N-2 reduced the free water content, while K-1 had the lowest freezable water content and highest binding capacity for deeply adsorbed water. The N-2 and K-1 induced more ordered protein secondary structures with stronger intermolecular disulfide bonds, which were maximally improved in K-1. This study provides more comprehensive theories for the strengthening effect of NaCl and kansui on FCNs quality.

Initializing LSTM internal states via manifold learning

We present an approach, based on learning an intrinsic data manifold, for the initialization of the internal state values of long short-term memory (LSTM) recurrent neural networks, ensuring consistency with the initial observed input data. Exploiting the generalized synchronization concept, we argue that the converged, "mature" internal states constitute a function on this learned manifold. The dimension of this manifold then dictates the length of observed input time series data required for consistent initialization. We illustrate our approach through a partially observed chemical model system, where initializing the internal LSTM states in this fashion yields visibly improved performance. Finally, we show that learning this data manifold enables the transformation of partially observed dynamics into fully observed ones, facilitating alternative identification paths for nonlinear dynamical systems.

Establishing an efficient salinomycin biosynthetic pathway in three heterologous Streptomyces hosts by constructing a 106-kb multioperon artificial gene cluster

Salinomycin is a promising anticancer drug for chemotherapy. A highly productive biosynthetic gene cluster will facilitate the creation of analogs with improved therapeutic activity and reduced side effects. In this study, we engineered an artificial 106-kb salinomycin gene cluster and achieved efficient heterologous expression in three hosts: Streptomyces coelicolor CH999, S. lividans K4-114, and S. albus J1074. The six-operon artificial gene cluster consists of 25 genes from the native gene cluster organized into five operons and five fatty acid β-oxidation genes into one operon. All operons are driven by strong constitutive promoters. For K4-114 and J1074 harboring the artificial gene cluster, salinomycin production in shake flask cultures was 14.3 mg L^-1 and 19.3 mg L^-1 , respectively. The production was 1.3-fold and 1.7-fold higher, respectively, than that of the native producer S. albus DSM41398. K4-114 and J1074 harboring the native gene cluster produced an undetectable amount of salinomycin and 0.5 mg L^-1 , respectively. CH999 harboring the artificial gene cluster produced 10.3 mg L^-1 of salinomycin, which was 92% of the production by DSM41398. The efficient heterologous expression system based on the 106-kb multioperon artificial gene cluster established in this study will facilitate structural diversification of salinomycin, which is valuable for drug development and structure-activity studies.

RedEx: a method for seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters

Biosynthesis reprograming is an important way to diversify chemical structures. The large repetitive DNA sequences existing in polyketide synthase genes make seamless DNA manipulation of the polyketide biosynthetic gene clusters extremely challenging. In this study, to replace the ethyl group attached to the C-21 of the macrolide insecticide spinosad with a butenyl group by refactoring the 79-kb gene cluster, we developed a RedEx method by combining Redαβ mediated linear-circular homologous recombination, ccdB counterselection and exonuclease mediated in vitro annealing to insert an exogenous extension module in the polyketide synthase gene without any extra sequence. RedEx was also applied for seamless deletion of the rhamnose 3′-O-methyltransferase gene in the spinosad gene cluster to produce rhamnosyl-3′-desmethyl derivatives. The advantages of RedEx in seamless mutagenesis will facilitate rational design of complex DNA sequences for diverse purposes.

Graphene-based temperature sensors suspended by anodic aluminum oxide

In this paper, we investigate the substrate effect in graphene temperature sensors. Recently, there have been many research studies done on temperature sensors using the nanofabrication technique. However, the sensitivity and response time need to be improved. In this study, we propose a new type of temperature sensor that consists of graphene and Anodic Aluminum Oxide (AAO). In this device, graphene and AAO are used as the sensing material and the substrate, respectively. We characterize the sensitivity and the response time using the experimental results and simulation data. The real-time resistance change of graphene is monitored depending on the temperature, and the response time is also analyzed by COMSOL Multiphysics. To confirm the porous substrate effect, we compare the device performance of the AAO substrate to the performance of the glass substrate. From these results, the suspended graphene on the AAO substrate shows about two times higher sensitivity and a much faster response time than the glass substrate.

