Gene discovery using the maize genome database ZmDB

Zea mays DataBase (ZmDB) is a repository and analysis tool for sequence, expression and phenotype data of the major crop plant maize. The data accessible in ZmDB are mostly generated in a large collaborative project of maize gene discovery, sequencing and phenotypic analysis using a transposon tagging strategy and expressed sequence tag (EST) sequencing. ESTs constitute most of the current content. Database search tools, convenient links to external databases, and novel sequence analysis programs for spliced alignment are provided and together serve as an efficient protocol for gene discovery by sequence inspection. ZmDB can be accessed at http://zmdb. iastate.edu. ZmDB also provides web-based ordering of materials generated in the project, including EST and genomic DNA clones, seeds of mutant plants and microarrays of amplified EST and genomic DNA sequences.

Recombinant hepatitis E capsid protein self-assembles into a dual-domain T = 1 particle presenting native virus epitopes

The three-dimensional structure of a self-assembled, recombinant hepatitis E virus particle has been solved to 22-A resolution by cryo-electron microscopy and three-dimensional image reconstruction. The single subunit of 50 kDa is derived from a truncated version of the open reading frame-2 gene of the virus expressed in a baculovirus system. This is the first structure of a T = 1 particle with protruding dimers at the icosahedral two-fold axes solved by cryo-electron microscopy. The protein shell of these hollow particles extends from a radius of 50 A outward to a radius of 135 A. In the reconstruction, the capsid is dominated by dimers that define the 30 morphological units. The outer domain of the homodimer forms a protrusion, which corresponds to the spike-like density seen in the cryo-electron micrograph. This particle retains native virus epitopes, suggesting its potential value as a vaccine.

Clinical implementation of wedge filter optimization in three-dimensional radiotherapy treatment planning

BACKGROUND AND PURPOSE

To describe a wedge filter optimization technique which automatically chooses the beam weights and wedge filters and to demonstrate the implementation of the algorithm in clinical three-dimensional (3D) radiotherapy treatment planning.

MATERIAL AND METHODS

Given the incident directions and beam energies of J beams, the dose distribution is a function of the beam weights, wedge angles, and wedge orientations. Instead of decomposing an incident field into a superposition of an open and two nominal wedged fields and then optimizing their weights, the algorithm optimizes the objective function with respect to the beam weights, wedge angles and wedge orientations directly. A salient feature of the algorithm is that no planner intervention was required in the selection of wedge filters during the optimization process. A dose-based objective function which incorporated the relative importance of structures was adopted in this work. The objective function was minimized by the method of simulated annealing. The technique was demonstrated by using a phantom study and two clinical cases.

RESULTS

For the phantom case, the classical wedge pair result was obtained, providing a useful test of the algorithm. Dose distributions and dose volume histograms for the target and surrounding organs were presented for the two clinical cases. It was also shown that dose homogeneity to the target could be compromised by increasing the relative importance factors to the surrounding organs.

CONCLUSIONS

A 3D wedge filter optimization algorithm has been developed. The technique has the potential to fully automate the 3D radiotherapy treatment planning process. In addition, treatment planning time and efforts were significantly reduced.

Comparative molecular field analysis as a tool to evaluate mode of action of chemical hybridization agents

The 3D-QSAR method of comparative molecular field analysis (CoMFA) was applied to three patent families of chemical hybridization agents (CHAs) in the MON21200 class of chemistry. The models for each CHA family gave good correlations between the variations in log percent male sterility and in the steric-electrostatic properties of the patent set. For all CHA families, observed sterility rates are generally higher for the sodium salts than for the corresponding esters. This is consistent with our CoMFA models which show that negative charge is favored in the region of the carboxylate group. The CoMFA models also indicated that for the MON21200 family increased steric bulk at the 4-position on the phenyl ring is associated with enhanced activity. However, for the RH0007 and the HYBRID families, male sterility is generally enhanced with increased steric bulk at the 2- or 3-position on the phenyl ring. Although the models cannot provide unambiguous conclusions about a common mode of action, similarities in the CoMFA contour maps provided some clues for a common agrophore for these three CHA families.

Estimation theory and model parameter selection for therapeutic treatment plan optimization

Treatment optimization is usually formulated as an inverse problem, which starts with a prescribed dose distribution and obtains an optimized solution under the guidance of an objective function. The solution is a compromise between the conflicting requirements of the target and sensitive structures. In this paper, the treatment plan optimization is formulated as an estimation problem of a discrete and possibly nonconvex system. The concept of preference function is introduced. Instead of prescribing a dose to a structure (or a set of voxels), the approach prioritizes the doses with different preference levels and reduces the problem into selecting a solution with a suitable estimator. The preference function provides a foundation for statistical analysis of the system and allows us to apply various techniques developed in statistical analysis to plan optimization. It is shown that an optimization based on a quadratic objective function is a special case of the formalism. A general two-step method for using a computer to determine the values of the model parameters is proposed. The approach provides an efficient way to include prior knowledge into the optimization process. The method is illustrated using a simplified two-pixel system as well as two clinical cases. The generality of the approach, coupled with promising demonstrations, indicates that the method has broad implications for radiotherapy treatment plan optimization.

Matching photon and electron fields with dynamic intensity modulation

A technique was developed to reduce the size and magnitude of the hot and cold spots in the abutting regions of photon and electron fields. The photon and electron fields were set up such that the photon field extended approximately 2 cm into the electron field in the abutting region. The region of the photon beam that overlapped the electron field was modulated using a multileaf collimator, effectively broadening the photon penumbra to make it complimentary to the electron penumbra. The computer calculations were verified using film measurements for abutting a 6 MV photon beam with a 9 MeV electron beam. A uniform dose was achieved at a prespecified depth of 2 cm, and dose uniformity was improved at the specified depth and beyond compared with unmodulated photon beams. A slight increase in dose inhomogeneity was seen at shallower depths. The overall areas of the hot and cold spots were significantly reduced. The technique also reduced the sensitivity of dose homogeneity to setup errors such that the magnitudes of the hot and cold spots were about half of those produced with unmodulated photon beam when an overlap or gap of 4 mm was introduced. The technique was applied to the treatment of a head and neck cancer and a lymphoma involving the right pleura with markedly reduced dose inhomogeneity in the abutting regions.

