A thermostable type I-B CRISPR-Cas system for orthogonal and multiplexed genetic engineering

Thermophilic cell factories have remarkably broad potential for industrial applications, but are limited by a lack of genetic manipulation tools and recalcitrance to transformation. Here, we identify a thermophilic type I-B CRISPR-Cas system from Parageobacillus thermoglucosidasius and find it displays highly efficient transcriptional repression or DNA cleavage activity that can be switched by adjusting crRNA length to less than or greater than 26 bp, respectively, without ablating Cas3 nuclease. We then develop an orthogonal tool for genome editing and transcriptional repression using this type I-B system in both thermophile and mesophile hosts. Empowered by this tool, we design a strategy to screen the genome-scale targets involved in transformation efficiency and established dynamically controlled supercompetent P. thermoglucosidasius cells with high efficiency ( ~ 108 CFU/μg DNA) by temporal multiplexed repression. We also demonstrate the construction of thermophilic riboflavin cell factory with hitherto highest titers in high temperature fermentation by genome-scale identification and combinatorial manipulation of multiple targets. This work enables diverse high-efficiency genetic manipulation in P. thermoglucosidasius and facilitates the engineering of thermophilic cell factories.

[Development of highly efficient electrocompetent cells for electroporation of Geobacillus thermoglucosidasius NCIMB 11955]

Geobacillus thermoglucosidasius is a kind of Gram-positive facultative anaerobic bacteria. The fast growth rate under high temperature and less susceptibility to microbial contamination enable G. thermoglucosidasius to be a desirable producer of biofuels and high-value-added chemicals for the next-generation industrial biotechnology. However, compared with the classical model strain Escherichia coli, the applications of G. thermoglucosidasius are hampered by its low transformation efficiency. This study aimed at obtaining competent cells with high transformation efficiency through inactivating restriction enzymes, adding cell membrane inhibitors and cell wall weakening agents. The results showed that the electro-transformation efficiency achieved 1.2×104 CFU/(μg DNA) by knocking out four genes encoding restriction enzymes. Adding a certain amount of tween 80, dl-threonine and glycine further increased the competent efficiency about 22.5, 44, and 334 times, respectively. The electro-transformation efficiency was enhanced to 4.6×106 CFU/(μg DNA) under the optimized conditions, laying a foundation for genetic manipulation and metabolic engineering of G. thermoglucosidasius.

Identification of genes and proteins associated with anagen wool growth

Identifying genes of major effect for wool growth would offer strategies for improving the quality and increasing the yield of fine wool. In this study, we employed the Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin (more wool growing) in Aohan fine wool sheep (a Chinese indigenous breed) in comparison with groin skin (no wool growing) at the anagen stage of the wool follicle. A microarray study revealed that 4772 probes were differentially expressed, including 2071 upregulated and 2701 downregulated probes, in the comparisons of body side skin vs. groin skin (S/G). The microarray results were verified by means of quantitative PCR. A total of 1099 probes were assigned to unique genes/transcripts. The number of distinct genes/transcripts (annotated) was 926, of which 352 were upregulated and 574 were downregulated. In S/G, 13 genes were upregulated by more than 10 fold, whereas 60 genes were downregulated by more than 10 fold. Further analysis revealed that the majority of the genes possibly related to the wool growth could be assigned to categories including regulation of cell division, intermediate filament, cytoskeletal part and growth factor activity. Several potential gene families may participate in hair growth regulation, including fibroblast growth factors, transforming growth factor-β, WNTs, insulin-like growth factor, vascular endothelial growth factors and so on. Proteomic analysis also revealed 196 differentially expressed protein points, of which 121 were identified as single protein points.

Variable drug metabolism genes in Arab population

Cataloging interethnic differences in the distribution of genotypes of drug metabolic genes provides valuable information for profiling the pharmacogenetics of a population. We used PCR analysis to catalog the frequencies of alleles and genotypes for CYP1A1, NAT2, GSTs, MTHFR, MTR (MS) and NQO*1 in Arabs. The frequencies of alleles and/or genotypes for CYP1A1*2A, GSTT1 null, GSTT1 and GSTM1 double null, and GSTP1 A1578G in Arabs were significantly higher than those reported in Caucasians. However, the distribution of NAT2 acetylator phenotypes in both populations was similar. In contrast, the frequencies of MTHFR 677T allele and the combined (677+1298) genotypes for low activity were lower than those reported in Caucasians. Other alleles in Arabs, including CYP1A1 T3801C and GSTP1 A1578G were present in frequencies similar to Africans. The overall profile of variations in metabolism genes in Arabs is thus unique.

[A herbalogical study on traditional Mongolian medicine "lideri"]

By herbalogical study and investigation, "lideri" used by Mongolia doctors in different areas mainly contains 10 species from 4 genera of 4 families, but the quality materials only contains 3 species, Tinospora sinensis (Lour.) Merr., T. cordifolia Miers and T. capillipes Gagnep.

