Novel mutation in TGA stop-codon of bovine SIX6 gene

As a transcriptional regulatory gene of the SIX family, SIX6 (also known as OPTX2, SIX9), probably affects pituitary development and secretion of hormones, suggesting that this gene is a potential candidate gene for studying association with growth trait in animals. Therefore, this study is first of all focused on detecting sequence variations in a bovine SIX6 gene and on its effects on growth traits in 1087 cattle from five Chinese cattle breeds using DNA sequencing and HhaI-ACRS-PCR methods. Herein, a novel mutation (NC_007308: g 2015T > C) in the TGA stop-codon of a bovine SIX6 gene was found, which leads to an ORF shift and extension of the encoded protein for four amino acids (Arg223-Gln224-Arg225-Val226). The frequency of allele "C" varied from 0.255 (Chinese Holsteins) to 0.614 (Hasake). They all were in the Hardy-Weinberg equilibrium except Jiaxian Red and Hasake cattle. Using amino acid sequence alignment and online prediction software, a new helix in the C-terminal domain of the mutated bovine SIX6 protein was revealed, which possibly affects pituitary development and hormone secretion. So, relationship analysis between this polymorphism and growth traits in the Nanyang breed was carried out based on a proper linear model. Although no statistically significant associations were observed (P > 0.05), the presented work preliminarily demonstrated a novel mutation in the TGA stop-codon which extends the spectrum of genetic variations of the bovine SIX6 gene and might be of interest in terms of its association with other biophysical and biochemical indexes.

Characterization of Eu- and heterochromatin of citrus with a focus on the condensation behavior of 45S rDNA chromatin

To characterize the properties of eu- and heterochromatic regions in Citrus species, the chromosomal distribution of different histone H3 marks, DNA methylation sites (5mC) and 45S ribosomal DNA sites were determined for C. clementina, C. paradisi, C. sinensis, and for the hybrid Ortanique C. reticulata × C. sinensis. Our data show that in the relatively small genomes of investigated Citrus species (genome size ranges from 378-400 Mbp) the euchromatin is characterized by histone H3 lysine 4 mono-, di- and trimethylation (H3K4me1/ 2/3) and histone H3 lysine 9 trimethylation (H3K9me3). In contrast, histone H3 lysine 9 mono- and dimethylation (H3K9me1/2), histone H3 lysine 27 mono-, di- and trimethylation (H3K27me1/2/3) as well as 5-methylcytosine (5mC) were enriched at certain heterochromatin fractions. Whereas H3K9me1/2 and H3K27me1 were preferentially enriched at the chromomycin A(3)-bright (CMA(+)) heterochromatin, H3K27me2/3 showed a higher accumulation at the DAPI brightly-stained heterochromatin. 5mC signals were associated with most of the CMA(+) areas as well as with the DAPI strongly-stained heterochromatin fraction. Therefore, extensive methylation of DNA as well as of H3K9me1/2 and H3K27me1/2/3, and depletion of H3K4me1/2/3 and H3K9me3 appear to be specific features of heterochromatin in Citrus. Transcriptionally active decondensed 45S rDNA sites were found DNA hypomethylated, while the silenced condensed sites were strongly 5mC methylated. Although the number of chromosomal 45S rDNA sites differed between the species, the number of transcriptionally active rDNA sites remains constant.

Characterization of phytase from three ferns with differing arsenic tolerance

Phytase is involved in many physiological activities in plants including phosphorus metabolism and stress response. The effects of arsenic on phytase activities in arsenic-hyperaccumulator Pteris vittata were determined. Two arsenic-sensitive ferns (Pteris ensiformis and Nephrolepis exaltata) were included for comparison purpose. Fern phytase was extracted with Tris-HCl buffer (pH 7.6) followed by ammonium sulfate partial purification to characterize its properties and arsenic stress responses. The phytase showed an optimum pH of 5.0 and temperature of 40 °C except for P. vittata with 40-70 °C. Phytase from P. vittata was the first plant-phytase showing high heat resistance with no loss of activity by heating it at 70 °C, which may have application in feed industry. Phytase activity was inhibited by arsenate but not by arsenite. The fact that P. vittata phytase was the most heat-tolerant (40-70 °C) and had the highest resistance to arsenate among the three ferns suggest that phytase may play a role in arsenic detoxification and arsenic hyperaccumulation in P. vittata.

