Multiple copies of a linear donor fragment released in situ from a vector improve the efficiency of zinc-finger nuclease-mediated genome editing

Homologous recombination (HR) is a strategy for genetic correction. The efficiency of HR can be increased by creating a targeted double-strand break (DSB) via zinc-finger nucleases (ZFNs) and/or by introducing linear donor DNA intracellularly. Some studies have suggested that increased copy numbers of linear donor DNA may further improve HR efficiency. However, the introduction of multiple copies of a linear donor fragment remains a challenge, particularly in cell types with low transfection efficiency. In this study, we developed a vector that carries tandem repeats of a donor fragment, with each repeat flanked by ZFN target sequence fragments (TSFs). The cleavage of the flanking TSF sequence by ZFN would lead to the release of multiple linear fragment. We demonstrated that this novel vector carrying five copies of a linearizable donor fragment, when co-transfected with a ZFN-expressing vector in 293 cells, showed improved HR efficiency about 30 times, as compared with vector carry nonlinearizable donor. For the application of gene therapy, we then introduced this system into an adenoviral vector, which also revealed markedly improved ZFN-mediated HR efficiency in cells. The novel strategies presented here have the potential to promote the application of ZFNs in both basic research and disease therapy.

The inhibitory effect of melatonin on colonic motility disorders induced by water avoidance stress in rats

OBJECTIVES

Psychological stress is involved in the etiology of functional gastrointestinal disease (FGID). Accumulations of chronic continuous stress associate with the symptoms of the gastrointestinal tract (GIT) including abdominal discomfort, pain, constipation or diarrhea. Melatonin (MT) is a neurohormone which mainly synthesized in the pineal gland and GIT, has been shown to alleviate the stress and regulate the intestinal motility. Although melatonin attenuated abnormal defecation induced by stress, the mechanisms of the effect are not fully elucidated. This study sought to investigate the effect of melatonin (MT) on colonic smooth muscle contractility disorders induced by chronic water avoidance stress (WAS).

MATERIALS AND METHODS

36 adult Wistar rats were divided into three groups [Control+V (vehicle solution), WAS+V, WAS+MT]. The WAS+V and WAS+MT groups were suffered from WAS for one hour daily for 10 days. Melatonin was given 30 min before stress session in the WAS+MT group. Colonic motility was assessed using the numbers of fecal pellet output. The concentrations of melatonin and serotonin (5-HT) were measured through ELISA method. The contractions of isolated colonic strips were assessed through isometric force transducer.

RESULTS

The numbers of fecal output was increased in the WAS+V group, and melatonin attenuates the increased fecal pellet output induced by WAS. The concentrations of 5-HT was increased by WAS, and melatonin decreased the augment in the concentration of 5-HT. In the part of contraction recording of colonic smooth muscle, melatonin inhibited the fortified spontaneous contraction induced by WAS, and decreased the amplitude of spontaneous contraction stimulated by Ach and KCl after WAS treatment.

CONCLUSIONS

Melatonin could inhibit WAS-induced fecal output pellets by inactivating the 5-HT pathway, may interact with calcium channel and inhibit the influx of calcium.

