Bayesian methods for estimating GEBVs of threshold traits

Estimation of genomic breeding values is the key step in genomic selection (GS). Many methods have been proposed for continuous traits, but methods for threshold traits are still scarce. Here we introduced threshold model to the framework of GS, and specifically, we extended the three Bayesian methods BayesA, BayesB and BayesCπ on the basis of threshold model for estimating genomic breeding values of threshold traits, and the extended methods are correspondingly termed BayesTA, BayesTB and BayesTCπ. Computing procedures of the three BayesT methods using Markov Chain Monte Carlo algorithm were derived. A simulation study was performed to investigate the benefit of the presented methods in accuracy with the genomic estimated breeding values (GEBVs) for threshold traits. Factors affecting the performance of the three BayesT methods were addressed. As expected, the three BayesT methods generally performed better than the corresponding normal Bayesian methods, in particular when the number of phenotypic categories was small. In the standard scenario (number of categories=2, incidence=30%, number of quantitative trait loci=50, h² = 0.3), the accuracies were improved by 30.4%, 2.4%, and 5.7% points, respectively. In most scenarios, BayesTB and BayesTCπ generated similar accuracies and both performed better than BayesTA. In conclusion, our work proved that threshold model fits well for predicting GEBVs of threshold traits, and BayesTCπ is supposed to be the method of choice for GS of threshold traits.

The identification of c-Kit-positive cells in the intestine of chicken

The ultrastructure of the interstitial cells of Cajal (ICC) has been examined in birds, but the distribution of these cells remains obscure because a suitable marker is lacking. In the present study, the identification and expression of c-Kit-positive cells in the chicken intestine were demonstrated by means of in situ hybridization histochemistry and the expression of the c-Kit gene by real-time quantitative PCR. Two types of cells stained positive for c-Kit mRNA. The first group consisted of spindle-shaped or bipolar cells identified as ICC. The ICC were found at a variety of locations: at the level of the myenteric plexus between the circular and longitudinal muscle and intermingled with smooth muscle cells within muscle bundles in the circular and longitudinal muscle layers. The ICC were also identified along the submucosal layer. The second group was composed of round-shaped cells, which resembled mast cells. Mast cells were mainly found in the lamina propria region as well as in the submucosal layer. The expression of the c-Kit gene by real-time quantitative PCR revealed the expression of c-Kit mRNA throughout the lamina muscularis and mucosa of the intestine; however, the quantitation was variable in different regions. This study reveals conclusively for the first time the distribution of ICC, quantifies the expression of c-Kit mRNA in the intestine of adult chicken, and also compares the c-Kit-positive cell types morphologically.

Kinematic control of redundant robots and the motion optimizability measure

This paper treats the kinematic control of manipulators with redundant degrees of freedom. We derive an analytical solution for the inverse kinematics that provides a means for accommodating joint velocity constraints in real time. We define the motion optimizability measure and use it to develop an efficient method for the optimization of joint trajectories subject to multiple criteria. An implementation of the method for a 7-dof experimental redundant robot is present.

A study of classification of spontaneous intraventricular haemorrhage: a report of 324 cases

In order to develop a practical classification of spontaneous intraventricular haemorrhage (IVH), a correlation was made between clinical and computed tomographic (CT) factors in 324 patients with IVH between September 1988 and December 1996. Spontaneous IVH was graded according to age, blood pressure, clinical conditions, conscious state on admission, primary site of bleeding, volume of intraparenchymal haematoma, degree of midline shift, degree of hydrocephalus and location of IVH, producing a score up to 20. A score of 0-5 was Grade I, 6-10 Grade II, 11-15 Grade III, 16-20 Grade IV. The mortality of each Grade, respectively, was 1.6%, 22.5%, 76% and 100%. The authors propose that this grading system may be a practical schema in the evaluation of the prognosis for IVH.