Optimization of importance factors in inverse planning

Inverse treatment planning starts with a treatment objective and obtains the solution by optimizing an objective function. The clinical objectives are usually multifaceted and potentially incompatible with one another. A set of importance factors is often incorporated in the objective function to parametrize trade-off strategies and to prioritize the dose conformality in different anatomical structures. Whereas the general formalism remains the same, different sets of importance factors characterize plans of obviously different flavour and thus critically determine the final plan. Up to now, the determination of these parameters has been a 'guessing' game based on empirical knowledge because the final dose distribution depends on the parameters in a complex and implicit way. The influence of these parameters is not known until the plan optimization is completed. In order to compromise properly the conflicting requirements of the target and sensitive structures, the parameters are usually adjusted through a trial-and-error process. In this paper, a method to estimate these parameters computationally is proposed and an iterative computer algorithm is described to determine these parameters numerically. The treatment plan selection is done in two steps. First, a set of importance factors are chosen and the corresponding beam parameters (e.g. beam profiles) are optimized under the guidance of a quadratic objective function using an iterative algorithm reported earlier. The 'optimal' plan is then evaluated by an additional scoring function. The importance factors in the objective function are accordingly adjusted to improve the ranking of the plan. For every change in the importance factors, the beam parameters need to be re-optimized. This process continues in an iterative fashion until the scoring function is saturated. The algorithm was applied to two clinical cases and the results demonstrated that it has the potential to improve significantly the existing method of inverse planning. It was noticed that near the final solution the plan became insensitive to small variations of the importance factors.

Synchronizing dynamic multileaf collimators for producing two-dimensional intensity-modulated fields with minimum beam delivery time

PURPOSE

Leaf motion synchronization of dynamic multileaf collimators (DMLC) for intensity-modulated radiotherapy (IMRT) is important in improving dose distribution and reducing "tongue-and-groove" effects for a prescribed intensity profile. Leaf synchronization could also be used in transforming a one-dimensional leaf-setting algorithm into a two-dimensional leaf-setting algorithm. In this work, we aim to develop a generalized leaf synchronization method for delivering IMRT with the minimized beam delivery time and the optimized subfield variations for a leaf-setting sequence.

METHODS AND MATERIALS

With the leaf synchronization procedure, all active MLC leaf pairs start and finish off a leaf sequence simultaneously. In this work, the MLC leaf pairs were synchronized under the condition that the resulting leaf sequence produces the desired intensity profile with the minimum beam delivery time. The parameter of the leaf synchronization function was determined through the least-square minimization of the area variations of all subfields within a leaf sequence. The leaf synchronization and optimization procedure were applied and analyzed for clinical relevant intensity profiles for treating the head-and-neck cancer patients using IMRT.

RESULTS

The total monitor units and the optimized beam delivery time of generating a two-dimensional intensity profile was proven through this work to be the global minimum of all leaf-setting sequences including the unsynchronized leaf-setting sequences. The optimized parameter for subfield variations of the synchronized leaf trajectories was found to be dependent on individual intensity profiles. For all our studied cases, the unsynchronized leaf trajectories always have significantly larger subfield variations than the synchronized leaf trajectories.

CONCLUSION

It is important and also feasible to synchronize and optimize dynamic MLC leaf motions while still keeping the total beam delivery time minimum for delivering arbitrary two-dimensional intensity-modulated fields.

Required and nonessential functions of nuclear factor-kappa B in bone cells

Nuclear factor-kappa B (NF-kappaB) is a set of five polypeptide transcription factors, called p50, p52, p65 (also called Rel A), Rel B, and c-Rel, which regulate the expression of a variety of genes involved in immune and inflammatory responses. They were originally named because they were considered essential regulators of B cell kappa light chain expression. More recent studies indicate that NF-kappaB proteins are involved in the regulation of a variety of other cell functions, including cell proliferation, responses to stress, and apoptosis. NF-kappaB heterodimers reside in the cytoplasm of cells bound to inhibitory proteins, the two commonest of which are IkappaBalpha and IkappaBbeta, which prevent NF-kappaB from entering the nucleus. When cells are stimulated, IkappaB is phosphorylated by specific IkappaB kinases and subsequently is ubiquitinated and degraded in proteosomes. This allows NF-kappaB to translocate to the nucleus to regulate the expression of a growing list of genes, including the proinflammatory cytokines, interleukin-1 (IL-1), IL-6, and tumor necrosis factor. IL-1 and tumor necrosis factor in turn also regulate the expression of NF-kappaB. Thus, once activated, NF-kappaB may be involved in upregulatory loops, which can amplify the effects of the initiating stimulus. Because these proinflammatory cytokines have been implicated in the pathogenesis of estrogen deficiency and inflammation-related bone loss, it is likely that NF-kappaB has a significant role in the increased generation and function of osteoclasts in these circumstances. However, an unexpected and essential role of NF-kappaB in the formation of osteoclasts during development was discovered recently after the generation of knockout mice, which lack the expression of the p50 and p52 subunits. This paper will describe recent studies that reveal an essential role for NF-kappaB signaling in the generation of osteoclasts and that suggest that NF-kappaB may also play a key central role in the activation and survival of osteoclasts in conditions in which osteoclastogenesis is upregulated.