Surgical procedures and their cost estimates among women with newly diagnosed endometriosis: a US database study

OBJECTIVE

This descriptive study assessed the rate and costs of surgical procedures among newly diagnosed endometriosis patients.

METHODS

Utilizing the Medstat MarketScan database, commercially insured women aged 18-45 with endometriosis newly diagnosed during 2006-2007 were identified. Each endometriosis patient was matched to four women without endometriosis (population controls) based on age and region of residence. Surgical procedures received during the 12 months post-diagnosis were assessed. Costs of surgical procedures were the amount paid by the insurance companies.

RESULTS

This study identified 15,891 women with newly diagnosed endometriosis and 63,564 population controls. More than 65% of endometriosis patients received an endometriosis-related surgical procedure within 1 year of the initial diagnosis. The most common procedure was therapeutic laparoscopy (31.6%), followed by abdominal hysterectomy (22.1%) and vaginal hysterectomy (6.8%). Prevalence and type of surgery performed varied by patient age, including a hysterectomy rate of approximately 16% in patients younger than 35 and 37% among patients aged 35-45 years. Average costs ranged from $4,289 (standard deviation [SD]: $3,313) for diagnostic laparoscopy to $11,397 (SD: $8,749) for abdominal hysterectomy.

LIMITATIONS

Diagnosis of endometriosis cannot be validated against medical records, and information on the severity of endometriosis-related symptoms is not available in administrative claims data.

CONCLUSIONS

Over 65% of patients had endometriosis-related surgical procedures, including hysterectomy, within 1 year of being diagnosed with endometriosis. The cost of surgical procedures related to endometriosis places a significant financial burden on the healthcare system.

Disruption and formation of surface salt bridges are coupled to DNA binding by the integration host factor: a computational analysis

Revealing the thermodynamic driving force of protein-DNA interactions is crucial to the understanding of factors that dictate the properties and function of protein-DNA complexes. For the binding of DNA to DNA-wrapping proteins, such as the integration host factor (IHF), Record and co-workers proposed that the disruption of a large number of preexisting salt bridges is coupled with the binding process [Holbrook, J. A., et al. (2001) J. Mol. Biol. 310, 379]. To test this proposal, we have conducted explicit solvent MD simulations (multiple ∼25-50 ns trajectories for each salt concentration) to examine the behavior of charged residues in IHF, especially concerning their ability to form salt bridges at different salt concentrations. Of the 17 cationic residues noted by Record and co-workers, most are engaged in salt bridge interactions for a significant portion of the trajectories, especially in the absence of salt. This observation suggests that, from a structural point of view, their proposal is plausible. However, the complex behaviors of charged residues observed in the MD simulations also suggest that the unusual thermodynamic characteristics of IHF-DNA binding likely arise from the interplay between complex dynamics of charged residues both in and beyond the DNA binding site. Moreover, a comparison of MD simulations at different salt concentrations suggests that the strong dependence of the IHF-DNA binding enthalpy on salt concentration may not be due to a significant decrease in the number of stable salt bridges in apo IHF at high salt concentrations. In addition to the Hofmeister effects quantified in more recent studies of IHF-DNA binding, we recommend consideration of the variation of the enthalpy change of salt bridge disruption at different salt concentrations. Finally, the simulation study presented here explicitly highlights the fact that the electrostatic properties of DNA-binding proteins can be rather different in the apo and DNA-bound states, which has important implications for the design of robust methods for predicting DNA binding sites in proteins.

Transcription factor Sox11b is involved in spinal cord regeneration in adult zebrafish

Adult zebrafish have the ability to recover from spinal cord injury and exhibit re-growth of descending axons from the brainstem to the spinal cord. We performed gene expression analysis using microarray to find damage-induced genes after spinal cord injury, and found that Sox11b mRNA is up-regulated at 11 days after injury. However, the functional relevance of Sox11b for regeneration is not known. Here, we report that the up-regulation of Sox11b mRNA after spinal cord injury is mainly localized in ependymal cells lining the central canal and in newly differentiating neuronal precursors or immature neurons. Using an in vivo morpholino-based gene knockout approach, we demonstrate that Sox11b is essential for locomotor recovery after spinal cord injury. In the injured spinal cord, expression of the neural stem cell associated gene Nestin, and the proneural gene Ascl1a (Mash1a), which are involved in the self-renewal and cell fate specification of endogenous neural stem cells, respectively, is regulated by Sox11b. Our data indicate that Sox11b promotes neuronal determination of endogenous stem cells and regenerative neurogenesis following spinal cord injury in the adult zebrafish. Enhancing Sox11b expression to promote proliferation and neurogenic determination of endogenous neural stem cells after injury may be a promising strategy in restorative therapy after spinal cord injury in mammals.