Deregulated expression of the clock genes in gliomas

Growing evidence shows that the deregulation of the circadian clock plays an important role in the development of malignant tumors, including gliomas. However, the molecular mechanisms of genes controlling circadian rhythm in glioma cells have not been explored. Using reverse transcription polymerase chain reaction and immunohistochemistry techniques, we examined the expression of the most important clock genes, clock, in 67 gliomas.Our results revealed that asynchronized expression of the clock gene was found in cancerous tissues in comparison with paired non-cancerous tissues. The expression levels of clock mRNA in grade III or IV glioma was significantly different from the surrounding non-tumor tissues (P < 0.01). The difference in the expression of clock in low-grade (grades 1 and II) gliomas and the surrounding non-glioma tissues was insignificant (P > 0.05). The intensity of immunoactivity for Clock in highgrade gliomas was significantly higher than that of low-grade gliomas (r = -0.403, P 5 0.012 , < 0.05), non-tumor tissues around high-grade gliomas (r = -0.376, P = 0.027 < 0.05), while there was no difference in the intensity of immunoactivity for Clock between low-grade gliomas and the surrounding non-tumor tissues (P > 0.05). The expression of PCNA (Proliferating Cell Nuclear Antigen) protein in highgrade gliomas was significantly higher than that of low-grade gliomas (P < 0.05). In this study, we found that the expression of clock in glioma cells and in the surrounding non-tumor cells. The expression of clock in highgrade gliomas was significantly higher than that of the low-grade gliomas and non-glioma. Therefore, we suggest that disturbances in clock expression may result in the disruption of the control of normal circadian rhythm, thus benefiting the survival of glioma cells and promoting carcinogenesis.

Inverse energy cascade and emergence of large coherent vortices in turbulence driven by Faraday waves

We report the generation of large coherent vortices via inverse energy cascade in Faraday wave driven turbulence. The motion of floaters in the Faraday waves is three dimensional, but its horizontal velocity fluctuations show unexpected similarity with two-dimensional turbulence. The inverse cascade is detected by measuring frequency spectra of the Lagrangian velocity, and it is confirmed by computing the third moment of the horizontal velocity fluctuations. This is observed in deep water in a broad range of wavelengths and vertical accelerations. The results broaden the scope of recent findings on Faraday waves in thin layers [A. von Kameke et al., Phys. Rev. Lett. 107, 074502 (2011)].

Removal of methyl blue from aqueous solution by magnetic carbon nanotube

Magnetic carbon nanotube (mCNT) was formed via direct mixing of carbon nanotube (CNT) with magnetic nanoparticle (MNP) in dye solution. When the mass ratio of MNP to CNT was 4:1, all CNT were magnetically collected. The adsorption performance of mCNT was evaluated using methyl blue (MB) as a model adsorbate. Equilibrium of MB adsorption was attained in 60 min, and maximum adsorption occurred at pH 3-6. MB adsorption was independent of ionic strength and followed pseudo-second-order kinetics. According to the Langmuir isotherm, adsorption capacity of mCNT for MB was 115.34 mg g(-1). Thermodynamic analysis suggested MB adsorption onto mCNT was a spontaneous process. Reusability study results showed that 97.06, 96.26, 94.33, 92.91 and 90.14% of MB were removed in five consecutive cycles. The study suggests that the mCNT has a great potential application in dye removal from industrial wastewater.

Oscillon dynamics and rogue wave generation in Faraday surface ripples

We report new experimental results which suggest that the generation of extreme wave events in the Faraday surface ripples is related to the increase in the horizontal mobility of oscillating solitons (oscillons). The analysis of the oscillon trajectories in a horizontal plane shows that at higher vertical acceleration, oscillons move chaotically, merge and form enclosed areas on the water surface. The probability of the formation of such craters, which precede large wave events, increases with the increase in horizontal mobility.