Association of genetic and environmental factors with dental caries among adolescents in south China: A cross-sectional study

AIM

The objective of this study was to investigative genetic and environmental factors that contribute to caries susceptibility among adolescents in south China.

MATERIALS AND METHODS

A cross-sectional study was conducted among 1055 adolescents aged 13-14 years old in south China. The International Caries Detection and Assessment System (ICDAS) was used to identify caries. Environmental variables were analysed by regression models. Twenty-three single nucleotide polymorphisms (SNPs) in 14 genes were identified from saliva samples. Regression analysis was used for the evaluation of effects of SNP markers using the minor allele as the effect allele.

RESULTS

Our results suggest that gender, Cariostat score and Plaque Index were associated with dental caries. After the adjustment by age and gender, the G allele in AMBN (rs13115627) nominally was a protective factor for caries under additive model (P=0.028; OR=0.782; 95% CI, 0.627-0.974). However, the association did not meet the Bonferroni correction significance cut-off for multiple testing.

CONCLUSION

Gender, Cariostat score and Plaque Index were associated with dental caries in this population. No selected SNPs showed a significant association with dental caries under either additive model or dominance model.

Intrinsic Fluoride Tolerance Regulated by a Transcription Factor

Fluoride facilitates the remineralization of dental hard tissues and affects bacterial activities. Therefore, it is extensively used as an anti-caries agent in clinical practice and daily life. Although some studies focused on understanding Streptococcus mutans' response to fluoride, the mechanism regulating intrinsic fluoride tolerance is not yet clear. Since the TetR family of transcription factors is associated with multidrug resistance, our aim was to evaluate whether they are related to fluoride tolerance in S. mutans. A mutant library including each S. mutans TetR gene was constructed and the transcription factor fluoride related transcriptional regulator (FrtR) was identified. The in-frame deletion of the S. mutans frtR gene resulted in decreased cell viability under fluoride in both the planktonic state and single-/dual-species biofilms. This in-frame frtR mutant was used for RNA-sequencing and the fluoride related permease gene (frtP) was found as 1 of the downstream genes directly regulated by FrtR. The recombinant FrtR protein was purified, and conserved DNA binding motifs were determined using electrophoretic mobility shift and DNase I footprinting assays. Finally, a series of mutant and complement strains were constructed to perform the minimum inhibitory concentration (MIC) assays, which indicated that frtP upregulation led to the increase of fluoride sensitivity. Collectively, our results indicate that FrtR is an important transcription factor regulating the frtP expression in S. mutans, thus affecting the intrinsic fluoride tolerance. Therefore, this study provides novel insights into a potential target to increase the S. mutans sensitivity to fluoride for a better prevention of dental caries.

MiR-363-3p modulates cell growth and invasion in glioma by directly targeting pyruvate dehydrogenase B

OBJECTIVE

This study is designed to investigate the role of miR-363-3p in the cancer development of glioma.

PATIENTS AND METHODS

The expression of miR-363-3p in glioma and adjacent noncancerous tissue was measured using quantitative RT-PCR. The expression of a target gene of miR-363-3p, pyruvate dehydrogenase B (PDHB), was determined by Western blot. The level of miR-363-3p was increased or decreased by transfected with miR-363-3p mimic or miR-363-3p inhibitor, respectively. The impact of miR-363-3p on cell growth, apoptosis and invasion was determined by CCK-8 (Cell Counting Kit) assay, flow cytometry, and transwell assay. The role of PDHB in mediating the oncogenic activities was demonstrated by co-transfected PDHB vector and miR-363-3p mimic.

RESULTS

Our results have shown that miR-3663-3p level was significantly higher in glioma tissue. Furthermore, miR-363-3p functions as onco-miRNA, promotes cell proliferation, protects against apoptosis, and enhances invasion by directly targeting PDHB.

CONCLUSIONS

MiR-363-3p is an onco-miRNA, which can be considered as a potential therapeutic target in glioma.