A simple method for calculating the statistical power for detecting a QTL located in a marker interval

We developed a simple method for calculating the statistical power for detecting a QTL located in an interval flanked by two markers. The statistical method for QTL detection is assumed to be the Haley and Knott's simple regression method of interval mapping. This method allows us to answer one of the fundamental questions in designing a QTL mapping experiment: What is the minimum marker density required to detect a QTL explaining a certain heritable proportion of the phenotypic variance (denoted by h(2)) with a power gamma under a Type I error alpha in an F(2) or other mating designs with a sample size n? Computing the statistical power only requires the ability to evaluate a non-central F-distribution function and the inverse function of this distribution.

Zero-field remote detection of NMR with a microfabricated atomic magnetometer

We demonstrate remote detection of nuclear magnetic resonance (NMR) with a microchip sensor consisting of a microfluidic channel and a microfabricated vapor cell (the heart of an atomic magnetometer). Detection occurs at zero magnetic field, which allows operation of the magnetometer in the spin-exchange relaxation-free (SERF) regime and increases the proximity of sensor and sample by eliminating the need for a solenoid to create a leading field. We achieve pulsed NMR linewidths of 26 Hz, limited, we believe, by the residence time and flow dispersion in the encoding region. In a fully optimized system, we estimate that for 1 s of integration, 7 x 10(13) protons in a volume of 1 mm(3), prepolarized in a 10-kG field, can be detected with a signal-to-noise ratio of approximately 3. This level of sensitivity is competitive with that demonstrated by microcoils in 100-kG magnetic fields, without requiring superconducting magnets.

Homogeneous nanocrystalline cubic silicon carbide films prepared by inductively coupled plasma chemical vapor deposition

Silicon carbide films with different carbon concentrations x(C) have been synthesized by inductively coupled plasma chemical vapor deposition from a SiH(4)/CH(4)/H(2) gas mixture at a low substrate temperature of 500 °C. The characteristics of the films were studied by x-ray photoelectron spectroscopy, x-ray diffraction, scanning electron microscopy, high-resolution transmission electron microscopy, Fourier transform infrared absorption spectroscopy, and Raman spectroscopy. Our experimental results show that, at x(C) = 49 at.%, the film is made up of homogeneous nanocrystalline cubic silicon carbide without any phase of silicon, graphite, or diamond crystallites/clusters. The average size of SiC crystallites is approximately 6 nm. At a lower value of x(C), polycrystalline silicon and amorphous silicon carbide coexist in the films. At a higher value of x(C), amorphous carbon and silicon carbide coexist in the films.

Mechanisms of the reactions of W AND W+ with H2O: computational studies

The mechanism of the reactions of W and W(+) with the water molecule have been studied for several lower-lying electronic states of tungsten centers at the CCSD(T)/6-311G(d,p)+SDD and B3LYP/6-31G(d,p)+SDD levels of theory. It is shown that these reactions are essentially multistate processes, during which lower-lying electronic states of the systems cross several times. They start with the formation of initial prereaction M(H(2)O) complexes with M-H(2)O bonding energies of 9.6 and 48.2 kcal/mol for M = W and W(+), followed by insertion of the metal center into an O-H bond with 20.0 and 53.3 kcal/mol barriers for neutral and cationic systems, respectively. The overall process of M + H(2)O --> t-HM(OH) is calculated to be highly exothermic, 48.4 and 48.8 kcal/mol for M = W and W(+). From the HM(OH) intermediate the reaction may proceed via several different channels, among which the stepwise HM(OH) --> HMO + H --> (H)(2)MO and concerted HM(OH) --> (H)(2)MO pathways are more favorable and can compete (energetically) with each other. For the neutral system (M = W), the concerted process is the most favorable, whereas for the charged system (M = W(+)), the stepwise pathway is slightly more favorable. From the energetically most favorable intermediate (H)(2)MO the reactions proceed via H(2)-molecule formation with a 53.1 kcal/mol activation barrier for the neutral system. For the cationic system, H-H formation and dissociation is an almost barrierless process. The overall reaction of W and W(+) with the water molecule leading to H(2) + MO formation is found to be exothermic by 48.2 and 39.8 kcal/mol, respectively. In the gas phase with the collision-less conditions the reactions W((7)S) + H(2)O --> H(2) + WO((3)Sigma(+)), and W(+)((6)D) + H(2)O --> H(2) + WO(+)((4)Sigma(+)) are expected to proceed via a 10.4 and 5.1 kcal/mol overall energy barrier corresponding to the first O-H dissociation at the TS1. On the basis of these PESs, we predict kinetic rate constants for the reactions of W and W(+) with H(2)O.

