Controlling DNA Fragmentation in MALDI-MS by Chemical Modification

Fragmentation has proven to be a major factor limiting accessible mass range, sensitivity, and mass resolution in the analysis of DNA by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Previous work has shown that this DNA fragmentation is strongly dependent on both the MALDI matrix and the nucleic acid sequence employed. Fragmentation is initiated by nucleobase protonation, leading to cleavage of the N-glycosidic bond with base loss, followed by cleavage of the phosphodiester backbone. In this study, asymmetric oligonucleotides incorporating cytidine and cytidine analogs such as 5-methyl-2'-deoxycytidine, 5-bromo-2'-deoxycytidine, aracytidine, and 2'-fluorodeoxycytidine nucleosides were used to systematically investigate the influence of the structural changes on the stability of the N-glycosidic bond. Modifications of the deoxyribose sugar ring by replacing the 2'-hydrogen with more electron-withdrawing groups such as the hydroxyl or fluoro group stabilize the N-glycosidic bond to a greater extent than the C5 nucleobase modifications. 2'-Hydroxyl and 2'-fluoro groups respectively are shown to partially or completely block fragmentation at the modified nucleosides. Mixtures of oligonucleotides incorporating such modifications demonstrate remarkably extended accessible mass range, as well as increased sensitivity and mass resolution. The stabilization provided by these chemical modifications also expands the range of matrices useful for nucleic acid analysis, yielding in some cases greatly improved performance.

RFLP analysis of the progeny from Oryza alta Swallen x Oryza sativa L

RFLP analyses were carried out in the progeny from a cross of two phylogenetically distant rice species, wild rice Oryza alta Swallen (CCDD, 2n = 48) and cultivated rice O. sativa L. (AA, 2n = 24). The sterile plants gave heterozygous RFLP patterns at most of the loci detected. They looked more like their wild rice parent, with 36 chromosomes in their root-tip cells and pollen mother cells. In two partially fertile plants, however, most of the markers that were used showed RFLP patterns similar to the cultivated parent, O. sativa. By cytological study, it was found that nearly one-third of the chromosomes had been eliminated in the partially fertile plants. Their seeds have short awns, which is a characteristic of their wild parent, O. alta. An introgression occurred in one of the partially fertile plants, which led to the discussion about a nonconventional mechanism in wide hybridization for transference of wild rice chromosome segments to cultivated rice chromosomes.

MicroCT Imaging and In Vivo Temperature Elevations in Implanted Prostatic Tumors in Laser Photothermal Therapy Using Gold Nanorods

In this study, in vivo animal experiments are performed on implanted xenograph prostatic tumors in nude mice to investigate enhanced laser energy absorption in the tumors by an intratumoral injection of gold nanorod solutions. In vivo temperature mapping of the tumors during laser photothermal therapy has shown the feasibility of elevating tumor temperatures higher than 50 °C using only 0.1 ml nanorod solution and a low laser irradiance of 1.6 W/cm2 incident on the tumor surface. The temperature profile suggests that normal tumor tissue still absorbs some amount of the laser energy without nanorod presence; however, the injected nanorods ensure that almost all the laser energy is absorbed and confined to the targeted tumors. The inverse relationship between the temperature elevations and the tumor size implies a relatively uniform spreading of the nanorods to the entire tumor, which is also shown by microcomputed tomography (microCT) imaging analyses. The feasibility of detecting 250 OD gold nanorod solution injected to the tumors is demonstrated via a high resolution microCT imaging system. Compared to other nanostructures, the gold nanorods used in this study do not accumulate surrounding the injection site. The relatively uniform deposition of the nanorods in the tumors observed by the microCT scans can be helpful in future study in simplifying theoretical simulation of temperature elevations in tumors during laser photothermal therapy.

Characterization of the phenotype of high collagen-producing fibroblast clones in systemic sclerosis, using a new modified limiting-dilution method

BACKGROUND

Overproduction of type I collagen in fibroblasts of systemic sclerosis (SSc) is the hallmark of fibrosis. Establishment and characterization of the phenotype of SSc fibroblasts has been hindered by the heterogeneity between fibroblasts and the lack of adequate cloning methods.

AIM

To establish and investigate the characteristics of the SSc high collagen-producing fibroblast phenotype.

METHODS

Primary cultured fibroblasts from skin biopsies of patients with SSc and normal controls were cloned by a new modified limiting-dilution method. All clones were divided into different subpopulations based on their α1(I) procollagen (COL1A1) mRNA level detected by real-time reverse transcriptase PCR assay. In the different subpopulations, cell growth and cycle distribution were analysed by MTT and flow cytometry, COL1A1 promoter activity was examined by transient transfection, and the binding activity of Sp1 to the COL1A1 proximal promoter was investigated by quantitative chromatin immunoprecipitation.

