BL-1023 improves behavior and neuronal survival in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-intoxicated mice.

The therapeutic potential of BL-1023, a chemical combination of L-3,4-dihydroxyphenylalanine (L-DOPA) and gamma-aminobutyric acid (GABA), was investigated in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) intoxicated mice. Such animals exhibit nigrostriatal degeneration, characteristic of human Parkinson's disease. Drug was administered during and after the development of MPTP-induced nigrostriatal lesions followed by measures of motor function and behavior, surviving nigrostriatal dopaminergic neurons and termini, and striatal dopamine levels. When administered after lesion development, BL-1023 improved motor function of MPTP-mice as measured by rotarod, total floor and vertical plane movements, and stereotypic movements in open field activity tests compared to MPTP-mice without treatment. This also paralleled modest nigral dopaminergic neuronal protection. Such significant improvements in motor function, behaviors, and dopaminergic neuronal numbers were not seen when BL-1023 was administered during MPTP-induced lesion development. The data demonstrate select abilities of BL-1023 to increase dopaminergic neuronal survival and improve motor function in MPTP-mice.

Survey of US fuel ethanol plants.

The ethanol industry is growing in response to increased consumer demands for fuel as well as the renewable fuel standard. Corn ethanol processing creates the following products: 1/3 ethanol, 1/3 distillers grains, and 1/3 carbon dioxide. As the production of ethanol increases so does the generation of its coproducts, and viable uses continually need to be developed. A survey was mailed to operational US ethanol plants to determine current practices. It inquired about processes, equipment used, end products, and desired future directions for coproducts. Results indicated that approximately one-third of plant managers surveyed expressed a willingness to alter current drying time and temperature if it could result in a higher quality coproduct. Other managers indicated hesitation, based on lack of economic incentives, potential cost and return, and capital required. Respondents also reported the desire to use their coproducts in some of the following products: fuels, extrusion, pellets, plastics, and human food applications. These results provide a snapshot of the industry, and indicate that operational changes to the current production of DDGS must be based upon the potential for positive economic returns.

Quaternary stratigraphy, sediment characteristics and geochemistry of arsenic-contaminated alluvial aquifers in the Ganges-Brahmaputra floodplain in central Bangladesh.

This study focuses on the Quaternary stratigraphy, sediment composition, mineralogy, and geochemistry of arsenic (As)-contaminated alluvial aquifers in the Ganges-Brahmaputra floodplain in the central Bangladesh. Arsenic concentrations in 85 tubewells in Manikganj area, 70 km northwest of Dhaka City, range from 0.25 microg/L to 191 microg/L with a mean concentration of 33 microg/L. Groundwater is mainly Ca-HCO(3) type with high concentrations of dissolved As, Fe, and Mn, but low level of SO(4). The uppermost aquifer occurs between 10 m and 80 m below the surface that has a mean arsenic concentration of 35 microg/L. Deeper aquifer (>100 m depth) has a mean arsenic concentration of 18 microg/L. Sediments in the upper aquifer are mostly gray to dark-gray, whereas sediments in the deep aquifer are mostly yellowing-gray to brown. Quartz, feldspar, mica, hornblende, garnet, kyanite, tourmaline, magnetite, ilmenite are the major minerals in sediments from both aquifers. Biotite and potassium feldspar are dominant in shallow aquifer, although plagioclase feldspar and garnet are abundant in deep aquifer sediments. Sediment composition suggests a mixed provenance with sediment supplies from both orogenic belts and cratons. High arsenic concentrations in sediments are found within the upper 50 m in drilled core samples. Statistical analysis shows that As, Fe, Mn, Ca, and P are strongly correlated in sediments. Concentrations of Cd, Cu, Ni, Zn, and Bi also show strong correlations with arsenic in the Manikganj sediment cores. Authigenic goethite concretions, possibly formed by bacteria, are found in the shallow sediments, which contain arsenic of a concentration as high as 8.8 mg/kg. High arsenic concentrations in aquifers are associated with fine-grained sediments that were derived mostly from the recycled orogens and relatively rapidly deposited mainly by meandering channels during the Early to Middle Holocene rising sea-level conditions.

Pilot study of the knowledge and attitude towards evidence based medicine of otolaryngology higher surgical trainees.