A New Rice Disease, Black Sheath Spot, Caused by Curvularia fallax in China

In July 2011, we observed a new rice disease, black sheath spot, on tillering rice plants in Huayuan County, Hunan Province, China. Field surveys indicated that this disease covered a ~1,000-ha paddy field, mainly on Y series 2-line hybrid rice cultivars, especially Y Liangyou 7 and Y Liangyou 302, in hills of which 10 to 70% infection was observed (average of 45%), causing estimated damages up to $1.2 million (US). The diseased rice plants were cultivated with standard practices. Weather, flooding, herbicide damage, and fertilizer application did not appear to account for the symptoms. Typical symptoms of the disease included elliptical spots, about 10 × 5 mm, dark brown to black and with a diffuse yellow-brown margin. The leaf blades with diseased sheaths became yellow and blighted. After 7 days of growth on PDA, groups of cylindrical and branched stromata scattered over dark green colony. Conidia averaged 30.4 × l2.5 μm and contained five cells with three dark central cells. The morphology of spores was consistent with that of C. fallax (1). We inoculated 8-cm healthy rice sheath segments with culture disk of an isolate HNAH001. Sheath segments were divided into four groups: I) disks on wounded sheath surfaces; II) disks on non-wounded sheath surfaces; III) disks between the leaf sheath and stem, and IV) a sterilized water control. The segments were maintained in moist, covered plates in a 25°C incubator after inoculation. After another 24 h, circular brown lesions, less than 10 mm long, appeared on all inoculated segments in treatments I,II, and III. Treatment I induced the most serious symptoms. No lesions developed on control segments. For further verification of pathogenicity, we sprayed a spore suspension of HNHY001 on healthy rice plants at the boot stage. Black spots reappeared on the sheaths after 5 days. No lesions appeared on the stems or the leaf blades of inoculated rice plants. We recovered HNHY001 from the spots on inoculated plants and completed all steps of Koch's postulates. For molecular identification of the fungus, DNA was extracted from mycelia and used as a template for PCR with a primer pair of ITS 5 and ITS 4 targeting the rDNA-ITS. The sequence of the PCR product (Accession No. JQ360963) had 100% identity with rDNA-ITS of Cochliobolus geniculatus (teleomorphic state of C. geniculata) and C. affinis in GenBank after a BLAST search and clustered with them after a phylogenetic analysis. There was no sequence of C. fallax on the BLAST list because ITS sequence of C. fallax had not yet been submitted to any nucleotide databank. Hosokawa et al. concluded that C. fallax and C. affinis are synonyms for C. geniculata (2), which is supported by our results from BLAST and phylogenetic analysis. In view of its relative straight conidia and branching stromata, we suggest that the causal agent of black sheath spot of rice be C. fallax. Although Curvularia spp. were reported as pathogens responsible for black kernel of rice, there is no report of sheath spot of rice caused by Curvularia (3). To our knowledge, this is the first report of a rice sheath disease caused by C. fallax. It seems likely the disease exists in areas beyond Huayuan County. Further field inspection and molecular identification are necessary. References: (1) K. B. Boedijn. Bull. Jard. Bot. Buitenzorg, ser. 3 13:129, 1933. (2) M. Hosokawa et al. Mycoscience 44:227, 2003. (3) S. H. Ou. Page 317 in: Rice Diseases, 2nd Edition, Commonwealth Mycological Institute, Kew, UK, 1985.

Propagating solitons generated by localized perturbations on the surface of deep water

We report experimental evidence of the propagating capillary solitary waves generated by a localized water surface perturbation. Solitons are formed at the air-water interface with a solid plunger and then propagate with velocities proportional to their amplitudes. The shape of the forward front of such solitons is independent of the plunger shape and is given by the hyperbolic secant profile. We find that the nonlinearity of capillary waves is responsible for a small dispersion in the capillary wave group velocity and the soliton existence. This dispersion can be further reduced by adding minute concentrations of proteins to water.

Parametrically excited water surface ripples as ensembles of oscillons

We show that ripples on the surface of deep water which are driven parametrically by monochromatic vertical vibration represent ensembles of oscillating solitons, or quasiparticles, rather than waves. The horizontal mobility of oscillons determines the broadening of spectral lines and transitions from chaos to regular patterns. It is found that microscopic additions of proteins to water dramatically affect the oscillon mobility and drive transitions from chaos to order. The shape of the oscillons in physical space determines the shape of the frequency spectra of the surface ripple.