Dental abnormalities associated with failure of tooth eruption in src knockout and op/op mice

c-src knockout and op/op mice develop osteopetrosis as a result of defective osteoclast function and osteoclast formation, respectively. The mutant mice can be distinguished readily from their wild-type littermates around 10-12 days after birth because their incisors do not erupt, but the morphology of their teeth and surrounding bone has not been reported previously in detail. Histologic examination of jaws of src-mutant mice reveals unerupted, abnormal incisors within their bony crypts. The tooth roots are distorted by foci of haphazard proliferation of odontogenic epithelium associated with primitive tooth structures that strongly resemble the tumor-like lesions in humans, known as odontomas. The crowns of the incisors are fused to the adjacent bone, and the developing periodontal ligament is disordered and hypocellular. Osteoclasts are present in the bone surrounding the distorted teeth, but as in other bones in these mice they lack ruffled borders and thus do not resorb effectively. Similar odontogenic proliferation is present around unerupted incisors in op/op mice which form very few osteoclasts, but the amount is significantly less than in src mutant mice. Molars fail to erupt in both types of mutant mice, but they are not accompanied by aberrant odontogenic proliferation. These findings and previous reports of similar abnormalities in jaws from op/op rats suggest that failure of incisor eruption and associated proliferation of odontogenic epithelium in osteopetrotic rodents are a direct result of defective osteoclastic bone resorption.

[Cloning of glycoprotein B gene from strain Rispens of Marek's disease virus and construction of recombinant fowlpox virus]

Purified DNAs from Chicken Embryo Fibroblast (CEF) cultures infected with MDV strain Rispens were used as templates. Specific fragment with the size of about 2.9 kb was successfully amplified through Polymerase Chain Reaction(PCR) and identified to be gB gene of MDV by dot blot hybridization with a digoxigenin-labelled MDV gB specific oligonucleotide probe. The gB gene from strain Rispens was cloned into pUC19 and FPV insertion vector pFG1175-1 to construct plasmid pMGB and pFGBR1775-1 respectively. DOSPER liposome-mediated transfection with insertion vector DNA pFGBR1175-1 was performed on CEF monolayers infected with FPV 3-4 h earlier. Recombinant FPV was clone purified. Immunofluorescence Assay(IFA) showed that MDV gB gene had been expressed in FPV.

A recombinant fowlpox virus vaccine expressing glycoprotein B gene from CVI988/Rispens strain of MDV: protection studies in different chickens

Recombinant fowlpox virus (rFPV) was constructed to express glycoprotein B (gB) gene from CVI988/Rispens strain of Marek's disease virus (MDV). The rFPV-gB/R alone and in combination with herpesvirus of turkey (HVT) preparations were evaluated for their protective efficacy against challenge with very virulent MDV strains Md5 and RB1B in different chickens. The rFPV-gB/R alone induced protection comparable to that by HVT vaccines in both Ab- SPF chickens and Ab+ production chickens. Significant protective synergism was observed in one of these two types of commercial production chickens when rFPV-gB/R was combined with HVT of either cell-associated or cell-free preparations. Immunogenesis studies showed that rFPV-gB/R, just like conventional vaccines, significantly reduced the level of viremia, splenocytes infection and feather follicle shedding of challenge virus in vaccinated chickens.

Interferon-induced guanylate binding protein-1 (GBP-1) mediates an antiviral effect against vesicular stomatitis virus and encephalomyocarditis virus

A cDNA encoding the human guanylate binding protein-1 (hGBP-1) was expressed in HeLa cells using a constitutive expression vector. Stably transfected clones expressing hGBP-1 exhibited resistance to the cytopathic effect mediated by both vesicular stomatitis virus (VSV) and encephalomyocarditis virus (EMCV) and produced less viral progeny than control cells following infection with these viruses. To study the role hGBP-1 plays in the IFN-mediated antiviral effect, cells were stably transfected with a construct expressing antisense RNA for hGBP-1. VSV infection of IFN-alpha-treated antisense RNA-expressing cells produced an amount of virus comparable to that produced in the parental cell line, while EMCV infection of the IFN-alpha-treated transfected cells and VSV and EMCV infection of the IFN-gamma-treated transfected cells produced far more virus than was produced in the parental cell line. These results demonstrate that GBP-1 mediates an antiviral effect against VSV and EMCV and plays a role in the IFN-mediated antiviral response against these viruses.

Identification of a novel activation-inducible protein of the tumor necrosis factor receptor superfamily and its ligand

Among members of the tumor necrosis factor receptor (TNFR) superfamily, 4-1BB, CD27, and glucocorticoid-induced tumor necrosis factor receptor family-related gene (GITR) share a striking homology in the cytoplasmic domain. Here we report the identification of a new member, activation-inducible TNFR family member (AITR), which belongs to this subfamily, and its ligand. The receptor is expressed in lymph node and peripheral blood leukocytes, and its expression is up-regulated in human peripheral mononuclear cells mainly after stimulation with anti-CD3/CD28 monoclonal antibodies or phorbol 12-myristate 13-acetate/ionomycin. AITR associates with TRAF1 (TNF receptor-associated factor 1), TRAF2, and TRAF3, and induces nuclear factor (NF)-kappaB activation via TRAF2. The ligand for AITR (AITRL) was found to be an undescribed member of the TNF family, which is expressed in endothelial cells. Thus, AITR and AITRL seem to be important for interactions between activated T lymphocytes and endothelial cells.