Isolation, culture and characterization of a primary fibroblast cell line from channel catfish

A primary cell line (designated as CCf) derived from caudal fin tissue of channel catfish, Ictalurus punctatus, was developed using explant techniques. The cell line grew fastest in media supplied with FBS and channel catfish serum. The duplication time of the cell line under optimal conditions was ∼56 h at a plating density of 1.1 × 10(5) cells/ml. The cell line has been propagated continuously for 25 passages (1:4 dilution per passage), cryopreserved, and recovered successfully at different passages. The cultured cells had fibroblastic morphology, and synthesized fibronectin and Type I and III collagens in the cytoplasm. The cell line maintained the normal diploid chromosome number (58) of channel catfish throughout the experiment. Nucleolus organizer regions were located on the short arms of a pair of medium-sized submetacentrics, which is typical for channel catfish. This study provides a method for acquiring a cell line from juvenile catfish without sacrifice, and is especially useful for early screening of valuable fishes.

Functional-characterization of developing tumor vascular system and drug delivery (review)

This review summarizes our recent experiments on the process of tumor vascularization and character of tumor vessels. By vitalscopic observation with transparent chambers in rats, we found that the sites where tumor vessels originated were usually terminal portions of terminal arterioles and that an intricate tumor vascular network was constructed from incorporated preexisting vessels and newly formed vessels by three different modes, i.e., sprouting, cross-connecting and splitting. Observation and hydrogen clearance studies showed that tumor blood flow changed remarkably during the development of the tumor vascular network. At an early stage of tumor growth, there were some regions of high flow in the tumor. At an advanced stage, however, there was a rapid increase in low-flow or no-flow areas which were resistant to access of anticancer drugs and oxygen. Angiotensin II-induced hypertension produced a several-fold increase in tumor blood flow without increasing tissue blood flow of normal tissues. These good conditions for drug delivery to tumor tissue are able to enhance therapeutic effects of chemotherapy, irradiation, antibody and photodynamic therapy.

Control of Campylobacter jejuni in chicken breast meat by irradiation combined with modified atmosphere packaging including carbon monoxide

Campylobacter is one of the leading causes of human foodborne illnesses originating from meat and poultry products. Cross-contamination of this organism occurs in many poultry processing plants, and can occur in the kitchens and refrigerators of consumers. Therefore, new intervention strategies are needed for meat and poultry products to better protect consumers from this pathogen. Vacuum or modified atmosphere packaging is a common packaging technique used by the meat and poultry industry to extend the shelf life of meat products. In addition, irradiation has been well established as an antibacterial treatment to reduce pathogens on meat and poultry products. Irradiation in combination with high-CO(2) + CO modified atmosphere packaging (MAP) was investigated in this study for the control of Campylobacter jejuni in chicken breast meat. The radiation sensitivity (D(10)-value) of this foodborne pathogen in chicken breast meat was similar in vacuum or high-O(2) MAP (0.31 ± 0.01 kGy in vacuum packaging and 0.29 ± 0.03 kGy in MAP). C. jejuni survived in both vacuum and high-CO(2) MAP through 6 weeks of refrigerated storage. Irradiation was effective for eliminating C. jejuni from meat or poultry packaged in vacuum or MAP, and should reduce the chance of cross-contamination in retail stores or home kitchens. However, irradiated off-odor and sour aroma were observed for raw, irradiated chicken breast packaged with either vacuum or MAP. Therefore, additional means to mitigate quality changes appear necessary for these products.