First Report of Artichoke Bacterial Stem Rot Caused by Pectobacterium carotovorum subsp. carotovorum in China

A new disease on globe artichoke (Cynara scolymus L.) was observed in the springs of 2008 and 2009 and during the spring and fall seasons of 2010 in commercial fields (nearly 1,000 ha) in Changde, Hunan Province, China. Characteristic symptoms were wilting and necrosis of the outermost leaves and dark brown discoloration of the vascular tissue and pith of the stem base. Eventually, the plants wilted and died. Nearly 5, 35, and 4% (2008, 2009, and 2010, respectively) of the artichoke fields were destroyed because of the disease. Manual weeding and cuttings often led to the development of typical soft rot during propagation. To investigate the causal agent of the disease, isolations were made from rotted stems of field artichoke plants on nutrient agar (NA). Bacteria consistently isolated from the diseased tissues formed gray-white, glossy, convex, translucent, and round colonies on NA. The bacterial cells were gram-negative rods with two to eight peritrichous flagella. Ten isolates were negative for oxidase, arginine dehydrolase, H₂S, gelatin liquefaction, and tryptophan ammonialyase. Isolates were positive for catalase, reduced NO₃ to NO₂, indole, glucuroide, galactosidase, Voges-Proskauer test, and β-galactosidase, along with being facultatively anaerobic and insensitive to erythromycin (40 μg/ml). Negative results were obtained for utilization of maltose, gluconate, and phenylacetic acid, and positive results were obtained from arabinose, glucose, mannose, N-acetyl-glucosamine, mannitol, and sodium citrate for all isolates. Acid was produced from glucose, inositol, rhamnose, melibiose, arabinose, mannitol, sucrose, and amarogentin. All test results were similar to reference strain PCC1000 (GenBank Accession No. JF721959) of Pectobacterium carotovorum subsp. carotovorum. These isolates could also cause soft rot of Chinese cabbage stem, carrot slice, pepper, lettuce and artichoke stems, and tomato and potato slices within 48 h at 28°C in an artificial inoculation test (3). PCR amplification was carried out by utilizing universal 16S rDNA primer pair 16SF/16SR and pel gene primers Y1/Y2 (1). The 16S rDNA and pel gene sequences of isolate HNXDT002 (GenBank Accession Nos. JF721958 and JF721960, respectively) had 99 and 93% nucleotide identity with strains of P. carotovorum subsp. carotovorum (GenBank Accession Nos. U80197 and CP001657, respectively). Pathogenicity was confirmed by needle-stab inoculation (1 × 10⁸ CFU/ml) at the stem on three healthy artichoke plants held at 28°C for 48 h. Sterile distilled water was used as a negative control. Within 72 h after inoculation, water-soaking and soft-rot symptoms were observed on all inoculated artichoke plants, while controls remained healthy. The bacterium was recovered only from rotted stems of inoculated plants. In recent years, P. carotovorum was reported on such plants as Pinellia ternata (4) and Chinese cabbage (2) in China. To our knowledge, this is the first report of bacterial rot disease caused by P. carotovorum subsp. carotovorum on artichoke in China. References: (1) D. J. Brenner et al. Bergey's Manual of Systematic Bacteriology. Vol. 2. Springer, NY, 2005. (2)Y. Fang et al. Acta Microbiol. Sinica 44:136, 2004. (3) H. Yi-Bo et al. Acta Phytopathol. Sinica 37:338, 2007. (4) F. X. Ying et al. Plant Dis. 91:1359, 2007.

In vivo biocompatibility and degradation behavior of Mg alloy coated by calcium phosphate in a rabbit model

