Direct immobilization of gangliosides onto gold-carboxymethyldextran sensor surfaces by hydrophobic interaction: applications to antibody characterization

We describe a novel immobilization technique to investigate interactions between immobilized gangliosides (GD3, GM1, and GM2) and their respective antibodies, antibody fragments, or binding partners using an optical biosensor. Immobilization was performed by direct injection onto a carboxymethyldextran sensor chip and did not require derivatization of the sensor surface or the ganglioside. The ganglioside appeared to bind to the sensor surface by hydrophobic interaction, leaving the carbohydrate epitope available for antibody or, in the case of GM1, cholera toxin binding. The carboxyl group of the dextran chains on the sensor surface did not appear to be involved in the immobilization as evidenced by equivalent levels of immobilization following conversion of the carboxyl groups into acyl amino esters, but rather the dextran layer provided a hydrophilic coverage of the sensor chip which was essential to prevent nonspecific binding. This technique gave better reactivity and specificity for anti- ganglioside monoclonal antibodies (anti-GD3: KM871, KM641, R24; and anti-GM2: KM966) than immobilization by hydrophobic interaction onto a gold sensor surface or photoactivated cross-linking onto carboxymethydextran. This rapid immobilization procedure has facilitated detailed kinetic analysis of ganglioside/antibody interactions, with the surface remaining viable for a large number of cycles (>125). Kinetic constants were determined from the biosensor data using linear regression, nonlinear least squares and equilibrium analysis. The values of kd, ka, and KAobtained by nonlinear analysis (KAKM871 = 1.05, KM641 = 1.66, R24 = 0.14, and KM966 = 0.65 x 10(7) M- 1) were essentially independent of concentration and showed good agreement with data obtained by other analytical methods.      

Mathematics reflecting sensorimotor organization

 This review combines short presentations of several mathematical approaches that conceptualize issues in sensorimotor neuroscience from different perspectives and levels of analysis. The intricate organization of neural structures and sensorimotor performance calls for characterization using a variety of mathematical approaches. This review points out the prospects for mathematical neuroscience: in addition to computational approaches, there is a wide variety of mathematical approaches that provide insight into the organization of neural systems. By starting from the perspective that provides the greatest clarity, a mathematical approach avoids specificity that is inaccurate in characterizing the inherent biological organization. Approaches presented include the mathematics of ordered structures, motion-phase space, subject-coincident coordinates, equivalence classes, topological biodynamics, rhythm space metric, and conditional dynamics. Issues considered in this paper include unification of levels of analysis, response equivalence, convergence, relationship of physics to motor control, support of rhythms, state transitions, and focussing on low-dimensional subspaces of a high-dimensional sensorimotor space. Received: 28 August 2001 / Accepted in revised form: 11 July 2002 Correspondence to: e-mail: mccollum@ohsu.edu Acknowledgements. I would like to express many thanks for the critical comments on this review offered by William L. Bloch, Jan E. Holly, Gerhard Magnus, and Patrick D. Roberts.     

Characterization of the wound-induced material in Citrus paradisi fruit peel by carbon-13 CP-MAS solid state NMR spectroscopy

Grapefruit, Citrus paradisi, were injured, inoculated with Penicillium digitatum and incubated under conditions favourable for the accumulation of defence related material. Histochemical examination revealed that tissues adjacent to inoculated injuries contained phloroglucinol-HCl (PG-HCl) reactive material. Solvent washed cell wall preparations of intact and injured-inoculated peel were further purified using a mixture of cell wall degrading enzymes. Samples from injured inoculated tissue contained PG-HCl reactive globular material in addition to the fragments of xylem and cuticle found in controls. The principal chemical moieties of the material that accumulates in grapefruit injuries during wound-healing were studied by solid state 13C cross-polarization magic angle spinning NMR. A complete assignment of the NMR signals was made. From the analysis evidence was found that cellulose and hemicellulose are the biopolymers present in the intact peel samples, in addition, relevant quantities of cutin were found in the residues of enzyme digest. The NMR difference spectrum intact- wounded peels showed resonances which were attributed to all major functional groups of the aromatic-aliphatic suberin polyester of new material produced by the wounds. Information on the latter polyester was obtained by analyzing the T(1)rho (1H) relaxation.     