The objective of this survey is to provide an insight into the knowledge and attitude of the higher surgical trainees in Otolaryngology towards evidence based medicine and evaluate their understanding of medical statistics and use of evidence based medicine in patient management. A self administered anonymous questionnaire was distributed to twenty Specialist Registrars in Otolaryngology in Ireland during an annual National Otolaryngology Meeting. Of these, nineteen attempted the questionnaire and eighteen completed it. Three previously published questionnaires [Meserve et al. (2005) Med. Educ. Online.10, 1; McColl et al. (1998) BMJ.316, 361; Khan et al. (1999) J. Obst. Gynaecol.19, 231] were used in this survey. In general, there was a moderately welcoming attitude towards evidence based medicine. However, the survey findings indicate the need for incorporation of formal teaching of critical appraisal skills into medical education with a greater emphasis on involvement and dissemination of evidence based medicine in day to day practice.

Post-acute dispositions of older adults hospitalized for depression.

This study addressed factors associated with six-month post-acute dispositions (continuous community stay, medical hospitalization, psychiatric rehospitalization, nursing home placement, death) for older adults hospitalized for depression and discharged to the community. The sample included 199 older adults; and data were collected via medical records, interviews with discharge planners, patients, and family members. Over half of the sample remained in the community throughout the observation period; 23% experienced psychiatric re-admission and 10% entered a nursing home. Several factors associated with nursing home placement were identified: less improvement in depression during the hospitalization, lower Global Assessment of Functioning (GAF) scores at discharge; and less mental health service use in the post-acute period. Those at higher risk of psychiatric re-admission had more previous psychiatric hospitalizations and were marginally more likely to be married and have lower Brief Psychiatric Rating Scale (BPRS) scores at discharge. Differentiating those at risk for nursing home placement may be easier than differentiating those at risk of psychiatric readmission.

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of alpha and alpha+beta proteins [60-70 residues with C(alpha) rms deviation (rmsd) <6 A]. However, for alpha+beta proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two alpha and three alpha+beta, with sizes of 53-235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue alpha+beta protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-A C(alpha) rmsd. So far this protein is the largest alpha+beta protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly alpha-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 A rmsd, except the 32 C-terminal residues, most of which form a beta-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction.

The protein folding problem: global optimization of the force fields.

The evolutionary development of a theoretical approach to the protein folding problem, in our laboratory, is traced. The theoretical foundations and the development of a suitable empirical all-atom potential energy function and a global optimization search are examined. Whereas the all-atom approach has thus far succeeded for relatively small molecules and for alpha-helical proteins containing up to 46 residues, it has been necessary to develop a hierarchical approach to treat larger proteins. In the hierarchical approach to single- and multiple-chain proteins, global optimization is carried out for a simplified united residue (UNRES) description of a polypeptide chain to locate the region in which the global minimum lies. Conversion of the UNRES structures in this region to all-atom structures is followed by a local search in this region. The performance of this approach in successive CASP blind tests for predicting protein structure by an ab initio physics-based method is described. Finally, a recent attempt to compute a folding pathway is discussed.

Genetic Diversity of Sclerotinia homoeocarpa Isolates from Turfgrasses from Various Regions in North America.

Sixty-seven isolates of Sclerotinia homoeocarpa, causing dollar spot disease in creeping bentgrass, annual bluegrass, Bermudagrass, and perennial ryegrass turf, collected from 23 golf courses in various geographical regions of the United States and Canada between 1972 and 2001, were characterized by vegetative compatibility, genetic diversity, and pathogenicity. Eleven vegetative compatibility groups (VCGs A to K) were identified among the isolates tested in this study, and five of them (VCGs G to K) were new. VCG B was the most predominant group, typifying 33 isolates (51%) tested. S. homoeocarpa isolates collected from golf courses in Pennsylvania belonged to seven VCGs (A, B, E, F, G, I, and K), whereas three groups were observed in those collected from New York (B, E, and G) and New Jersey (E, H, and I). Two isolates, one each from Pennsylvania and Canada, were incompatible when paired with the tester isolates in all possible combinations, and did not fall into any known VCG. An isolate collected from Canada was compatible with tester isolates from two VCGs (C and D). Genetic analyses using amplified fragment length polymorphism (AFLP) showed the presence of two genetically distinct groups, designated as major group and the minor group. The major group included 36 isolates collected from various golf courses in the United States and Canada. Two isolates collected from bermudagrass in Florida formed a separate cluster, the minor group. Isolates that belonged to the major group were further divided into two subgroups (1 and 2). Subgroup 1 consisted of all the isolates that belonged to VCGs A, E, G, H, and I. Three of the four isolates that belonged to VCG K also were clustered with isolates of subgroup 1. Subgroup 2 consisted of all the isolates from VCG B, and one each from VCGs F and K. Pathogenicity assays on Penncross creeping bentgrass showed significant differences (P = 0.05) in virulence among the isolates. Overall, a relationship between virulence and VCGs was observed, in which certain virulence groups corresponded to specific VCGs; however, such a relationship was not observed between virulence and AFLPs. Close similarity among isolates of S. homoeocarpa collected from different locations in the United States and Canada suggests that isolates of the same genotype could be involved in outbreaks of dollar spot epidemics at multiple locations.