Pituitary adenoma and vestibular schwannoma: case report and review of the literature

The concurrence of the intracranial multiple primary tumors (MPTs) consisting of acoustic neuroma (AN) and pituitary adenoma is very rare. Here, we report a 42-year-old female who presented with left AN associated with pituitary adenoma. A total of three such cases have been reported before and which also presented with left AN with pituitary adenoma. Recently, a new "field cancerization" model has been proposed, which could explain MPTs and is consistent with the pathogenesis of such cases. The model also indicates that when a pituitary tumor or AN is detected separately, we might consider the development of "expanding field" after oncological treatment especially after radiotherapy in order to prevent the second field tumor occurring.

Six novel coding SNPs of the nucleophosmin 1 (<i>NPM1</i>) gene and their associations with growth traits in bovine (Brief Report)

Abstract. The Nucleophosmin 1 (NPM1) gene encodes a multifunctional nucleolar phosphoprotein that has crucial roles in the control of different aspects of cell growth and homeostasis, such as ribosome biogenesis, centrosome duplication, cell cycle progression, apoptosis and cell differentiation (GRISENDI et al. 2006, NAOE et al. 2006). As mutants of NPM1 gene impact protein synthesis, NPM1 is an essential protein in mouse development and cell growth (MAGGI et al. 2008). The bovine NPM1 gene contains one exon and locates at chromosome 9. In previous work, the 12-bp deletion was detected in bovine NPM1 gene coding region. (HUANG et al. 2010). In this study, the coding region of bovine NPM1 gene has been scanned by PCR-SSCP, DNA sequencing and forced PCR-RFLP methods for SNPs in 1 032 individuals belonging to four Chinese cattle breeds. Association of six mutations of NPM1 gene with growth traits was analyzed.

Soil-test N recommendations augmented with PEST-optimized RZWQM simulations

Improved understanding of year-to-year late-spring soil nitrate test (LSNT) variability could help make it more attractive to producers. We test the ability of the Root Zone Water Quality Model (RZWQM) to simulate watershed-scale variability due to the LSNT, and we use the optimized model to simulate long-term field N dynamics under related conditions. Autoregressive techniques and the automatic parameter calibration program PEST were used to show that RZWQM simulates significantly lower nitrate concentration in discharge from LSNT treatments compared with areas receiving fall N fertilizer applications within the tile-drained Walnut Creek, Iowa, watershed (>5 mg NL(-1) difference for the third year of the treatment, 1999). This result is similar to field-measured data from a paired watershed experiment. A statistical model we developed using RZWQM simulations from 1970 to 2005 shows that early-season precipitation and early-season temperature account for 90% of the interannual variation in LSNT-based fertilizer N rates. Long-term simulations with similar average N application rates for corn (Zea mays L.) (151 kg N ha(-1)) show annual average N loss in tile flow of 20.4, 22.2, and 27.3 kg N ha(-1) for LSNT, single spring, and single fall N applications. These results suggest that (i) RZWQM is a promising tool to accurately estimate the water quality effects of LSNT; (ii) the majority of N loss difference between LSNT and fall applications is because more N remains in the root zone for crop uptake; and (iii) year-to-year LSNT-based N rate differences are mainly due to variation in early-season precipitation and temperature.

Novel 12-bp deletion in the coding region of the bovine NPM1 gene affects growth traits

The nucleophosmin 1 gene (NPM1) encodes a multifunctional nucleolar phosphoprotein that plays a crucial role in the control of various aspects of cell growth and homeostasis. In this study, the coding region of the NPM1 gene was screened in 1035 individuals of 4 Chinese cattle breeds by DNA sequencing and polyacrylamide gel electrophoresis. A novel 12-bp deletion mutation was identified in the coding region of the NPM1 gene. The PCR products of primer NPM1-P2 exhibited 3 genotypes and 2 alleles: 178 bp (denoted as W) and 166 bp (denoted as D). Genotype DD and allele D were predominant in the studied populations. Association analysis with growth traits in the Nanyang breed (N = 265) showed that the animals with genotype DD had significantly greater birth weight, body weight, body length, and heart girth than those with genotype WD (P < 0.01 or P < 0.05) at birth and after 6 months and 12 months, but not at 18 and 24 months of age. Results of this study suggest that the NPM1 gene is a candidate gene for growth traits in cattle.