The effects of force inhibition by sodium vanadate on cross-bridge binding, force redevelopment, and Ca2+ activation in cardiac muscle

Strongly bound, force-generating myosin cross-bridges play an important role as allosteric activators of cardiac thin filaments. Sodium vanadate (Vi) is a phosphate analog that inhibits force by preventing cross-bridge transition into force-producing states. This study characterizes the mechanical state of cross-bridges with bound Vi as a tool to examine the contribution of cross-bridges to cardiac contractile activation. The K(i) of force inhibition by Vi was approximately 40 microM. Sinusoidal stiffness was inhibited with Vi, although to a lesser extent than force. We used chord stiffness measurements to monitor Vi-induced changes in cross-bridge attachment/detachment kinetics at saturating [Ca(2+)]. Vi decreased chord stiffness at the fastest rates of stretch, whereas at slow rates chord stiffness actually increased. This suggests a shift in cross-bridge population toward low force states with very slow attachment/detachment kinetics. Low angle x-ray diffraction measurements indicate that with Vi cross-bridge mass shifted away from thin filaments, implying decreased cross-bridge/thin filament interaction. The combined x-ray and mechanical data suggest at least two cross-bridge populations with Vi; one characteristic of normal cycling cross-bridges, and a population of weak-binding cross-bridges with bound Vi and slow attachment/detachment kinetics. The Ca(2+) sensitivity of force (pCa(50)) and force redevelopment kinetics (k(TR)) were measured to study the effects of Vi on contractile activation. When maximal force was inhibited by 40% with Vi pCa(50) decreased, but greater force inhibition at higher [Vi] did not further alter pCa(50). In contrast, the Ca(2+) sensitivity of k(TR) was unaffected by Vi. Interestingly, when force was inhibited by Vi k(TR) increased at submaximal levels of Ca(2+)-activated force. Additionally, k(TR) is faster at saturating Ca(2+) at [Vi] that inhibit force by > approximately 70%. The effects of Vi on k(TR) imply that k(TR) is determined not only by the intrinsic properties of the cross-bridge cycle, but also by cross-bridge contribution to thin filament activation.

Automated sample preparation and purification of homogenized brain tissues

A robotic homogenized tissue sample transferring method has been developed by using a Packard MultiProbe II 8-tip system. It enables robotically transferring homogenized tissue samples from individual test tubes into a 96-well format plate for further sample purification and analysis. Extensive validation has been made to establish the accuracy and variability of this method. This automatic tissue sample transferring approach combined with automatic tissue homogenization, has significantly increased the throughput of tissue sample preparation in screening of drug candidates using liquid chromatography coupled with highly sensitive and selective tandem mass spectrometry (LC-MS/MS).

Engineered CD8+ cytotoxic T cells with fiber-modified adenovirus-mediated TNF-alpha gene transfection counteract immunosuppressive interleukin-10-secreting lung metastasis and solid tumors