Recent advances in bone biology provide insight into the pathogenesis of bone diseases

Bone is modeled during embryonic development by endochondral and membranous ossification and is continuously remodeled thereafter under the influence of local and systemic factors to provide structural support and assist in calcium homeostasis. Recent studies of knockout and transgenic mice have increased understanding of the regulation of bone modeling during development and of remodeling of mature bone and have shed new light on the pathogenesis of a number of bone disorders. For example, fibroblast growth factor receptor-3, parathyroid hormone-related protein, and tartrate-resistant acid phosphatase affect the function of chondrocytes during endochondral ossification (the latter two by regulating their life spans and thus growth plate thickness and bone length). Some ubiquitously expressed genes seem unexpectedly to have unique functions that are largely confined to bone cells: M-CSF, C-Fos, PU.1, and NF-kappaB are required for osteoclast formation, whereas c-Src and Mitf (microphthalmia transcription factor) are required for osteoclast activity after the cells have formed. Knockout of these genes results in osteopetrosis, a disorder characterized by persistence in marrow cavities of unresorbed osteocartilaginous matrix and, as in some affected humans, by increased mortality. Some proteins seem to act as negative regulators of bone cell function, for example osteoprotegerin (a soluble TNF receptor) in osteoclasts; osteocalcin, bone sialoprotein, and 5-lipoxygenase in osteoblasts. Regulation of osteoclast life span may be an important mechanism by which estrogen and bisphosphonates prevent bone loss in conditions characterized by increased bone resorption, such as postmenopausal osteoporosis. The unique requirement of bone cells for certain gene products raises the possibility that these cells may have specific responses to inhibitory or stimulatory agents, and that signaling molecules in these response pathways could be specific targets for novel therapies to treat or prevent common bone diseases.

Dosimetric verification of a commercial inverse treatment planning system

A commercial three-dimensional (3D) inverse treatment planning system, Corvus (Nomos Corporation, Sewickley, PA), was recently made available. This paper reports our preliminary results and experience with commissioning this system for clinical implementation. This system uses a simulated annealing inverse planning algorithm to calculate intensity-modulated fields. The intensity-modulated fields are divided into beam profiles that can be delivered by means of a sequence of leaf settings by a multileaf collimator (MLC). The treatments are delivered using a computer-controlled MLC. To test the dose calculation algorithm used by the Corvus software, the dose distributions for single rectangularly shaped fields were compared with water phantom scan data. The dose distributions predicted to be delivered by multiple fields were measured using an ion chamber that could be positioned in a rotatable cylindrical water phantom. Integrated charge collected by the ion chamber was used to check the absolute dose of single- and multifield intensity modulated treatments at various spatial points. The measured and predicted doses were found to agree to within 4% at all measurement points. Another set of measurements used a cubic polystyrene phantom with radiographic film to record the radiation dose distribution. The films were calibrated and scanned to yield two-dimensional isodose distributions. Finally, a beam imaging system (BIS) was used to measure the intensity-modulated x-ray beam patterns in the beam's-eye view. The BIS-measured images were then compared with a theoretical calculation based on the MLC leaf sequence files to verify that the treatment would be executed accurately and without machine faults. Excellent correlation (correlation coefficients > or = 0.96) was found for all cases. Treatment plans generated using intensity-modulated beams appear to be suitable for treatment of irregularly shaped tumours adjacent to critical structures. The results indicated that the system has potential for clinical radiation treatment planning and delivery and may in the future reduce treatment complexity.

Theoretical considerations of monitor unit calculations for intensity modulated beam treatment planning

A treatment planning system to compute intensity modulated radiotherapy (IMRT) treatments using inverse planning was investigated. The system was designed to optimize the intensity patterns required to treat a specified target volume with specified normal structure constraints. A beam model that uses the convolution of pencil beams was used to compute the dose distributions. A multileaf collimator leaf-setting sequence intended to produce the intensity pattern was computed along with the monitor units required to deliver each of a number of fixed-gantry modulated fields. Computer calculations are commonly verified using an independent manual procedure. It is difficult to calculate treatment delivery monitor units for this variant of IMRT using manual methods. Since manual calculations are not feasible, it is important both to understand and to verify the calculation of treatment monitor units by the planning system algorithm. A formal analysis was made of the dose calculation model and the monitor unit calculation embedded in the algorithm. Experimental verification of the dose delivered by plans computed with the methodology demonstrated an agreement of better than 4% between the dose model and measurements.

Functional implications of genetic interactions between genes encoding small GTPases involved in vesicular transport in yeast

Ras-related, guanine nucleotide-binding proteins of the Ypt/Rab family play a key role at defined steps in vesicular transport, both in yeast and in mammalian cells. In yeast, Ypt1p has an essential function late in endoplasmic reticulum (ER) to Golgi transport, and the redundant Ypt31/Ypt32 GTPases have been proposed to act in transport through and/or from the Golgi. Here we report that mutant alleles of YPT31 and YPT32, whose gene products have a reduced affinity for GTP, are able to suppress the dominant lethal phenotype of YPT1(N121I). Co-expression of YPT1(N121I) and the suppressor YPT31(N126I) allow essentially undisturbed secretory transport in the absence of the respective wild-type GTPases. Such mutant cells massively overaccumulate 60-100 nm vesicles and are heat sensitive. It appears likely that the mutant GTPases, which are defective in nucleotide binding, compete for the binding of common interacting protein(s). These and other genetic interactions between YPT1, YPT31/32, ARF1 and SEC4 described here strongly support the view that Ypt31p and Ypt32p have a central, Golgi-associated function in anterograde or retrograde transport.

Identification and characterization of immunoreactive calcitonin gene-related peptide from lymphocytes of the rat

There is accumulating evidence that the immune system can produce neuropeptides. In the light of these facts, we obtained direct evidences to prove that T lymphocytes also synthesize and secrete calcitonin gene-related peptide (CGRP), a neuropeptide localized within primary sensory nerves. By using CGRP specific RIA, CGRP-like immunoreactivity (LI) was found in the extracts of rat lymphocytes from thymus and mesenteric lymph node. The intracellular concentration of lymphocyte-derived CGRP-LI of rat thymus and mesenteric lymph node was 745+/-39 and 447+/-33 fg/10(6) cells, respectively. CGRP-LI in lymphocytes was shown to co-elute with synthetic rat CGRP and sensory neuron-derived CGRP by reverse-phase HPLC. In addition, the CGRP-LI located in the T lymphocytes was also shown by immunocytochemical method examined by electron microscopy. The CGRP mRNA detected by RT-PCR was also present in these lymphocytes and was also identified to be the same one in sensory neurons. These data suggest that CGRP is synthesized and secreted in T lymphocytes of both thymus and lymph node in the rat, and this is identified to be the same one in neuronal tissue. Lymphocyte-derived CGRP may act in an autocrine/paracrine mode and play an important role in certain physiological and pathophysiological conditions.