Development and validation of a liquid chromatography-tandem mass spectrometry method for the simultaneous determination of acrivastine and pseudoephedrine in human plasma and its application in pharmacokinetics

A specific, sensitive and accurate liquid chromatography-tandem mass spectrometry (LC-MS/MS) method has been developed for the simultaneous determination of acrivastine and pseudoephedrine in human plasma samples. Plasma samples were processed and analyzed on a Phenomenex Luna 3 μ CN 100A column (150 mm×2.0 mm) eluted with the mobile phase consisting of methanol and 0.01 mol/L ammonium acetate water solution containing 0.1% formic acid (45:55, v/v) at a flow rate of 0.2 mL/min. The analytes were detected by positive ion electrospray ionization in multiple reaction monitoring mode. The transitions of m/z 349→278, m/z 166→148 and m/z 256→167 were monitored for acrivastine, pseudoephedrine and diphenhydramine (IS), respectively. The method was specific and sensitive with a lower limit of quantitation (LLOQ) of 1.52 ng/mL for acrivastine and 8.13 ng/mL for pseudoephedrine. The method showed good linearity in the range of 1.52~606.0 0 ng/mL for acrivastine and 8.13~813.12 ng/mL for pseudoephedrine (r≥0.996). The mean recovery were ranged 91.82% ~ 98.46% for acrivastine and 90.77% ~ 92.05% for pseudoephedrine. Validation results, such as accuracy, precision and repeatability were within the required limits. The method was successfully applied in a pharmacokinetic study of the acrivastine and pseudoephedrine hydrochloride compound capsule in humans.

Delineation of the cardiac substructures based on PET-CT and contrast-enhanced CT in patients with left breast cancer treated with postoperative radiotherapy

The aim of this study is to evaluate the volume differences between contrast-enhanced CT-based left ventricle (LV) and PET-CT-based LV and assess the impact of dose on the substructure volume differences in patients with left breast cancer treated with adjuvant radiotherapy. From October 2008 to February 2009, 14 patients with post-operatively confirmed left breast cancer were enrolled in the current study. The patients were scanned using contrast-enhanced CT for simulation, and (18)F-FDG PET-CT was employed to display the structure of the left ventricle of each before radiotherapy (RT). The LV was delineated based on both contrast-enhanced CT and PET-CT. And other substructures, such as the left anterior descending coronary artery (LAD), were contoured in each patient, with the six-field simple intensity modulated radiotherapy (sIMRT) technique created for all. The mean volumes of the left ventricle based on contrast-enhanced CT (LV-CT) and PET-CT (LV-PET) were found to be 107.296 cm(3) and 112.931 cm(3), respectively (p = 0.06). The volume of LV receiving ≥ 50% prescription dose was significantly correlated with the volume of the heart receiving the same dosage (γ = 0.869). There was less correlation between the volume of LAD and that of the heart under the same condition (γ = 0.22). As a conclusion, the left ventricle can be delineated effectively based on the image of PET-CT, the contrast-enhanced CT based LV can serve as an appropriate alternative. Moreover, the volume of LV receiving high dose in RT closely correlated with the volume of the heart using sIMRT technique, which may pave the way for further exploring radiation-induced cardiac injuries in patients with left breast cancer.

Ultrastructural identification of different subtypes of interstitial cells of Cajal in the chicken ileum

Ultrastructural characteristics of different subtypes of interstitial cells of Cajal (ICC) remain unclear in birds; however, birds have significant economical and scientific notability. Our aim was to describe and classify ICC in the chicken gut. The ileum of normal adult Three Yellow broiler chickens (n=10) were studied by transmission electron microscopy (TEM). The ICC were spindle- or stellate-shaped with ramified cell processes. They had numerous mitochondria, abundant intermediate filaments, fusiform nuclei (oval or indented), with a dense band of peripheral heterochromatin, and formed close contacts by true gap junctions with each other and with neighboring smooth muscle cells (SMC). The ICC were in close contact with enteric nerves, but true gap junctions were not found between them. A new subtype of ICC located in the lamina propria mucosae has been discovered. Some of the ICC showed typical features of SMC, including a basal lamina, caveolae, and dense bodies. Lacking intermediate filaments and caveolae distinguished them from the fibroblast-like cells showing well-developed secretory organelles, including coated vesicles and a patchy basal lamina. The ultrastructural features and distribution of ICC in chicken intestine is similar to mammals. They may play similar key regulatory roles in gastrointestinal motility. The new subtype of ICC discovered in the lamina propria mucosae may play a role in the regulation of secretion and absorption.