[Study on the role of human papillomavirus in carcinogenesis of oral papillomas by in situ hybridization]

OBJECTIVE

To explore the role of human papillomavirus (HPV) infection on carcinogenesis of oral squamous cell papillomas (SCP).

METHODS

By using digoxin labelled HPV 6/11 and HPV 16/18 probes, through hybridization in situ technique, the HPV DNA sequence in 30 cases of oral SCP were detected.

RESULTS

Among them, 16 cases (53.3%) were positive for HPV 6/11 DNA. None of cases of SCP were positive for HPV 16/18 DNA.

CONCLUSION

Our results show that the frequent finding of HPV 6/11 DNA in oral SCP had close association between oral papillomas and HPV 6/11 infection.

[A herbalogical study on traditional Mongolian medicine dakesha]

By herbological study and investigation, "Dekesha" used by Mongolia doctors mainly contains 17 species from 3 genus of 3 family, but "Dakesha" in Inner Mongolia Standard of Medicinal Materials only contains 2 species which are Oxytropis myriophylla and O. hirta.

[Quantitative 3D measurements of the skull base by using spiral volumatric CT images]

OBJECTIVE

To study the spatial relationships of mandibular condyle and carotid canal, jugular fossa, foramen ovale, foramen spinosum when mandible in normal physical position.

METHODS

100 native adults were examined by spiral volumatric CT. The data were transferred to workstation, three-dimensional(3d) cranial base images were reconstructed, 3D measurements were performed by using specific 3d CT landmarks. 12 points were defined and 28 distances and angles were measured in the skull base from submandibular viewpoint. The internal pole of condyle and the condylar long axis were regarded as the center point and 0 degree axis in the reference frame.

RESULTS

Submandibular approach provided a clear vision of the internal pole of condyle and condylar long axis. The ECC was located at 12.01 +/- 2.71 mm, 5.14 +/- 1.22 degrees, Jug was located at 15.11 +/- 2.72 mm, -56.27 +/- 14.05 degrees according to the reference frame.

CONCLUSIONS

Quantitative measurements of 3D skull base can be very precise. Mandibular approach is easy to show the mandibular condyle. The reference frame is helpful to located other important structures of skull base in operation.

[Changes in blood coagulation affected by rifampicin administration]

OBJECTIVE

To study the characteristics of influence on coagulation by rifampicin (RFP) administration.

METHODS

Seventy-three patients, ages between 10 and 65 years(mean age 30.3 years), with tuberculosis of neck lymphnode were treated with 2HRZS/10HRE. The prothrombin time, activity, fibrinogen, II: C, V: C, VII: C, IX: C and alanine aminotransferase concentration in each case were observed during the period of RFP administration.

RESULTS

The prolongation of the PT and the reduction of the PA, FIB concentration in 48 cases were observed after 5-30 days following RFP administration. These changes depended on drug dosage and duration, especially the severe influence on coagulation were detected when the RFP were reused after the ALT normalized in seventh to tenth months. The ALT was (18 +/- 12) U/L in the tenth month, but the PT was (19.2 +/- 3.9) s and the FIB was (1.8 +/- 0.5) g/L respectively.

CONCLUSIONS

Not only the coagulation factors II, VII, IX, X, but also I V, VI and VIII were affected by RFP. The coagulation test is more sensitive than ALT test in the evaluation of liver injury. RFP should be stopped when FIB less than 1 g/L in spite of ALT in normal range.

Alterations in the level of phosphotyrosine signal transduction constituents in human parotid tumors

Human parotid tumors were evaluated for the activation of the phosphotyrosine signaling pathway by Western blot, enzyme activity assay, and reverse transcriptase-polymerase chain reaction. Warthin's tumor and mucoepidermoid carcinomas had the greatest level of tyrosine phosphorylated proteins identified in plasma membrane fractions. These tumors, along with pleomorphic adenocarcinoma, showed high levels of membrane expression of the tyrosine kinase receptor, c-erbB-2, and phosphatidylinositol-3-kinase. Expression of the epidermal growth factor receptor was confined to normal tissue. The level of mRNA for c-erb was elevated only in mucoepidermoid carcinomas. Messenger RNA levels for ras were unchanged from control levels in all tumors, while the level of src mRNA was higher in the tumor samples than the normal parotid tissue. The activities of several signal transduction kinases, including protein kinase A and C were elevated in tumor tissue (7.7- to 18.9- and 0.4- to 3.7-fold higher, respectively), relative to surrounding normal tissue. While the level of glandular amylase was reduced (22%-0% of normal levels) in the tumor tissue, epidermal growth factor (EGF) and transforming growth factor-alpha (TGFalpha) content was dramatically higher in the neoplastic tissue (10- to 170-fold and 4.6- to 6.0-fold, respectively). These results suggest that with the presence of elevated levels of EGF, TGFalpha, and the oncoprotein receptor c-erbB-2 in the membrane of parotid tumors, cell proliferation and activation of the phosphotyrosine signal transduction pathway may involve autocrine stimulation through the expression of high levels of growth factor and receptor in the same tissue.