Physical characteristics of a miniature multileaf collimator

A preliminary study of the physical characteristics of a miniature multileaf collimator (mMLC) used with 4 MV x rays is reported. The mMLC attached to the accessory mount of a class C or D Varian linear accelerator (Varian Oncology Systems, Palo Alto, CA) with a source to aperture distance of 65 cm. The field penumbra using the small leaves was found to be consistent with the anticipated field penumbra using photon jaws at the same source to aperture distance as the mMLC. The percentage depth dose values of square fields were found to be consistent with the fields collimated with the upper and lower jaws. Output factors for the very small fields were found to vary rapidly. Circular fields could be produced with depth dose characteristics similar to those produced using conical tertiary collimators, commonly used for radiosurgery, but with a broader penumbra.

Comparison of estrogen receptor alpha and beta subtypes based on comparative molecular field analysis (CoMFA)

A substantial body of evidence indicates that both humans and wildlife suffer adverse health effects from exposure to environmental chemicals that are capable of interacting with the endocrine system. The recent cloning of the estrogen receptor beta subtype (ER-beta) suggests that the selective effects of estrogenic compounds may arise in part by the control of different subsets of estrogen-responsive promoters by the two ER subtypes, ER-alpha and ER-beta. In order to identify the structural prerequisites for ligand-ER binding and to discriminate ER-alpha and ER-beta in terms of their ligand-binding specificities, Comparative Molecular Field Analysis (CoMFA) was employed to construct a three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) model on a data set of 31 structurally-diverse compounds for which competitive binding affinities have been measured against both ER-alpha and ER-beta. Structural alignment of the molecules in CoMFA was achieved by maximizing overlap of their steric and electrostatic fields using the Steric and Electrostatic ALignment (SEAL) algorithm. The final CoMFA models, generated by correlating the calculated 3D steric and electrostatic fields with the experimentally observed binding affinities using partial least-squares (PLS) regression, exhibited excellent self-consistency (r2 > 0.99) as well as high internal predictive ability (q2 > 0.65) based on cross-validation. CoMFA-predicted values of RBA for a test set of compounds outside of the training set were consistent with experimental observations. These CoMFA models can serve as guides for the rational design of ER ligands that possess preferential binding affinities for either ER-alpha or ER-beta. These models can also prove useful in risk assessment programs to identify real or suspected EDCs.

VEGI, a novel cytokine of the tumor necrosis factor family, is an angiogenesis inhibitor that suppresses the growth of colon carcinomas in vivo

A novel member of the tumor necrosis factor (TNF) family has been identified from the human umbilical vein endothelial cell cDNA library, named vascular endothelial growth inhibitor (VEGI). The VEGI gene was mapped to human chromosome 9q32. The cDNA for VEGI encodes a protein of 174 amino acid residues with the characteristics of a type II transmembrane protein. Its amino acid sequence is 20-30% identical to other members of the TNF family. Unlike other members of the TNF family, VEGI is expressed predominantly in endothelial cells. Local production of a secreted form of VEGI via gene transfer caused complete suppression of the growth of MC-38 murine colon cancers in syngeneic C57BL/6 mice. Histological examination showed marked reduction of vascularization in MC-38 tumors that expressed soluble but not membrane-bound VEGI or were transfected with control vector. The conditioned media from soluble VEGI-expressing cells showed marked inhibitory effect on in vitro proliferation of adult bovine aortic endothelial cells. Our data suggest that VEGI is a novel angiogenesis inhibitor of the TNF family and functions in part by directly inhibiting endothelial cell proliferation. The results further suggest that VEGI maybe highly valuable toward angiogenesis-based cancer therapy.

A three-dimensional algorithm for optimizing beam weights and wedge filters

An essential step towards optimizing and automating radiation therapy treatment planning is to develop an effective algorithm to find the optimal beam weights and wedge filters for a given set of beam directions and modalities. This problem is solved by introducing a variable transformation based on the universal and omni wedge principles. Instead of directly optimizing an objective function with respect to wedge angles and orientations, each field is first decomposed into a superposition of an open field and two orthogonal wedged fields. This transforms the problem of finding J beam weights, wedge angles, and orientations to that of optimizing a system with 3J beam weights (J open beams and 2J nominal wedged beams), where J is the total number of incident beam directions. An iterative algorithm based on a method originally developed for image reconstruction is used to find the 3J beam weights. The technique is applied to a few clinical cases. Treatment plans are improved compared to those obtained through the conventional manual trial and error planning process. In addition, planning time and effort are greatly reduced.

Fast iterative algorithms for three-dimensional inverse treatment planning

Three types of iterative algorithms, algebraic inverse treatment planning (AITP), simultaneous iterative inverse treatment planning (SIITP), and iterative least-square inverse treatment planning (ILSITP), differentiated according to their updating sequences, were generalized to three dimension with true beam geometry and dose model. A rapid ray-tracing approach was developed to optimize the primary beam components. Instead of recalculating the dose matrix at each iteration, the dose distribution was generated by scaling up or down the dose matrix elements of the previous iteration. This significantly increased the calculation speed. The iterative algorithms started with an initial intensity profile for each beam, specified by a two-dimensional pixel beam map of M elements. The calculation volume was divided into N voxels, and the calculation was done by repeatedly comparing the calculated and desired doses and adjusting the values of the beam map elements to minimize an objective function. In AITP, the iteration is performed voxel by voxel. For each voxel, the dose discrepancy was evaluated and the contributing pencil beams were updated. In ILSITP and SIITP, the iteration proceeded pencil beam by pencil beam instead of voxel by voxel. In all cases, the iteration procedure was repeated until the best possible dose distribution was achieved. The algorithms were applied to two examples and the results showed that the iterative techniques were able to produce superior isodose distributions.