Arterial remodeling of advanced basilar atherosclerosis: a 3-tesla MRI study

BACKGROUND

There are limited studies on wall imaging of human basilar artery (BA). Our aim was to investigate remodeling mode of advanced BA atherosclerosis using 3-T MRI.

METHODS

Thirty-two consecutive symptomatic patients with atherosclerotic BA stenosis >or=70% were imaged with a 3-T magnetic resonance scanner. Proton density-weighted (PDW) cross-sectional images with submillimeter voxel size were obtained. The vessel area (VA) and lumen area (LA) at the maximal lumen narrowing (MLN) site and reference site were measured. Intraobserver and interobserver variability was determined by intraclass correlation coefficient (ICC). Wall area (WA) was estimated by VA - LA. Plaque size (PS) was estimated by WA at MLN site--reference WA. Percent plaque burden was calculated as (PS/VA at MLN site) x 100%. Remodeling index (RI) was the ratio of VA at MLN site to reference VA. RI >or=1.05 was defined as positive remodeling (PR) and RI <1.05 as non-PR.

RESULTS

Measurements of cross-sectional BA images were available in 30 of 32 patients. Intraobserver or interobserver variability was small, with ICC ranging from 0.955 to 0.996. The mean RI of the 30 patients was 1.2 +/- 0.4. PR was found in 19 (63.3%) patients and non-PR in 11 (36.7%) patients. Compared with the non-PR group, the PR group had greater PS (15.0 +/- 9.3 mm(2) vs 6.4 +/- 3.9 mm(2), p = 0.007) and greater percent plaque burden (50.5 +/- 9.9% vs 28.5 +/- 12.7%, p < 0.0001).

CONCLUSIONS

3-T high-resolution PDW imaging is a reproducible tool for measuring BA dimensions. In patients with advanced BA atherosclerosis, PR lesions are more frequently observed and contain larger plaques than non-PR lesions.

Potential antidepressant properties of Radix Polygalae (Yuan Zhi)

Radix Polygalae ("Yuan Zhi", the roots of Polygala tenuifolia Willd., YZ) is an important herb used in traditional Chinese medicine to mediate depression. The present study was designed to verify the antidepressant effects of the standardized YZ ethanol extract (YZE) and its four fractions YZ-30, YZ-50, YZ-70 and YZ-90 on the tail suspension (TST) and forced swimming test (FST). Furthermore, the standardization of the fractions obtained from the separation procedures was carried out by high-performance liquid chromatography (HPLC)-fingerprint. The YZ-50 fraction (Oligosaccharide esters--enriched, oral (200 mg/kg) showed a significant anti-immobility like effects. The data of YZ-50 on the corticosterone-induced injure of SH-SY5Y human neuroblastoma cell indicated that YZ-50 may have biological effects on neuroprotection. Proliferation of cell lines was assessed by dimethylthiazoldiphenyltetrazoliumbromide (MTT) and 5-bromo-2'-deoxyuridine (BrdU) incorporation assays. It was found that YZ-50 and its two bioactive compounds, 3,6'-di-o-sinapoyl-sucrose (DISS) and tenuifoliside A(TEA) showed protection activities in SY5Y cells from the lesion. By using bioassay-screening methods, our results indicate that the presence of oligosaccharide esters such as DISS and TEA in this herb may be responsible for the cytoprotective activity effects.