Chemical synthesis of RNA using fast oligonucleotide deprotection chemistry.

The exocyclic amine protecting groups in oligonucleotide synthesis which require 8-16 hours at 55 degrees C for deprotection in ammonia have been replaced with more labile base protecting groups (dimethylformamidine for adenine and guanine and isobutyryl for cytosine). Using these fast oligonucleotide deprotecting groups which require 2-3 hours at 55 degrees C for complete deprotection, a new set of cyanoethyl phosphoramidite ribonucleoside monomers and supports has been developed. Ribozymes and substrate RNAs which were synthesized with these phosphoramidites were assayed and were found to have full catalytic (biological) activity.     

Marsupials and monotremes sort genome treasures from junk

A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals (including humans) and more distant vertebrate species.     

Identification of a grapefruit cDNA belonging to a unique class of citrus dehydrins and characterization of its expression patterns under temperature stress conditions

Citrus fruits are sensitive to low temperatures and this often results in the development of chilling injuries during postharvest storage. In order to gain more insight into the molecular mechanisms involved in the acquisition of fruit chilling tolerance, we initiated a grapefruit ( Citrus paradisi, cv. Marsh Seedless) flavedo cDNA sequencing project and used it to identify a cDNA similar to other Poncirus trifoliata and Citrus unshiu dehydrin genes reported to be responsive to low temperatures. The grapefruit dehydrin cDNA, designated cor15 , encodes a predicted polypeptide of 15.1 kDa, that is almost completely identical with other reported citrus dehydrin proteins, except that it contains two large amino acid repeats, whereas P. trifoliata COR11 has only one such repeat and P. trifoliata COR19 and C. unshiu COR19 have three repeats. Together, the various grapefruit, P. trifoliata and C. unshiu dehydrins form a closely related and unique dehydrin gene family that differs from most other plant dehydrins in having an unusual K-segment similar to that of gymnosperms and in having a serine cluster (S-segment) at an unusual position at the carboxy-terminus. The grapefruit cor15 gene is consistently expressed in the fruit peel tissue at harvest, but its message levels dramatically decrease during storage at 2°C. However, a pre-storage hot water treatment, which enhances fruit chilling tolerance, elicited retention of the constant level of cor15 gene expression during cold storage and eliminated its decline. The hot water treatment had no inductive effect on cor15 gene expression when the fruit were held at non-chilling temperatures. The effects of other stresses, such as exposure to ethylene, UV irradiation and wounding, on cor15 gene expression, were temporary and persisted for 1-2 days after the treatments.     

Subnasal morphological variation in fossil hominids: a reassessment based on new observations and recent developmental findings

Quantitative and qualitative assessments of subnasal morphology in fossil hominids yield distinct patterns which have been used both to sort robust from nonrobust australopithecine taxa and to distinguish individual species. Recently, new developmental models have been applied to hominoid subnasal morphological variation. These studies require that certain features of the fossil hominid subnasal region, in particular the topography of the nasal cavity entrance and details of vomeral morphology, be reevaluated. This study does so for the robust and nonrobust australopithecines, early Homo (H. habilis/H. rudolfensis), and African H. erectus. Results reaffirm an overall similarity of the nonrobust Australopithecus subnasal morphological pattern with that of the chimpanzee. They further indicate that a vomeral insertion above the nasal surface of the premaxilla should be added to the list of traits characteristic of the robust australopithecine subnasal morphological pattern. Finally, reassessment of subnasal morphology in the early Homo and H. erectus samples from Africa suggest that these two taxa share a similar subnasal morphological pattern. This pattern consists of a smooth nasal cavity entrance, a horizontal nasal sill whose anterior edge is demarcated by a strong nasal crest, and a well-developed horizontal spine at the posterior edge of the nasal sill. Although none of the African fossil Homo specimens preserve a vomer, indirect evidence suggests that it would have inserted above the nasal sill.     