LIGHT, a novel ligand for lymphotoxin beta receptor and TR2/HVEM induces apoptosis and suppresses in vivo tumor formation via gene transfer

LIGHT is a new member of tumor necrosis factor (TNF) cytokine family derived from an activated T cell cDNA library. LIGHT mRNA is highly expressed in splenocytes, activated PBL, CD8(+) tumor infiltrating lymphocytes, granulocytes, and monocytes but not in the thymus and the tumor cells examined. Introduction of LIGHT cDNA into MDA-MB-231 human breast carcinoma caused complete tumor suppression in vivo. Histological examination showed marked neutrophil infiltration and necrosis in LIGHT expressing but not in the parental or the Neo-transfected MDA-MB-231 tumors. Interferon gamma (IFNgamma) dramatically enhances LIGHT-mediated apoptosis. LIGHT protein triggers apoptosis of various tumor cells expressing both lymphotoxin beta receptor (LTbetaR) and TR2/HVEM receptors, and its cytotoxicity can be blocked specifically by addition of a LTbetaR-Fc or a TR2/HVEM-Fc fusion protein. However, LIGHT was not cytolytic to the tumor cells that express only the LTbetaR or the TR2/HVEM or hematopoietic cells examined that express only the TR2/HVEM, such as PBL, Jurkat cells, or CD8(+) TIL cells. In contrast, treatment of the activated PBL with LIGHT resulted in release of IFNgamma. Our data suggest that LIGHT triggers distinct biological responses based on the expression patterns of its receptors on the target cells. Thus, LIGHT may play a role in the immune modulation and have a potential value in cancer therapy.

An optimized leaf-setting algorithm for beam intensity modulation using dynamic multileaf collimators

A leaf-setting algorithm is developed for generating arbitrary beam intensity profiles in discrete levels using dynamic multileaf collimators (DMLCs). The algorithm starts with the algebraic expression for the area under the beam profile. It is shown that the coefficients in this expression can be transformed into the specifications for the leaf-setting sequence. It is proven that the algorithm optimizes beam delivery time and total monitor units for the DMLC leaf setting for intensity modulated radiotherapy (IMRT). The algorithm is demonstrated to be applicable to both the 'step-and-shoot' and 'dynamic' type of beam delivery. The graphical interpretation and numerical implementation scheme of the algorithm is illustrated using a simplified example.

A test of the background selection hypothesis based on nucleotide data from Drosophila ananassae

We estimated DNA sequence variation within and between four populations of Drosophila ananassae at Om(1D) and vermilion (v) by using single-strand conformation polymorphism analysis and direct DNA sequencing. Om(1D) is located on the X chromosome in a region with a normal recombination rate; v is in a region of low recombination. In each population, levels of nucleotide diversity at v are reduced 10- to 25-fold relative to those at Om(1D). Divergence between D. ananassae and its sibling species D. pallidosa, however, is comparable for both loci. This lack of correlation between levels of polymorphism and divergence led to the rejection of a constant-rate, neutral model. To distinguish among alternative models, we propose a test of the background selection hypothesis based on the observed pattern of differentiation between populations. Although the degree of differentiation (measured by FST) among all pairs of subpopulations is similar at Om(1D), we found substantial differences at v. The two northern populations from Burma and Nepal are very homogeneous, whereas comparisons between northern and southern populations (e.g., between Nepal and middle India) produced large FST values. A coalescent-based simulation of the background selection model (in a geographically structured species with a finite number of demes) showed that the observed homogeneity among the northern populations is inconsistent with the background selection hypothesis. Instead, it may have been caused by a recent hitchhiking event that was limited to the northern species range.

Morphological evidence for the location of calcitonin gene-related peptide (CGRP) immunoreactivity in rat lymphocytes

Calcitonin gene-related peptide (CGRP) is widely distributed in sensory neurons and nerve fibers. It was shown recently in our laboratory that there was CGRP-immunoreactivity (CGRP-ir) in extract of rat lymphocyte of thymus and mesenteric lymph node by radioimmunoassay and reversed-phase HPLC. The aim of this study was to detect the CGRP-ir location in the rat lymphocyte by immunocytochemical method. Single cells isolated from thymus and mesenteric lymph node of male Wistar rat (200-250 g) were suspended in RPMI-1640 medium. After adhesion to plate wall and through nylon wool fiber columns, T cell-riched suspension was obtained. Immunocytochemical ABC method was performed in cell suspension, the specific antiserum (1:200 diluted) was rabbit anti-human CGRP. The cells were examined under light microscope after smeared on glass slide by Shandon Cytospin. The results showed that some lymphocytes were CGRP-ir positive. The positive granules were seen as ring, plaque, cap or spot distributing on the surface or inside the cell. The results indicate that CGRP-ir may be located in some rat T lymphocytes. This work provides new information about the interaction between the nervous and the immune systems. The functional significance of CGRP located in lymphocytes needs to be further studied.

Mesolimbic expression of neurotensin and neurotensin receptor during stress-induced gastric mucosal injury

Neurotensin is a neurotransmitter present in the brain and gastrointestinal tract. Intracerebroventricular injection of neurotensin protects rats from gastric mucosal injury caused by cold water restraint (CWR). Direct injection of neurotensin into the nucleus accumbens (NACB), part of the mesolimbic dopamine system, reduces gastric mucosal injury, suggesting that neurotensin confers protection on the mucosa through interaction with the mesolimbic system. The hypothesis is that the concentration of neurotensin in the mesolimbic system decreases during CWR, affecting the expression of neurotensin and the neurotensin receptor. After 1 h of CWR, neurotensin concentration significantly decreased 41% in the NACB and returned toward control concentrations after 2 h of CWR. The concentration of neurotensin mRNA significantly decreased 46% after 1 h CWR and returned toward control after 2 h. In contrast, neurotensin binding sites in the NACB increased from 159 to 228 fmol/mg protein after 1 h of CWR and increased significantly to 280 fmol/mg protein after 2 h CWR, whereas the level of neurotensin receptor mRNA significantly decreased 51 and 50% at 1 and 2 h, respectively. These studies show that neurotensin concentration within the mesolimbic system is transiently reduced by CWR stress and that the number of neurotensin binding sites increases, presumably in response to the decrease in neurotensin.