RESULTS

The clonogenicities of SSc and normal control fibroblasts were similar, but the mean COL1A1 mRNA level of clones and the percentage of the subpopulation with a high COL1A1 mRNA level were significantly higher in SSc fibroblasts than in controls. There was no significant difference on cell growth and cycle between different subpopulations of SSc and control fibroblasts. The COL1A1 proximal promoter activity and its binding activity to Sp1 in the clones were strongly correlated with their COL1A1 mRNA level.

CONCLUSION

Overproduction of collagen in an SSc fibroblast subpopulation seems to result mainly from the abnormally activated transcription of COL1A1 rather than from overproliferation of fibroblasts. The new modified limiting-dilution method provides a useful means for characterizing cells with heterogeneous phenotypes.

Alanyl-tRNA synthetase mutation in a family with dominant distal hereditary motor neuropathy

OBJECTIVE

To identify a new genetic cause of distal hereditary motor neuropathy (dHMN), which is also known as a variant of Charcot-Marie-Tooth disease (CMT), in a Chinese family.

METHODS

We investigated a Chinese family with dHMN clinically, electrophysiologically, and genetically. We screened for the mutations of 28 CMT or related pathogenic genes using an originally designed microarray resequencing DNA chip.

RESULTS

Investigation of the family history revealed an autosomal dominant transmission pattern. The clinical features of the family included mild weakness and wasting of the distal muscles of the lower limb and foot deformity, without clinical sensory involvement. Electrophysiologic studies revealed motor neuropathy. MRI of the lower limbs showed accentuated fatty infiltration of the gastrocnemius and vastus lateralis muscles. All 4 affected family members had a heterozygous missense mutation c.2677G>A (p.D893N) of alanyl-tRNA synthetase (AARS), which was not found in the 4 unaffected members and control subjects.

CONCLUSION

An AARS mutation caused dHMN in a Chinese family. AARS mutations result in not only a CMT phenotype but also a dHMN phenotype.

Polymorphic microsatellite loci for Japanese Spanish mackerel (Scomberomorus niphonius)

We isolated and characterized 21 polymorphic microsatellite loci in Japanese Spanish mackerel (Scomberomorus niphonius) using a (GT)(13)-enriched genomic library. Forty individuals were collected from Qingdao, China. We found 3 to 24 alleles per locus, with a mean of 8.8. The observed and expected heterozygosities ranged from 0.263 to 0.975 and from 0.385 to 0.946, with means of 0.655 and 0.685, respectively. Deviation from Hardy-Weinberg proportions was detected at three loci. Two loci showed evidence for null alleles. These microsatellite markers will be useful for population genetic analysis of Japanese Spanish mackerel.

Blood pressure and obesity among adolescents: a school-based population study in China

BACKGROUND

There is little information regarding the obesity epidemical situation and risk factors of childhood hypertension (HTN) in China. The present study aimed to determine the prevalence of HTN/prehypertension (PHTN), as well as the associated risk factors, among adolescents in Changsha city, China.

METHODS

A total of 88,974 adolescents from 49 middle schools in Changsha city between 12 and 17 years of age were examined during 2009. Body weight, height, and blood pressure (BP) were measured in all adolescents. HTN and PHTN were defined according to sex- and age-specific Chinese reference data. Overweight and obesity were also defined according to sex- and age-specific Chinese reference data.

RESULTS

It was determined that the prevalence of PHTN and HTN were 7.2 and 3.1%, respectively. Furthermore, 14.6% of male adolescents were overweight and 7.0% were obese, whereas 8.6% of female adolescents were overweight and 2.9% were obese. The risk ratio (RR) of HTN were significantly higher in overweight (RR: 2.8, 95% confidence interval (CI): 2.6-3.2) and obese (RR: 8.7, 95% CI: 8.1-9.5) adolescents adjusted for age, sex, and height.

CONCLUSIONS

Chinese reference data were used to evaluate BP and body mass index (BMI) of children and adolescents. Higher prevalence of HTN was associated with higher BMI percentiles. Being overweight or obese markedly increased the risk of both HTN and PHTN among adolescents between 12 and 17 years of age in Changsha city, China.