T-cell suppression derived from tumor-secreted immunosuppressive interleukin (IL)-10 becomes a major barrier to CD8+ T-cell immunotherapy of tumors. Tumor necrosis factor-alpha (TNF-alpha) is a multifunctional cytokine capable of activating T and dendritic cells (DCs) and counteracting IL-10-mediated DC inhibition and regulatory T-cell-mediated immune suppression. In this study, we constructed a recombinant adenovirus (MF)AdVTNF with fiber-gene modified by RGD insertion into the viral knob's H1 loop and a melanoma cell line B16(OVA/IL-10) engineered to express ovalbumin (OVA) and to secrete IL-10 (2.2 ng/ml/10(6) cells/24 h). We transfected OVA-specific CD8+ T cells with (MF)AdVTNF, and found a fivefold increase in transgene human TNF-alpha secretion (4.3 ng/ml/10(6) cells/24 h) by the engineered CD8+ T(TNF) cells transfected with (MF)AdVTNF, compared to that (0.8 ng/ml/10(6) cells/24 h) by CD8+ T cells transfected with the original AdVTNF without viral fiber modification. The engineered CD8+ T(TNF) cells exhibited enhanced cytotoxicity and elongated survival in vivo after adoptive transfer. TNF-alpha derived from both the donor CD8+ T cells and the host cells plays an important role in donor CD8+ T-cell survival in vivo after adoptive transfer. We also demonstrated that the transfected B16(OVA/IL-10) tumor cells secreting IL-10 are more resistant to in vivo CD8+ T-cell therapy than the original B16(OVA) tumor cells without IL-10 expression. Interestingly, the engineered CD8+ T(TNF) cells secreting transgene-coded TNF-alpha, but not the control CD8+ T(control) cells without any transgene expression eradicated IL-10-secreting 12-day lung micrometastasis in all 10/10 mice and IL-10-secreting solid tumors ( approximately 5 mm in diameter) in 6/10 mice. Transfer of the engineered CD8+ T(TNF) cells further induced both donor- and host-derived memory CD8+ T cells, leading to a stronger long-term antitumor immunity against the IL-10-secreting B16(OVA/IL-10) tumor cell challenges. Therefore, CD8+ T cells engineered to secrete TNF-alpha may be useful when designing strategies for adoptive T-cell therapy of solid tumors.

Dosimetry for a Study of Low-Dose Radiation Cataracts among Chernobyl Clean-up Workers

A cohort of 8,607 Ukrainian Chernobyl clean-up workers during 1986-1987 was formed to study cataract formation after ionizing radiation exposure. Study eligibility required the availability of sufficient exposure information to permit the reconstruction of doses to the lens of the eye. Eligible groups included civilian workers, such as those who built the "sarcophagus" over the reactor, Chernobyl Nuclear Power Plant Workers, and military reservists who were conscripted for clean-up work. Many of the official doses for workers were estimates, because only a minority wore radiation badges. For 106 military workers, electron paramagnetic resonance (EPR) measurements of extracted teeth were compared with the recorded doses as the basis to adjust the recorded gamma-ray doses and provide estimates of uncertainties. Beta-particle doses to the lens were estimated with an algorithm devised to take into account the nature and location of Chernobyl work, time since the accident, and protective measures taken. A Monte Carlo routine generated 500 random estimates for each individual from the uncertainty distributions of the gamma-ray dose and of the ratio of beta-particle to gamma-ray doses. The geometric mean of the 500 combined beta-particle and gamma-ray dose estimates for each individual was used in the data analyses. The median estimated lens dose for the cohort was 123 mGy, while 4.4% received >500 mGy.

Extensive nuclear localization of alpha-synuclein in normal rat brain neurons revealed by a novel monoclonal antibody