The smell of Tokishakuyaku-san (TJ-23) induces generation of regulatory T cells and prolongation of survival of fully allogeneic cardiac grafts in mice

Oral administration of Tokishakuyaku-san (TJ-23), a Japanese herbal medicine, induces prolongation of cardiac allograft survival and generates regulatory cells in mice. Because herbal medicines usually have unique odor, and because smell is supposed to modulate the immune system, we examined whether the odor of TJ-23 induced prolonged allograft survival and regulatory cell generation. Naïve CBA mice (H2(k)) and olfactory-dysfunctional CBA mice after a stereotaxic operation underwent transplantation of C57BL/6 (B6, H2(b)) hearts, receiving fumigated water only or TJ-23 until rejection. Untreated or treated with water fumigation CBA mice rejected B6 cardiac grafts acutely (median survival times [MSTs], 7 and 8.5 days). When CBA mice were treated with fumigation of TJ-23, allograft survival was significantly prolonged (MST, 48 days). Olfactory-dysfunctional CBA mice treated with fumigation of TJ-23 rejected grafts acutely (MST, 7 days). Treatment with fumigation of TJ-23 also suppressed splenocytes proliferation and interferon-γ production. Secondary CBA recipients of whole splenocytes or CD4(+) cells from primary TJ-23-treated CBA recipients of B6 cardiac allografts at 30 days after grafting showed prolonged survival of B6 hearts (MST, >60 days). Flow cytometry studies showed increased CD4(+)CD25(+)Foxp3(+) regulatory cells in recipients given fumigation of TJ-23. In conclusion naïve but not olfactory-dysfunctional CBA mice treated with fumigation of TJ-23 displayed prolonged survival of fully allogeneic cardiac allografts and generation of regulatory cells.

Music exposure induced prolongation of cardiac allograft survival and generated regulatory CD4⁺ cells in mice

In clinical practice, music has been used to decrease stress, heart rate, and blood pressure and to provide a distraction from disease symptoms. We investigated sound effects on alloimmune responses in murine heart transplantation. Naïve and eardrum-ruptured CBA/N (CBA, H2(K)) underwent transplantation of a C57BL/6 (B6, H2(b)) heart and were exposed to 1 of 3 types of music-opera (La Traviata), classical (Mozart), and New Age (Enya)-or 1 of 6 different single sound frequencies for 7 days. An adoptive transfer study was performed to determine whether regulatory cells were generated in allograft recipients. Cell-proliferation, cytokine, and flow cytometry assessments were also performed. CBA recipients of a B6 graft exposed to opera and classical music had significantly prolonged allograft survival (median survival times [MSTs], 26.5 and 20 days, respectively), whereas those exposed to 6 single sound frequencies and New Age did not (MSTs, 7, 8, 9, 8, 8, 8, and 11 days, respectively). Untreated and eardrum-ruptured CBA rejected B6 grafts acutely (MSTs, 7 and 8.5 days, respectively). Adoptive transfer of whole splenocytes, CD4(+) cells, and CD4(+)CD25(+) cells from opera-exposed primary recipients resulted in significantly prolonged allograft survival in naive secondary recipients (MSTs, 36, 68, and >50 days, respectively). Cell-proliferation, interleukin (IL)-2 and interferon-γ were suppressed in opera-exposed mice, whereas IL-4 and IL-10 from opera-exposed recipients were up-regulated. Flow cytometry studies showed an increased CD4(+)CD25(+)Foxp3(+) cell population in splenocytes from opera-exposed mice. In conclusion, exposure to some types of music may induce prolonged survival of fully allogeneic cardiac allografts and generate CD4(+)CD25(+)Foxp3(+) regulatory cells.