Requirement for NF-kappaB in osteoclast and B-cell development

NF-kappaB is a family of related, dimeric transcription factors that are readily activated in cells by signals associated with stress or pathogens. These factors are critical to host defense, as demonstrated previously with mice deficient in individual subunits of NF-kappaB. We have generated mice deficient in both the p50 and p52 subunits of NF-kappaB to reveal critical functions that may be shared by these two highly homologous proteins. We now demonstrate that unlike the respective single knockout mice, the p50/p52 double knockout mice fail to generate mature osteoclasts and B cells, apparently because of defects that track with these lineages in adoptive transfer experiments. Furthermore, these mice present markedly impaired thymic and splenic architectures and impaired macrophage functions. The blocks in osteoclast and B-cell maturation were unexpected. Lack of mature osteoclasts caused severe osteopetrosis, a family of diseases characterized by impaired osteoclastic bone resorption. These findings now establish critical roles for NF-kappaB in development and expand its repertoire of roles in the physiology of differentiated hematopoietic cells.

Rescue of osteoclast function by transgenic expression of kinase-deficient Src in src-/- mutant mice

The Src tyrosine kinase has been implicated in a wide variety of signal transduction pathways, yet despite the nearly ubiquitous expression of c-src, src-/- mice show only one major phenotype-osteopetrosis caused by an intrinsic defect in osteoclasts, the cells responsible for resorbing bone. To explore further the role of Src both in osteoclasts and other cell types, we have generated transgenic mice that express the wild-type and mutated versions of the chicken c-src proto-oncogene from the promoter of tartrate resistant acid phosphatase (TRAP), a gene that is expressed highly in osteoclasts. We demonstrate here that expression of a wild-type transgene in only a limited number of tissues can fully rescue the src-/- phenotype. Surprisingly, expression of kinase-defective alleles of c-src also reduces osteopetrosis in src-/- animals and partially rescues a defect in cytoskeletal organization observed in src-/- osteoclasts. These results suggest that there are essential kinase-independent functions for Src in vivo. Biochemical examination of osteoclasts from these mice suggest that Src may function in part by recruiting or activating other tyrosine kinases.

QSAR models for binding of estrogenic compounds to estrogen receptor alpha and beta subtypes

We have developed Quantitative Structure-Activity Relationship (QSAR) models based on Comparative Molecular Field Analysis (CoMFA) for 31 estrogenic chemicals whose relative binding affinity (RBA) is available for both ER-alpha and ER-beta. The models demonstrated a significant correlation (r2>0.95) between the CoMFA-calculated steric/electrostatic fields and corresponding RBA data and a good predictive capability (q2>0.6) based on cross-validation. The CoMFA models and contour plots obtained for ER-alpha and ER-beta suggest a close similarity between the receptors in terms of mode of binding and provide a rational basis for ligand selectivity.

Antitumor activity of the novel human breast cancer growth inhibitor, mammary-derived growth inhibitor-related gene, MRG

A novel human tumor growth inhibitor was identified by differential cDNA sequencing. The predicted amino acid sequence of this tumor-suppressing factor has a significant sequence homology to mouse mammary-derived growth inhibitor and thus was named mammary-derived growth inhibitor-related gene (MRG). MRG was found to be expressed in normal and benign human breast tissues but not in breast carcinomas. In situ hybridization analysis demonstrated a stage-specific MRG expression as follows. MRG was barely detectable in breast carcinomas, showed partial and weak expression in benign hyperplasia, but was expressed at a high level in normal breast epithelial cells. To determine if MRG can modulate in vivo growth of human breast cancers, we transfected a full-length MRG cDNA into MDA-MB-231 human breast cancer cells and studied the orthotopic growth of MRG transfectants versus control transfectants in the mammary fat pad of athymic nude mice. Overexpression of MRG in human breast cancer cells significantly suppressed cell proliferation in vitro and tumor growth in an orthotopic nude mouse model. These results suggest that MRG has tumor-suppressing activity, and the loss of MRG expression may be involved in the development and progression of breast cancer.

Cystatin E is a novel human cysteine proteinase inhibitor with structural resemblance to family 2 cystatins

A new member of the human cystatin superfamily, called cystatin E, has been found by expressed sequence tag (EST) sequencing in amniotic cell and fetal skin epithelial cell cDNA libraries. The sequence of a full-length amniotic cell cDNA clone contained an open reading frame encoding a putative 28-residue signal peptide and a mature protein of 121 amino acids, including four cysteine residues and motifs of importance for the inhibitory activity of Family 2 cystatins like cystatin C. Recombinant cystatin E was produced in a baculovirus expression system and isolated. An antiserum against the recombinant protein could be used for affinity purification of cystatin E from human urine, as confirmed by N-terminal sequencing. The mature recombinant protein processed by insect cells started at amino acid 4 (cystatin C numbering), and displayed reversible inhibition of papain and cathepsin B (Ki values of 0.39 and 32 nM, respectively), in competition with substrate. Cystatin E is thus a functional cysteine proteinase inhibitor despite relatively low amino acid sequence similarities with human cystatins (26-34% identity with sequences for the Family 2 cystatins C, D, S, SN, and SA; <30% with the Family 1 cystatins, A and B, and domains 2 and 3 of the Family 3 cystatin, kininogen). Unlike other human low Mr cystatins, cystatin E is a glycoprotein, carrying an N-linked carbohydrate chain at position 108. Northern blot analysis revealed that the cystatin E gene is expressed in most human tissues, with the highest mRNA amounts found in uterus and liver. A strikingly high incidence of cystatin E clones in cDNA libraries from fetal skin epithelium and amniotic membrane cells (>0.5% of clones sequenced) indicates a protective role of cystatin E during fetal development.