Telmisartan alleviates rosiglitazone-induced bone loss in ovariectomized spontaneous hypertensive rats

In the present study, we systematically examined telmisartan, an angiotensin AT(1) receptor antagonist, on rosiglitazone-induced bone loss in ovariectomized spontaneously hypertensive rats. Telmisartan (5 mg/kg/d, 90 days) was found to be able to significantly alleviate rosiglitazone (10 mg/kg/d, 90 days)-induced decrease in BMD of femur and lumbar vertebrae. The BMD changes were associated with positive biomechanical changes of lumbar vertebrae, improvements in microarchitecture of tibial metaphysic and normalized serum osteocalcin (OC) levels and urinary deoxypyridinoline/creatinine (DPD/Cr) ratio. MicroCT analysis of the tibial metaphysis showed that telmisartan significantly prevented the decreases in bone volume/tissue volume (BV/TV), connect density (Conn. D.), trabecular number (Tb. N.) and trabecular thickness (Tb. Th.), and increase in trabecular separation (Tb. Sp.) induced by rosiglitazone. Histomorphometric analysis also showed that telmisartan had protective effects on rosiglitazone-reduced bone formation indices such as histomorphometric bone volume fraction (BV/TV-Histo), mineralizing surface/bone surface (MS/BS), mineral apposition rate (MAR) and bone formation rate (BFR/BS). Our study clearly showed that telmisartan alleviated rosiglitazone-induced bone loss in ovariectomized spontaneous hypertensive rats. The relief of bone loss provides a possible therapeutic application of telmisartan with rosiglitazone for the treatment of elderly women patients afflicted with metabolic syndrome.

Modeling nutrient flows in the food chain of China

Increasing nitrogen (N) and phosphorus (P) inputs have greatly contributed to the increasing food production in China during the last decades, but have also increased N and P losses to the environment. The pathways and magnitude of these losses are not well quantified. Here, we report on N and P use efficiencies and losses at a national scale in 2005, using the model NUFER (NUtrient flows in Food chains, Environment and Resources use). Total amount of "new" N imported to the food chain was 48.8 Tg in 2005. Only 4.4.Tg reached households as food. Average N use efficiencies in crop production, animal production, and the whole food chain were 26, 11, and 9%, respectively. Most of the imported N was lost to the environment, that is, 23 Tg N to atmosphere, as ammonia (57%), nitrous oxide (2%), dinitrogen (33%), and nitrogen oxides (8%), and 20 Tg to waters. The total P input into the food chain was 7.8 Tg. The average P use efficiencies in crop production, animal production, and the whole food chain were 36, 5, and 7%, respectively. This is the first comprehensive overview of N and P balances, losses, and use efficiencies of the food chain in China. It shows that the N and P costs of food are high (for N 11 kg kg(-1), for P 13 kg kg(-1)). Key measures for lowering the N and P costs of food production are (i) increasing crop and animal production, (ii) balanced fertilization, and (iii) improved manure management.

Variants in ACAD10 are associated with type 2 diabetes, insulin resistance and lipid oxidation in Pima Indians

AIMS/HYPOTHESIS

A prior genome-wide association study in Pima Indians identified a variant within the ACAD10 gene that is associated with early-onset type 2 diabetes. Acylcoenzyme A dehydrogenase 10 (ACAD10) catalyses mitochondrial fatty acid beta-oxidation, which plays a pivotal role in developing insulin resistance and type 2 diabetes. Therefore, ACAD10 was analysed as a positional and biological candidate for type 2 diabetes.

METHODS

Twenty-three SNPs were genotyped in 1,500 Pima Indians to determine the linkage disequilibrium pattern across ACAD10. Association with type 2 diabetes was determined by genotyping four tag single nucleotide polymorphisms (SNPs) in a population-based sample of 3,501 full-heritage Pima Indians; two associated SNPs were further genotyped in a second population-based sample of 3,723 American Indians. Associations with quantitative traits were assessed in 415 non-diabetic full heritage Pima individuals who had been metabolically phenotyped.

RESULTS

SNPs rs601663 and rs659964 were associated with type 2 diabetes in the full-heritage Pima Indian sample (p=0.04 and 0.0006, respectively), and rs659964 was further associated with type 2 diabetes in the second American Indian sample (p=0.04). Combination of these two samples provided the strongest evidence for association (p=0.009 and 0.00007, for rs601663 and rs659964, respectively). Quantitative trait analyses identified nominal associations with both lower lipid oxidation rate and larger subcutaneous abdominal adipocyte size, which is consistent with the known physiology of ACAD10, and also identified associations with increased insulin resistance.

CONCLUSIONS/INTERPRETATION

We propose that ACAD10 variation may increase type 2 diabetes susceptibility by impairing insulin sensitivity via abnormal lipid oxidation.