Failure of fallow deer (Dama dama) to develop chronic wasting disease when exposed to a contaminated environment and infected mule deer (Odocoileus hemionus)

We monitored a herd of fallow deer (Dama dama) for evidence of prion infection for 7 yr by periodic postmortem examination of animals from the herd. The fallow deer were exposed to the chronic wasting disease (CWD) agent from mule deer by living in a paddock considered contaminated with infectivity from its history of housing CWD infected deer and, after the first year of the study, by comingling with infected mule deer (Odocoileus hemionus). At least 8 of 12 mule deer serving as sentinels for prion transmission and 25 additional mule deer serving as sources of infectivity developed clinical CWD or were otherwise confirmed to be infected with CWD via lymphoid tissue immunohistochemistry (IHC). In contrast, none of the 41 exposed fallow deer showed clinical signs suggestive of CWD, IHC staining of disease-associated prion in lymphoid or brain tissues, or evidence of spongiform degeneration in sections of brain stem at the level of the obex when sampled 18 mo to 7 yr after entering the mule deer paddock. The absence of clinical disease and negative IHC results in fallow deer housed in the same contaminated paddock for up to 7 yr and almost continuously exposed to CWD-infected mule deer for up to 6 yr suggests a species barrier or other form of resistance preventing fallow deer infection by the CWD agent or delaying progression of the disease in this species.     

Analysis of bronchoalveolar lavage fluid proteome from systemic sclerosis patients with or without functional, clinical and radiological signs of lung fibrosis

Lung fibrosis is a major cause of mortality and morbidity in systemic sclerosis (SSc). However, its pathogenesis still needs to be elucidated. We examined whether the alteration of certain proteins in bronchoalveolar lavage fluid (BALF) might have a protective or a causative role in the lung fibrogenesis process. For this purpose we compared the BALF protein profile obtained from nine SSc patients with lung fibrosis (SSc_Fib+) with that obtained from six SSc patients without pulmonary fibrosis (SSc_Fib-) by two-dimensional gel electrophoresis (2-DE). Only spots and spot-trains that were consistently expressed in a different way in the two study groups were taken into consideration. In total, 47 spots and spot-trains, corresponding to 30 previously identified proteins in human BALF, showed no significant variation between SSc_Fib+ patients and SSc_Fib- patients, whereas 24 spots showed a reproducible significant variation in the two study groups. These latter spots corresponded to 11 proteins or protein fragments, including serum albumin fragments (13 spots), 5 previously recognized proteins (7 spots), and 4 proteins (3 spots) that had not been previously described in human BALF maps, namely calumenin, cytohesin-2, cystatin SN, and mitochondrial DNA topoisomerase 1 (mtDNA TOP1). Mass analysis did not determine one protein-spot. The two study groups revealed a significant difference in BALF protein composition. Whereas levels of glutathione S-transferase P (GSTP), Cu–Zn superoxide dismutase (SOD) and cystatin SN were downregulated in SSc_Fib+ patients compared with SSc_Fib- patients, we observed a significant upregulation of α1-acid glycoprotein, haptoglobin-α chain, calgranulin (Cal) B, cytohesin-2, calumenin, and mtDNA TOP1 in SSc_Fib+ patients. Some of these proteins (GSTP, Cu–Zn SOD, and cystatin SN) seem to be involved in mechanisms that protect lungs against injury or inflammation, whereas others (Cal B, cytohesin-2, and calumenin) seem to be involved in mechanisms that drive lung fibrogenesis. Even if the 2-DE analysis of BALF did not provide an exhaustive identification of all BALF proteins, especially those of low molecular mass, it allows the identification of proteins that might have a role in lung fibrogenesis. Further longitudinal studies on larger cohorts of patients will be necessary to assess their usefulness as predictive markers of disease.