Synuclein was initially named for its localization in both presynaptic nerve terminals and portions of nuclear envelope. However, subsequent studies only confirmed the presynaptic localization of this protein in the brain; its nuclear localization in the neurons remained elusive. Here, two new monoclonal antibodies against alpha-synuclein (alpha-SYN) were produced. Epitope mapping using phage peptide display showed that the epitopes of the two antibodies were localized in two distinct specific sequences of the C-terminal domain of alpha-SYN. One antibody named 3D5 recognized amino acids 115-121 of alpha-SYN and the other antibody named 2E3 identified the amino acids 134-138 of the protein. Western blot analysis demonstrated that both 2E3 and 3D5 detected a 19 kD protein from rat and human brain homogenates, which was identical to the molecular size of recombinant alpha-SYN. However, immunohistochemical staining on normal adult rat brain sections showed that the two antibodies revealed distinct patterns of subcellular localization of alpha-SYN immunoreactivity. Both 3D5 and 2E3 detected the presynaptic alpha-SYN but only 3D5 detected the nuclear alpha-SYN. The nuclear localization of alpha-SYN was further confirmed by Western blot analysis in isolated nuclear fraction where the same size of alpha-SYN was detected, and by immunoelectron microscopy using colloidal gold probes where gold particles were specifically localized in portions of peri- and intra-nucleus. The nuclear positive neurons were distributed extensively in almost all the brain regions. This is the first report well characterizing the extensive localization of alpha-SYN in the neuronal nuclei throughout the brain in normal conditions. This finding indicates an important physiological function of this molecule in the nuclei of brain neurons, which deserves further investigations.

Cataracts among Chernobyl Clean-up Workers: Implications Regarding Permissible Eye Exposures

The eyes of a prospective cohort of 8,607 Chernobyl clean-up workers (liquidators) were assessed for cataract at 12 and 14 years after exposure. The prevalence of strictly age-related cataracts was low, as expected (only 3.9% had nuclear cataracts at either examination), since 90% of the cohort was younger than 55 years of age at first examination. However, posterior subcapsular or cortical cataracts characteristic of radiation exposure were present in 25% of the subjects. The data for Stage 1 cataracts, and specifically for posterior subcapsular cataracts, revealed a significant dose response. When various cataract end points were analyzed for dose thresholds, the confidence intervals all excluded values greater than 700 mGy. Linear-quadratic dose-response models yielded mostly linear associations, with weak evidence of upward curvature. The findings do not support the ICRP 60 risk guideline assumption of a 5-Gy threshold for "detectable opacities" from protracted exposures but rather point to a dose-effect threshold of under 1 Gy. Thus, given that cataract is the dose-limiting ocular pathology in current eye risk guidelines, revision of the allowable exposure of the human visual system to ionizing radiation should be considered.

Enhanced T-cell immunity induced by dendritic cells with phagocytosis of heat shock protein 70 gene-transfected tumor cells in early phase of apoptosis

The dual role of heat shock protein 70 (HSP70), as antigenic peptide chaperone and danger signal, makes it especially important in dendritic cell (DC)-based vaccination. In this study, we investigated the impacts of apoptotic transgenic MCA/HSP tumor cells expressing HSP70 on DC maturation, T-cell stimulation and vaccine efficacy. We found that DCs with phagocytosis of MCA/HSP in early phase of apoptosis expressed more pMHC I complexes, stimulated stronger cytotoxic T lymphocyte (CTL) responses (40% specific killing at an E:T cell ratio of 50) and induced immune protection in 90% of mice against MCA tumor cell challenge, compared with 25% specific CTL killing activity and 60% immune protection seen in mice immunized with DC with phagocytosis of MCA/HSP in late phase of apoptosis (P<0.05). Similar results were confirmed in another EG7 tumor model also expressing HSP70. Taken together, our data demonstrate that HSP70 on apoptotic tumor cells stimulate DC maturation, and DC with phagocytosis of apoptotic tumor cells expressing HSP70 in early phase of apoptosis more efficiently induced tumor-specific CTL responses and immunity than DCs with phagocytosis of apoptotic tumor cells in late phase of apoptosis. These results may have an important impact in designing DC-based antitumor vaccines.