Ab initio folding of multiple-chain proteins.

Our previous methodology for ab initio prediction of protein structure is extended here to treat multiple-chain proteins. This involved modification of our united-residue (UNRES) force field and our Conformational Space Annealing (CSA) Global Optimization procedure. Good results have been obtained for both a four- and a three-helix protein from the CASP3 exercise.

Perception of 3D surface orientation from skew symmetry.

In this paper, we investigate how symmetry can be used to perceive 3D surface orientation. When a symmetric planar object is viewed from an angle, the projected contour has skew symmetry, which provides partial information about the 3D orientation of the object. For a given skew symmetry, this information can be characterized by a constraint curve of possible slant/tilt combinations that are consistent with a mirror-symmetric interpretation. These constraint curves move around when an object is rotated within a plane, and depend on what we will term the spin of the object: the angle between its axis of symmetry and the direction of tilt. To test the influence of symmetry constraint curves, we presented subjects with stereo images of symmetric objects that varied in spin, and had them perform an orientation-matching task. We found that the judgments showed biases that depended on the spin of the objects. Since other sources of information depend only on slant and tilt, not on spin, the biases imply that skew symmetry contributed to subjects' judgments. In a second experiment, we introduced conflicts between stereo and symmetry cues, and found that the spin-dependent biases can be modulated by selectively changing stereo slant. We propose an explanation of these results involving the optimal integration of stereo and skew symmetry, and present a Bayesian model that can account for the pattern of biases.

Intracellular trafficking of pigeon beta-very low density lipoprotein and low density lipoprotein at low and high concentrations in pigeon macrophages.

Foam cell formation occurs in vitro at lipoprotein concentrations above 50 microgram/ml in pigeon macrophages. Hypothetically, intracellular trafficking of lipoproteins at higher concentrations may differ from uptake of lipoproteins associated with low concentrations, revealing a separate atherogenic endocytic pathway. Macrophage intracellular trafficking of pigeon beta-very low density lipoprotein (beta-VLDL) and low density lipoprotein (LDL) at low concentrations (12 microgram/ml) near the saturation of high affinity binding sites and high lipoprotein concentrations (50-150 microgram/ml) used to induce foam cell formation were examined. Pigeon beta-VLDL and LDL, differentially labeled with colloidal gold, were added simultaneously to contrast trafficking of beta-VLDL, which causes in vitro foam cell formation, with LDL, which does not. The binding of lipoproteins to cell surface structures, distribution of lipoproteins in endocytic organelles, and the extent of colabeling in the endocytic organelles were determined by thin-section transmission electron microscopy. At low concentrations, the intracellular trafficking of pigeon LDL and beta-VLDL was identical. At high concentrations, LDL was removed more rapidly from the plasma membrane and reached lysosomes more quickly than beta-VLDL. No separate endocytic route was present at high concentrations of beta-VLDL; rather, an increased residence on the plasma membrane, association with nonmicrovillar portions of the plasma membrane, and slower trafficking in organelles of coated-pit endocytosis reflected a more atherogenic trafficking pattern.

Detection of plant genes using a rapid, nonorganic DNA purification method.