Intranasal administration of TAT-haFGF(₁₄₋₁₅₄) attenuates disease progression in a mouse model of Alzheimer's disease

Human acidic fibroblast growth factor (haFGF), a neurotrophin-like growth factor in the brain, plays important roles in the development, differentiation and regeneration of brain neurons, which makes it potential to treat Alzheimer's disease (AD). In this study, haFGF(14-154) and TAT-haFGF(14-154) (haFGF(14-154) fused with the cell-penetrating peptide transactivator of transcription protein transduction domain (TAT-PTD)) were intranasally administrated for 5 weeks to investigate the effects on senescence-accelerated mouse prone-8 (SAMP8) mice (a mouse model of AD). Results showed that TAT-PTD could increase the concentration of haFGF in the brain significantly, and TAT-haFGF(14-154) was more effective than haFGF(14-154) in the same dosage (300 μg/kg). Importantly, TAT-haFGF(14-154) improved the learning and memory abilities of SAMP8 mice in the behavioral test, and promoted the function of cholinergic system by measuring the relevant biomarkers (acetylcholine (ACh) level, acetylcholinesterase (AChE) and choline acetyltransferase (ChAT) activities). TAT-haFGF(14-154) also significantly reduced β-amyloid protein(1-42) (Aβ(1-42)) deposits as well as the levels of Aβ soluble forms in the mice brains and prevented the neurons from apoptosis. Besides, the oxidative stress impairment in the brain and serum was also ameliorated. The results suggest that TAT-haFGF(14-154) could attenuate the disease progression of SAMP8 AD mice, and the mechanism is related to the regulation of neurons microenvironment including neurotransmitters, Aβ pathology and oxidative stress.

CYP7A1 polymorphism influences the LDL cholesterol-lowering response to atorvastatin

WHAT IS KNOWN AND OBJECTIVE

Response to the lipid-lowering effect of the statins is known to show significant inter-individual variability. Our aim was to investigate whether genetic variants of the CYP3A5 gene, CYP7A1 gene and ABCG8 gene influence the lipid-lowering response to atorvastatin.

METHODS

One hundred and seven unrelated Chinese Han hypercholesterolemia patients were recruited from among the inpatients and outpatients of Tangshan Gongren Hospital of Hebei, China. Three polymorphisms of the CYP3A5 gene, seven polymorphisms of the CYP7A1 gene and seven polymorphisms of the ABCG8 gene were selected using a tagging single-nucleotide polymorphism (tSNP) strategy and genotyped using Snapshot platform.

RESULTS

SNP rs8192870, located in the first intron of the CYP7A1 gene, was associated with the LDL level lowering response to atorvastatin. The LDL levels were reduced by 27.89% for the GG/GA genotype carriers and 35.26% for the AA genotype carriers, respectively, after atorvastatin treatment (P = 0.021). The significance remained after adjusting for covariates. In addition, we observed that rs4148222 in the 11th intron of the ABCG8 gene significantly associated with the baseline levels of HDL (P = 0.046).

WHAT IS NEW AND CONCLUSION

CYP7A1 gene polymorphism influences the LDL-lowering effects of atorvastatin in Chinese Hans. If replicated by others, identification of the tagged functional variant would be needed.

Impact of climatic factors on genetic diversity of Stipa breviflora populations in Inner Mongolia

Genetic diversity of Stipa breviflora populations in the Inner Mongolian grasslands of China and its possible correlation with climatic factors was examined using geographic information systems and random amplified polymorphism DNA analysis. A total of 308 bands were produced with 28 arbitrary decamer oligonucleotide. Three major findings were demonstrated. First, the genetic diversity of S. breviflora was high but lower than that of Stipa grandis and Stipa krylovii. Second, genetic distances between the populations analyzed using the unweighted pair group method and the Mantel test had a highly positive correlation with geographical distances, indicating that spatial separation of this species in the studied area produced genetic shift in the population. Finally, both canonical correspondence and Pearson's analyses revealed strong correlations between genetic differentiation and temperature in the area. We therefore conclude that temperature variations play an important role in genetic differentiations among the investigated S. breviflora populations.