Ectopic expression of glucagon receptor in skeletal muscles improves glucose homeostasis in a mouse model of diabetes

AIMS/HYPOTHESIS

Excessive secretion of glucagon partially contributes to the development of diabetic hyperglycaemia. However, complete blocking of glucagon action will lead to adverse effects, since glucagon exerts certain beneficial effects via its receptor in many organs. We aimed to study the effects of a 'decoy receptor' for circulating glucagon on modulating beta cell function and glucose homeostasis in mice by over-producing the glucagon receptor (GCGR) in skeletal muscles.

METHODS

We generated transgenic mice in which the expression of Gcgr is driven by the muscle specific creatine kinase (Mck) promoter, and assessed the effects of glucagon on the modulation of glucose homeostasis under conditions of extremes of glucose influx or efflux.

RESULTS

Mck/Gcgr mice showed increased circulating levels of glucagon and insulin, resulting in an unchanged ratio of glucagon-to-insulin. The levels of hepatic glucose-6-phosphatase (G6PC) and fructose-1,6-bisphosphatase (F1,6P2ase) were significantly decreased, whereas the phosphorylation level of pancreatic cAMP-response-element-binding-protein (CREB) was significantly increased in these transgenic mice. Under basal conditions, the mice displayed normal blood glucose levels and unchanged glucose tolerance and insulin sensitivity when compared with their age-matched wild-type (WT) littermates. However, following multiple low-dose streptozotocin injections, Mck/Gcgr mice exhibited a delay in the onset of hyperglycaemia compared with the WT controls. This was associated with preserved beta cell mass and beta cell secretory capacity in response to glucose challenge.

CONCLUSIONS/INTERPRETATION

We suggest that mild and chronic hyperglucagonaemia, through a strategy involving neutralising peripheral glucagon action, provides beneficial effects on beta cell function and glucose homeostasis. Mck/Gcgr mice thus represent a novel mouse model for studying the physiological effects of glucagon.

Microelectronic-sensing assay to detect presence of Verotoxins in human faecal samples

AIMS

 To develop a novel Vero cell assay that implements a real-time cell electronic sensing (RT-CES) system for the determination of the presence of verotoxin-producing Escherichia coli (VTEC). The assay overcomes the major drawbacks in conventional Vero cell assay, for example, labour-intensive and time-consuming.

METHODS AND RESULTS

 Cells were grown onto the surfaces of microelectronic sensors that are integrated into the bottom surfaces of the microtiter plate. Cellular viability was monitored in real-time and quantified based on changes in the sensor's electrical impedance. For cell viability measurement, the data generated on the RT-CES system correlated well with those obtained by the Vero cell assay for Verotoxins. To assess cytotoxicity, test cells growing on microelectronic sensors were treated with either supernatant from pure cultures, or stool samples. The specific neutralizing antibodies of VT1 and VT2 were used to identify specific toxins in the samples.

CONCLUSIONS

 The RT-CES assay provides a sensitive measurement comparable to conventional crystal violet assay. The assay has been successfully and specifically used to identify VTEC in human faecal samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

 The RT-CES assay significantly shortens the testing time from 48 to 72 h required by the crystal violet assay to only 15 h with automated operation.

Analysis of differentially expressed proteins involved in hand, foot and mouth disease and normal sera

We implemented 2-D DIGE technology on proteins prepared from serum obtained from children with hand, foot and mouth disease (HFMD) and controls, to study the differentially expressed proteins in control and HFMD serum samples. Proteins found to be differentially expressed were identified with matrix-assisted laser desorption/ionization time-of-flight/ time-of-flight mass spectrometry (MALDI-TOF/TOF MS) analysis. We identified 30 proteins from mild HFMD samples and 39 proteins from severe HFMD samples, compared with the normal controls. 25 proteins among them (14 up-regulated and 11 down-regulated proteins) are found in both HFMD groups. Classification analysis and protein-protein interaction map showed that they associate with multiple functional groups, including transporter activity and atalytic activity. These findings build up a comprehensive profile of the HFMD proteome and provide a useful basis for further analysis of the pathogenic mechanism and the regulatory network of HFMD.

High-fidelity, 160 fs, 5 μJ pulses from an integrated Yb-fiber laser system with a fiber stretcher matching a simple grating compressor

Although femtosecond microjoule Yb-fiber systems are attractive because of a straightforward power scalability, they inherently suffer from a lowered pulse fidelity as a result of complex dispersion and nonlinearity management. Here, we present an integrated Yb-fiber system delivering high-fidelity microjoule pulses compressible down to 160 fs. The system uses a dispersion compensating fiber stretcher that is specially designed to match the dispersion of a 1480 lines/mm grating compressor. Performance analysis suggests the further possibility of scaling the pulse energy to tens of microjoules without pulse quality deterioration using this dispersion management scheme.