We have developed a simple procedure for the preparation of plant genomic DNA using FTA paper. Plant leaves were crushed against FTA paper, and the genomic DNA was purified using simple, nonorganic reagents. The 18S rRNA gene and the gene encoding the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit (rbcL) from the chloroplast genome were detected by PCR amplification of DNA on FTA paper. DNA amplification was successful using extracts from 16 dicot and monocot plants. Studies of specific plant extracts revealed that extracts of leaf samples could be collected and stored at room temperature on FTA paper without a decrease in the DNA amplification success rate for more than a month. Both the 18S RNA gene and the rbcL gene were detected in the genomic DNA isolated from various soybean cultivars stored in this manner. Furthermore, by modestly increasing the number of cycles of DNA amplification, we were able to detect the uidA gene in transgenic tobacco and rice leaves as well as a single copy gene linked to the resistance gene of cyst nematode race 3 using genomic DNA isolated on FTA paper. These results demonstrate that genomic DNA isolated using FTA paper can be used for the detection of plant genes, from a wide range of plants with either high or low gene copy number and of either nuclear or cytoplasmic origin.

Application of amplified restriction fragment length polymorphism for genetic characterization of colletotrichum pathogens of alfalfa.

ABSTRACT Amplified restriction fragment length polymorphism (AFLP) was used to assess the levels of genomic variations among species and isolates of the genus Colletotrichum. Our objective was to characterize at the molecular level two alfalfa pathogens, isolates Arl-NW and 57RR, which are unusually aggressive to anthracnose-resistant alfalfa cultivars and whose taxa has been uncertain based on morphological criteria. The fingerprint patterns obtained were complex but did enable us to place these two isolates within the species C. trifolii and C. gloeosporioides, respectively. The diversity detected with AFLP among and within Colletotrichum species from alfalfa and other crops corroborated their published taxonomy based on morphology, ribosomal DNA sequence, and random amplified polymorphic DNA analyses. Similarity matrices generated with three primer pairs were highly correlated and, thus, were combined to determine the similarity among the fungal species and isolates that were analyzed. Analysis of the data generated with each of the primer pairs individually and application of either distance or parsimony methods supported the placement of these two isolates. The parsimony method of data analysis was more confirmatory in the placement of Phoma medicaginis as an out-group than the distance method, using either simple matching or Jaccard's coefficients to generate the similarity matrices. Our conclusion is that the AFLP technique will be useful for identification of individual isolates within complex genera such as Colletotrichum because of its ability to generate large numbers of polymorphisms and the consistency of polymerase chain reaction amplification.

Rapid optimization of electroporation conditions for plant cells, protoplasts, and pollen.

The optimization of electroporation conditions for maximal uptake of DNA during direct gene transfer experiments is critical to achieve high levels of gene expression in transformed plant cells. Two stains, trypan blue and fluorescein diacetate, have been applied to optimize electroporation conditions for three plant cell types, using different square wave and exponential wave electroporation devices. The different cell types included protoplasts from tobacco, a stable mixotrophic suspension cell culture from soybean with intact cell walls, and germinating pollen from alfalfa and tobacco. Successful electroporation of each of these cell types was obtained, even in the presence of an intact cell wall when conditions were optimized for the electroporation pulse. The optimal field strength for each of these cells differs, protoplasts having the lowest optimal pulse field strength, followed by suspension cells and finally germinating pollen requiring the strongest electroporation pulse. A rapid procedure is described for optimizing electroporation parameters using different types of cells from different plant sources.

Perceiving heading in the presence of moving objects.

In most models of heading from optic flow a rigid environment is assumed, yet humans often navigate in the presence of independently moving objects. Simple spatial pooling of the flow field would yield systematic heading errors. Alternatively, moving objects could be segmented on the basis of relative motion, dynamic occlusion, or inconsistency with the global flow, and heading determined from the background flow. Displays simulated observer translation toward a frontal random-dot plane, with a 10 deg square moving independently in depth. The path of motion of the object was varied to create a secondary focus of expansion (FOE') 6 deg to the right or left of the actual heading point (FOE), which could bias the perceived heading. There was no effect when the FOE was visible, but when the object moved in front of it, perceived heading was biased toward the FOE' by approximately 1.9 degrees with a transparent object, and approximately 3.4 degrees with an opaque object. The results indicate that scene segmentation does not occur prior to heading estimation, which is consistent with spatial pooling weighted near the FOE. A simple template model based on large-field, center-weighted expansion units accounts for the data. This may actually represent an adaptive solution for navigation with respect to obstacles on the path ahead.