CADS: CRISPR/Cas12a-Assisted DNA Steganography for Securing the Storage and Transfer of DNA-Encoded Information.

Because DNA has the merit of high capacity and complexity, DNA steganography, which conceals DNA-encoded messages, is very promising in information storage. The classical DNA steganography method hides DNA with a "secret message" in a mount of junk DNA, and the message can be extracted by polymerase chain reaction (PCR) using specific primers (key), followed by DNA sequencing and sequence decoding. As leakage of the primer information may result in message insecurity, new methods are needed to better secure the DNA information. Here, we develop a pre-key by either mixing specific primers (real key) with nonspecific primers (fake key) or linking a real key with 3'-end redundant sequences. Then, the single-stranded DNA (ssDNA) trans cleavage activity of CRISPR/Cas12a is employed to cut a fake key or remove the 3'-end redundant sequences, generating a real key for further information extraction. Therefore, with the Cas12a-assisted DNA steganography method, both storage and transfer of DNA-encoding data can be better protected.

The CCTL (Cpf1-assisted Cutting and Taq DNA ligase-assisted Ligation) method for efficient editing of large DNA constructs in vitro.

As Cpf1 cleaves double-stranded DNA in a staggered way, it can be used in DNA assembly. However, the Cpf1 cleavage was found to be inaccurate, which may cause errors in DNA assembly. Here, the Cpf1 cleavage sites were precisely characterized, where the cleavage site on the target strand was around the 22nd base relative to the protospacer adjacent motif site, but the cleavage on the non-target strand was affected by the spacer length. When the spacer length was 20 nt or longer, Cpf1 mainly cleaved around the 14th and the 18th bases on the non-target strand; otherwise, with a shorter spacer (i.e. 17-19 nt), Cpf1 mainly cleaved after the 14th base, generating 8-nt sticky ends. With this finding, Cpf1 with a 17-nt spacer crRNA were employed for in vitro substitution of the actII-orf4 promoter in the actinorhodin biosynthetic cluster with a constitutively expressing promoter. The engineered cluster yielded more actinorhodin and produced actinorhodin from an earlier phase. Moreover, Taq DNA ligase was further employed to increase both the ligation efficiency and the ligation accuracy of the method. We expect this CCTL (Cpf1-assisted Cutting and Taq DNA ligase-mediated Ligation) method can be widely used in in vitro editing of large DNA constructs.

iBrick: a new standard for iterative assembly of biological parts with homing endonucleases.

The BioBricks standard has made the construction of DNA modules easier, quicker and cheaper. So far, over 100 BioBricks assembly schemes have been developed and many of them, including the original standard of BBF RFC 10, are now widely used. However, because the restriction endonucleases employed by these standards usually recognize short DNA sequences that are widely spread among natural DNA sequences, and these recognition sites must be removed before the parts construction, there is much inconvenience in dealing with large-size DNA parts (e.g., more than couple kilobases in length) with the present standards. Here, we introduce a new standard, namely iBrick, which uses two homing endonucleases of I-SceI and PI-PspI. Because both enzymes recognize long DNA sequences (>18 bps), their sites are extremely rare in natural DNA sources, thus providing additional convenience, especially in handling large pieces of DNA fragments. Using the iBrick standard, the carotenoid biosynthetic cluster (>4 kb) was successfully assembled and the actinorhodin biosynthetic cluster (>20 kb) was easily cloned and heterologously expressed. In addition, a corresponding nomenclature system has been established for the iBrick standard.

[Effect of gas-turbine green discoloring and drying processing methods on herbal quality of tetraploid Lonicerae Japonicae Flos].

OBJECTIVE: To study the effect of gas-turbine green discoloring and drying processing method on the quality of various Lonicerae Japonicae Flos herbs. METHOD: DIKMA DiamonsilTM-C18 column (4.6 mm x 250 mm, 5 microm) was adopted using HPLC Waters 1525 and eluted with acetonitrile and 0.1% phosphate acid as the mobile phase. The flow rate was 1.0 mL x min(-1) , the column temperature was 25 degrees C the detection wavelength was 355 nm. RESULT: After being processed by the gas-turbine green discoloring and drying method, tetraploid Lonicerae Japonicae Flos showed a green color. The contents of chlorogenic acid and galuteolin were 5.31% and 0.105% , both significantly higher by 18.0% and 32.1% than those of diploid Lonicerae Japonicae Flos processed by the same method. The content of chlorogenic acid in tetraploid Lonicerae Japonicae Flos processed the gas-turbine green discoloring and drying method were also remarkably higher than that of tetraploid and diploid Lonicerae Japonicae Flos processed by traditional processing method of natural drying. CONCLUSION: The gas-turbine green discoloring and drying processing method is a new-type drying method suitable for tetraploid Lonicerae Japonicae Flos. Under the condition of gas-turbine green discoloring and drying processing, tetraploid Lonicerae Japonicae Flos shows much higher quality than Lonicerae Japonicae Flos, suggesting that it is a good variety worth popularizing and applying.