Optimization of relative weights and wedge angles in treatment planning

An efficient technique to optimize beam weights and wedge angles in radiotherapy treatment planning has been developed. Based on the fact that a wedged field can be regarded as a superposition of an open field and a nominal wedged field, this approach reduces the problem of finding J beam weights and the corresponding wedge angles to optimizing a linear system with 2J unknowns (weights of J open beams and J nominal wedged beams), where J is the total number of incident beam directions. Two iterative algorithms similar to the iterative-least-square technique in image reconstruction are used to optimize the system. Application of the algorithms to two specific examples shows that this technique can reduce treatment planning time and effort, and promises to create a better solution for an arbitrarily complex treatment plan.

Signal transduction by DR3, a death domain-containing receptor related to TNFR-1 and CD95

Tumor necrosis factor receptor-1 (TNFR-1) and CD95 (also called Fas or APO-1) are cytokine receptors that engage the apoptosis pathway through a region of intracellular homology, designated the "death domain." Another death domain-containing member of the TNFR family, death receptor 3 (DR3), was identified and was shown to induce both apoptosis and activation of nuclear factor kappaB. Expression of DR3 appears to be restricted to tissues enriched in lymphocytes. DR3 signal transduction is mediated by a complex of intracellular signaling molecules including TRADD, TRAF2, FADD, and FLICE. Thus, DR3 likely plays a role in regulating lymphocyte homeostasis.

Iterative methods for inverse treatment planning

Iterative algorithms used in imaging science are generalized to study inverse treatment planning in radiotherapy. These algorithms consist of iteratively changing trial incident fluence functions which eventually yield a dose distribution consistent with the prescribed distribution. Application of the algorithms is presented for test cases of a circular phantom with cylindrically symmetric dose distributions. A comparison of the iterative beam profiles with previous analytic solutions shows excellent agreement, indicating that iterative techniques are promising to create sophisticated treatment plans. The relationship between the algorithms and several existing inverse treatment planning methods is discussed.

Antiinflammatory effect of Trichosanthes kirilowii Maxim, and its effective parts

This study was carried out to elucidate the antiinflammatory effect of 50% ethanol extract obtained from the fruit of Trichosanthes kirilowii Maxm, and its effective parts. The cut dried fruit was separated into the whole fruit, seeds and remaining parts, and each part was extracted with 50% ethanol. The antiinflammatory activity of these extracts was investigated on acetic acid-induced vascular permeability in mice, carrageenin-induced edema and cotton pellet-induced granuloma formation in rats, as well as writhing symptoms in mice. The whole fruit and seed extractions showed an antiinflammatory activity and analgesic activity, but the other part did not when given perorally. These results suggest that the antiinflammatory effect and analgesic effect induced by ethanol extract of the fruit of T. kirilowii may be due to the seeds contained in the fruit.

Accelerative effect of "nanshikon" and its constituents on the proliferation of granulation tissue in rats

The present study was carried out to examine the accelerative effect of the ether extract obtained from "Nanshikon" on the proliferation of granulation tissue induced by cotton pellet in rats and to elucidate its active principles. Among naphthoquinone derivatives, the ether extract contained mostly teracrylshikonin. At corresponding doses based on the contents of the naphthoquinone derivatives in the ether extract, the accelerative potencies of teracrylshikonin, beta, beta-dimethylacrylshikonin, and a mixture of alpha-methyl-n-butylshikonin and isovalerylshikonin were about the same. Also, the accelerative potencies of these compounds were somewhat weaker than that of the ether extract. From these results, it is suggested that the accelerative effect of the ether extract on the proliferation of granulation tissue is mainly due to teracrylshikonin, beta, beta-dimethylacrylshikonin and a mixture of alpha-methyl-n-butylshikonin and isovalerylshikonin contained in the ether extract, and the accelerative effect induced by ether extract might be an additive effect of these naphthoquinone derivatives.

cAMP response element-binding protein (CREB) interacts with transcription factors IIB and IID

cAMP response element-binding protein (CREB) participates in both constitutive and cAMP-induced transcription of cAMP-responsive genes. CREB-mediated constitutive transcription requires only CREB-binding sites and a minimal promoter region (containing the TATA through start sequences), indicating that CREB interacts directly with components of the general transcription machinery. In this study, a coimmunoprecipitation assay was used to test for interaction of CREB with the general transcription factors (TF) TFIIB and TFIID and the core component of TFIID, TATA-binding protein (TBP). Human TFIIB and TBP, tagged with distinct epitopes (eTFIIB and eTBP), were expressed in and purified from Escherichia coli, and holo-eTFIID, containing eTBP, was obtained from the HeLa cell line LTR alpha 3. 35S-Labeled CREB, synthesized in vitro and incubated with eTFIIB, was coimmunoprecipitated with antibody recognizing eTFIIB, indicating that CREB specifically binds to TFIIB. 35S-CREB was coimmunoprecipitated with antibody against eTBP, but only when incubated with the holo-eTFIID complex, not with eTBP alone. TFIIB interacted with TBP, but CREB was not coprecipitated with the eTBP antibody when incubated with eTBP plus TFIIB, so CREB did not form a stable ternary complex with TFIIB and TBP. Conversely, depletion of TFIIB from the holo-TFIID preparation did not diminish the level of interaction between CREB and TFIID. Thus, CREB interacts independently with TFIIB and TFIID, but not directly with TBP. A protein kinase A phosphorylation site mutant of CREB and wild-type CREB exhibited equivalent interaction with TFIIB, indicating that this phosphorylation is not required. Consistent with the role of CREB in promoting constitutive or basal transcription, the constitutive activation domain of CREB was sufficient for interaction with both TFIIB and TFIID.