This study is conducted to investigate the biocompatibility and biodegradation behavior of calcium phosphate-coated Mg alloy in vivo. Calcium phosphate (Ca-P) was coated on the Mg alloy (AZ31) by a chemical process. Samples of Ca-P coated rods, the naked alloy rods, and degradable polymer as controls were implanted into the thighbone of rabbits to investigate the bone response at the early stage. The reduction in implant volume was determined by micro-computed tomography and three-dimensional reconstruction of the remaining Mg alloy segmented from the bone matrix. It was observed that the biodegradation rate of naked Mg implant is faster than that of the coated ones. The bone-implant interface was characterized in sections by scanning electron microscopy with energy-dispersive spectroscopy. Biodegradation or reaction layer was formed on the surface of Mg alloy implants and direct contact with the surrounding bone. The layer was mainly composed of Ca, P, O, and Mg. After 8 weeks of post-operation, paraffin sections were generated for histomorphologic analysis; 100% implants were fixed and no inflammation was observed. Histological analysis showed that new bone tissue is formed around the Mg implants, and no fibrous capsule was found. Blood examination showed that the biodegradation of the Mg implant caused little change to blood composition. Ca-P coating on Mg alloy substrate might be an effective method to reduce the biodegradation rate of Mg alloy in vivo and improve the surface bioactivity of Mg alloy implants.

Gasless Laparoscopy versus Conventional Laparoscopy in Uterine Myomectomy: A Single-Centre Randomized Trial

In a single-centre, randomized trial, gasless laparoscopic myomectomy was compared with conventional laparoscopic myomectomy. The study examined feasibility, safety, reliability and post-operative outcomes. Estimated blood loss, duration of surgery, early post-operative outcomes and length of hospital stay were recorded. Compared with conventional laparoscopic myomectomy, gasless laparoscopy resulted in significantly lower intra-operative blood loss (median 100 ml vs 80 ml, respectively) and duration of surgery (median 94 min vs 71 min, respectively). Post-operative abdominal drainage volume was significantly lower after gasless laparoscopy than after conventional laparoscopy (median 100 ml vs 240 ml). There was no significant difference between duration of post-operative fever, post-operative time to flatus or length of hospital stay. Both forms of laparoscopy are suitable for uterine myomectomy, and comparison of these methods showed that gasless laparoscopy had potential advantages over conventional laparoscopy.

First Report of Anthracnose Caused by Glomerella acutata on Chili Pepper in China

A new anthracnose disease on chili pepper (cayenne pepper cv. Hongxiu 2003, fruiting type pepper) was found in Zhijiang County, Hunan, China in 2009. The disease was observed only on the fruits. Lesions were generally elongated, on which dark acervuli were arranged concentrically. Later, cracking of older lesions was observed. With a microscope, fungal conidia were observed to be 15.8 × 4.1 μm, fusiform or oval with one end acute, and single celled with two to seven oil globules. No setae were found on the acervuli. Eight isolates (HNZJ001-HNZJ008) showed no difference in colony feature when cultured on potato dextrose agar. All the isolates showed white growth at the early stages, but colonies turned pink when they produced powdery spores and then finally became red gray. The average colony diameter was 68.5 to 72.3 mm after 7 days with obvious gray black concentric rings because of the development of aerial and substrate mycelia. After a needle-prick inoculation with a suspension of 1 × 10⁶ spores per ml of HNZJ001 on 30 chili pepper fruits with three repeats, the same symptoms were observed and the same fungus was recovered. In bioassays, HNZJ001 caused lesions on both mature and immature fruits, while Glomerella cingulata strain LSQ1 (GenBank Accession No. HQ607386) used as a control did not infect immature fruits. PCR amplification was carried out by utilizing universal rDNA-ITS primer pair ITS4/ITS5. Sequencing of the PCR products of HNZJ001 (GenBank Accession No. GU059863) showed 100% identity to G. acutata (GenBank Accession No. EU008863) and Colletotrichum acutatum (GenBank Accession No. AF207794) after a BLAST search. The pathogen was identified as G. acutata (asexual stage: C. acutatum) on the basis of morphological characters and rDNA-ITS sequence analysis. Worldwide, it has been reported that pepper anthracnose might be caused by up to five species of Glomerella (Colletotrichum): G. cingulata, C. coccodes, C. capsici, C. dematium, and G. acutata (2), among which only the first three were previously reported in China. In recent years, G. acutata was reported on such plants as apple (3) and strawberry (1) in China, but not on pepper. To our knowledge, this is the first report of G. acutata on chili pepper in China. References: (1) X.-J. Ren et al. Acta Phytopathol. Sin. 38:325, 2008. (2) P. P. Than et al. Zhejiang Univ. Sci. B 9:764, 2008. (3) R. Zhang et al. Plant Dis. 92:1474, 2008.

Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure

A key issue in evolutionary biology is an improved understanding of the genetic mechanisms by which species adapt to various environments. Using DNA sequence data, it is possible to quantify the number of adaptive and deleterious mutations, and the distribution of fitness effects of new mutations (its mean and variance) by simultaneously taking into account the demography of a given species. We investigated how selection functions at eight housekeeping genes of four closely related, outcrossing species of wild tomatoes that are native to diverse environments in western South America (Solanum arcanum, S. chilense, S. habrochaites and S. peruvianum). We found little evidence for adaptive mutations but pervasive evidence for strong purifying selection in coding regions of the four species. In contrast, the strength of purifying selection seems to vary among the four species in non-coding (NC) regions (introns). Using F(ST)-based measures of fixation in subdivided populations, we suggest that weak purifying selection has affected the NC regions of S. habrochaites, S. chilense and S. peruvianum. In contrast, NC regions in S. arcanum show a distribution of fitness effects with mutations being either nearly neutral or very strongly deleterious. These results suggest that closely related species with similar genetic backgrounds but experiencing contrasting environments differ in the variance of deleterious fitness effects.

Turbulence decay rate as a measure of flow dimensionality

The dimensionality of turbulence in fluid layers determines their properties. We study electromagnetically driven flows in finite-depth fluid layers and show that eddy viscosity, which appears as a result of three-dimensional motions, leads to increased bottom damping. The anomaly coefficient, which characterizes the deviation of damping from the one derived using a quasi-two-dimensional model, can be used as a measure of the flow dimensionality. Experiments in turbulent layers show that when the anomaly coefficient becomes high, the turbulent inverse energy cascade is suppressed. In the opposite limit turbulence can self-organize into a coherent flow.

Primary oral leiomyosarcoma: a retrospective clinical analysis of 20 cases

PURPOSE

As a review and clinical analysis of primary oral leiomyosarcoma (LMS) cases in West China stomatology Hospital in the past 37 years, this study provides demographic, therapeutic and prognostic information of this rare tumor.

PATIENTS AND METHODS

In our study, 20 cases of primary oral LMS treated between 1972 and 2008 in West China Stomatology Hospital were analyzed retrospectively. A thorough review of clinical records was carried out and potential indicators of survival were analyzed.

RESULTS

The most common symptom of oral LMS presented as a painless mass. The median age of patients was 37 years, and the peak incidence age of this tumor was in the 2nd and 5th decades. There was no predilection of gender, and the male-to-female ratio was 11:9. The most frequently occurring site of oral leiomysarcoma was the jawbones. The prognosis of this tumor was poor as a result of the high local recurrence and the estimated 2 year survival was 17.6%. The bony involvement and method of therapy was observed to have an influence on the prognosis and survival of this tumor (P < 0.05).

CONCLUSION

There was a predilection site of jawbones for oral LMS, and bony involvement was a potential indicator suggesting a poorer prognosis. The recommended method of therapy on this tumor was aggressive, radical surgical resection; however, adjuvant radiotherapy and chemotherapy may also have a beneficial effect.

Capillary rogue waves

We report the first observation of extreme wave events (rogue waves) in parametrically driven capillary waves. Rogue waves are observed above a certain threshold in forcing. Above this threshold, frequency spectra broaden and develop exponential tails. For the first time we present evidence of strong four-wave coupling in nonlinear waves (high tricoherence), which points to modulation instability as the main mechanism in rogue waves. The generation of rogue waves is identified as the onset of a distinct tail in the probability density function of the wave heights. Their probability is higher than expected from the measured wave background.