159 LOCALIZATION OF CLAUDIN FAMILY PROTEINS IN PIG EMBRYOS DURING PRE-IMPLANTATION DEVELOPMENT

Tight junctions (TJ) are critical for blastocoel formation in mammalian pre-implantation embryos. Claudin family proteins, which are TJ proteins, are generally important for the barrier function of TJ. However, the expression and localization of claudin proteins are not clarified in mammalian pre-implantation embryos. The present study was designed to examine changes in the localization of claudin isoforms, claudin-1, -2, and -4, in pig parthenogenetic diploids through pre-implantation development. Oocyte–cumulus–granulosa cell complexes were collected from the follicles 4–6 mm in diameter, and then maturation-cultured. Only oocytes with a prominent first polar body were subjected to electro-stimulation after maturation, and they were treated with cytochalasin B to produce parthenogenetic diploids. Presumptive diploids were then cultured for 168 h and observed every 24 h. Embryos of each developmental stage from 2-cell to blastocyst were subjected to immunofluorescence staining of the anti-TJ proteins. Zona-free embryos were fixed and treated with rabbit anti-claudin-1 and -2 polyclonal antibodies or mouse anti-claudin-4 monoclonal antibody, followed by treatment with Alexa fluor 488-labeled goat anti-rabbit IgG antibody or goat anti-mouse IgG antibody. Some embryos were treated with rabbit anti-occludin antibody or anti-ZO-1 antibody for the detection of the TJ-net work. All embryos were counterstained with Hoechst 33342 and observed under an epifluorescence microscope after whole-mounting. The specific fluorescence for all TJ proteins examined was observed in embryos at all pre-implantation stages. Occludin and ZO-1 were detected in the cytoplasm before the morula stage (96 h), and localized toward the boundary region among cells from the morula and early blastocyst stages, reflecting the distribution of the tight junction in embryos. Claudin-1 and -2 localized in the cytoplasm at early-cleaving stages. They were detected in the nucleus after compaction, and the distribution of these proteins in the nucleus was dominant at the blastocyst stage. The distribution of the 2 claudin proteins in the nucleus was quite different; claudin-1 distributed rather homogeneously, but claudin-2 formed several bright spots in the nucleus. Claudin-4 also showed a unique distribution pattern in embryos; it was detected in the cytoplasm with strong fluorescence at the periphery of the nucleus of the 2- and 4-cell embryos. Claudin-4 changed its localization toward the boundary region of cells around the early blastocyst stage (120 h), and then the distribution of claudin-4 was restricted to the boundary region later in the blastocyst stage (144 h). These results indicate that claudin-4, but not claudin-1 and -2, is responsible for the formation of TJ in the pre-implantation embryos, although the function of these claudin proteins in the nucleus is unknown.

Progressive proliferative and dysplastic typhlocolitis in aging syrian hamsters naturally infected with Helicobacter spp.: a spontaneous model of inflammatory bowel disease

Helicobacter spp. have been implicated in a variety of gastrointestinal tract diseases, including peptic ulcer disease, gastric cancer, and inflammatory bowel disease (IBD), in humans and animals. Although most models of IBD are experimentally induced, spontaneous or natural models of IBD are rare. Herein, we describe a long-term study of chronic, progressive lesions that develop in the distal portion of the large bowel of unmanipulated Syrian hamsters naturally infected with Helicobacter spp. Twenty-four Syrian hamsters of three age groups (group A, 1 month [n = 4], group B, 7-12 months [n = 12], group C, 18-24 months [n = 12]), underwent complete postmortem examination. Results of microbial isolation and polymerase chain reaction and restriction fragment length polymorphism analyses confirmed the presence of Helicobacter spp. infection in the distal portion of the large bowel of all animals. Additionally, confounding pathogens, such as Clostridium difficile, Lawsonia intracellularis, and Giardia spp. that can cause proliferative enteritis, were absent in the hamsters of this study. Histopathologic scores for inflammation (P < 0.01), hyperplasia (P < 0.01), and dysplasia (P < 0.05) were significantly higher in the ileocecocolic (ICC) junction of animals in group C, relative to group A. Dysplastic lesions of various grades were detected in 5 of 11 hamsters in group C. Interestingly, the segment of the bowel that is usually colonized by Helicobacter spp. in hamsters had the most severe lesions. One hamster of group C developed a malignant fibrous histiocytoma, whereas another hamster developed a round cell sarcoma originating from the ICC junction. Thus, lesions in the distal portion of the large bowel of aging hamsters naturally colonized with Helicobacter spp. warrants developing the hamster as an animal model of IBD and potentially IBD-related cancer.