Interleukin-1 inhibits Sox9 and collagen type II expression via nuclear factor-kappaB in the cultured human intervertebral disc cells.

BACKGROUND: The most significant biological change in intervertebral disc degeneration is the decrease of chondrocyte specific gene and protein expression of Sox9 and collagen type II. Interleukin-1 (IL-1) is not expressed in the normal intervertebral disc tissue but increases in the degenerated intervertebral disc tissue. This suggests that IL-1 may play a role in regulation of the expression of Sox9 and collagen type II. METHODS: Human intervertebral disc cells were isolated and cultured. Sox9 and collagen type II expression during treatment with IL-1, with or without the nuclear factor-kappaB (NF-kappaB) activity inhibitor curcumin, were detected by using reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting, and the activity of the NF-kappaB signaling pathway was detected by the electrophoretic mobility shift assay (EMSA). RESULTS: IL-1 lowered the mRNA level and protein expression of Sox9 and collagen type II in the cultured intervertebral disc cells in a dose dependent manner (P < 0.05), and this effect was attenuated by curcumin. Curcumin alone had no effect on Sox9 and collagen type II expression (P > 0.05). IL-1 at concentrations of 0.1 ng/ml, 1 ng/ml and 10 ng/ml could stimulate the activity of NF-kappaB in the intervertebral disc cells in a dose dependent manner (P < 0.05) that was inhibited by curcumin. CONCLUSIONS: We demonstrated the previously unknown function of IL-1 in inhibiting Sox9 and collagen type II via NF-kappaB in the intervertebral disc cells. This inhibition can be attenuated by curcumin, which is an effective NF-kappaB activity inhibitor.

Photosynthetic responses to chromosome doubling in relation to leaf anatomy in Lonicera japonica subjected to water stress.

Gas exchange, chlorophyll fluorescence, and contents of some metabolites in two Japanese honeysuckle (Lonicera japonica Thunb.) cultivars, Damaohua (2n = 2x) and Jiufengyihao (2n = 4x), were compared with explore the function of chromosome doubling under water stress conditions. Water stress significantly decreased net photosynthesis rate, stomatal conductance, and transpiration rate of both cultivars. It also decreased electron transport rate, effective quantum yield of Photosystem II, photochemical quenching, and starch content, but increased non-photochemical quenching and contents of total soluble sugars, proline, and malondialdehyde. However, the tetraploid cultivar showed higher resistance to water stress than the diploid, as indicated by the fact that gas exchange, chlorophyll fluorescence, and metabolites were less affected for the tetraploid than the diploid. Moreover, the tetraploid recovered more quickly than the diploid after re-watering. Morphological and anatomical analysis further revealed that the tetraploid possessed less whole plant leaf area, higher leaf mass per unit area, thicker epidermis (both upper and lower) and palisade tissue, as well as denser pubescence. All of those specialised structures caused by chromosome doubling might lead to greater capacity in coping with drought stress. Our findings suggest that the effect of chromosome doubling on drought resistance in L. japonica could attribute to the improvement of structure and photosynthesis-related traits.

Prediction of protein structural class by amino acid and polypeptide composition.

A new approach of predicting structural classes of protein domain sequences is presented in this paper. Besides the amino acid composition, the composition of several dipeptides, tripeptides, tetrapeptides, pentapeptides and hexapeptides are taken into account based on the stepwise discriminant analysis. The result of jackknife test shows that this new approach can lead to higher predictive sensitivity and specificity for reduced sequence similarity datasets. Considering the dataset PDB40-B constructed by Brenner and colleagues, 75.2% protein domain sequences are correctly assigned in the jackknife test for the four structural classes: all-alpha, all-beta, alpha/beta and alpha + beta, which is improved by 19.4% in jackknife test and 25.5% in resubstitution test, in contrast with the component-coupled algorithm using amino acid composition alone (AAC approach) for the same dataset. In the cross-validation test with dataset PDB40-J constructed by Park and colleagues, more than 80% predictive accuracy is obtained. Furthermore, for the dataset constructed by Chou and Maggiona, the accuracy of 100% and 99.7% can be easily achieved, respectively, in the resubstitution test and in the jackknife test merely taking the composition of dipeptides into account. Therefore, this new method provides an effective tool to extract valuable information from protein sequences, which can be used for the systematic analysis of small or medium size protein sequences. The computer programs used in this paper are available on request.