High-affinity binding of Ca2+ to bovine alpha-lactalbumin in the absence and presence of EGTA.

Literature values for the Kd for Ca2+ in bovine alpha-lactalbumin range over 3 orders of magnitude. There is a difference between two results obtained with EGTA as a metal-ion buffer, partly because different values for the Kd of Ca2+-EGTA were used in the calculations, and a much wider difference between results obtained in the presence and absence of EGTA, which has been attributed to an interaction between EGTA and the protein. Titrations in a flow-dialysis cell showed that Mn2+ competed with Ca2+ for the high-affinity site on the protein, and the results, combined with a Kd for Mn2+ of 2.1 +/- 0.1 microM, which was determined fluorimetrically, gave a Kd for Ca2+ of 1.3 +/- 0.1 nM. When alpha-lactalbumin containing 45Ca2+ was titrated with EGTA in a flow-dialysis cell, and widely accepted metal-chelation data for EGTA were used in the calculations, a Kd for Ca2+ of 1.10 +/- 0.03 nM was obtained. The results from the two methods are so similar as to indicate that the affinity for Ca2+ was unaffected by the presence of EGTA.     

Inter-plot competition in yield trials of potatoes (Solanum tuberosum L.) with single-drill plots

An experiment was carried out to assess the significance of inter-plot competition in a yield trial of potato cultivars. Seventeen cultivars were deliberately chosen and assessed for yield in single-drill and four-drill plots. Inter-plot competition for fresh-weight yield was a significant factor in the single-drill plots. It was modelled using a common competition coefficient with a covariate based on neighbour fresh-weight yields. In contrast, there was no statistically significant inter-plot competition for specific gravity. After adjustment for inter-plot competition, varietal ranking in estimated monoculture yield differed little from that based on unadjusted means. However, there was a reduction in the range of yield estimates, and a closer agreement with the observed pure-stand yields from the inner two drills of the four-drill plots. The adjustment for monoculture performance was most pronounced for the higher and lower yielding varieties, as expected from the assumption that the performance of high yielding varieties was enhanced in a competitive environment at the expense of low yielding ones. A general and flexible method of estimating competition coefficients in variety trials, together with a suitable algorithm, was developed and is explained in an appendix. It was used to check for inter-plot competition in a number of potato trials with single-drill plots and a large number of entries. Competition was found in some trials but not in others. Thus, where potato tubers are grown in single-drill plots for assessment of fresh-weight yield, adjustment should be made for inter-plot competition when evidence of inter-drill competition is found.     

Site-directed mutants of charged residues in the active site of tyrosine hydroxylase

The active site of tyrosine hydroxylase consists of a hydrophobic cleft with an iron atom near the bottom. Within the cleft are several charged residues which are conserved across the family of pterin-dependent hydroxylases. We have studied four of these residues, glutamates 326 and 332, aspartate 328, and arginine 316 in tyrosine hydroxylase, by site-directed substitution with alternate amino acid residues. Replacement of arginine 316 with lysine results in a protein with a Ktyr value that is at least 400-fold greater and a V/Ktyr value that is 4000-fold lower than those found in the wild-type enzyme; substitution with alanine, serine, or glutamine yields insoluble enzyme. Arginine 316 is therefore critical for the binding of tyrosine. Replacement of glutamate 326 with alanine has no effect on the KM value for tyrosine and results in a 2-fold increase in the KM value for tetrahydropterin. The Vmax for DOPA production is reduced 9-fold, and the Vmax for dihydropterin formation is reduced 4-fold. These data suggest that glutamate 326 is not directly involved in catalysis. Replacement of aspartate 328 with serine results in a 26-fold higher KM value for tyrosine, a 8-fold lower Vmax for dihydropterin formation, and a 13-fold lower Vmax for DOPA formation. These data suggest that aspartate 328 has a role in tyrosine binding. Replacement of glutamate 332 with alanine results in a 10-fold higher KM value for 6-methyltetrahydropterin with no change in the KM value for tyrosine, a 125-fold lower Vmax for DOPA formation, and an only 3.3-fold lower Vmax for tetrahydropterin oxidation. These data suggest that glutamate 332 is required for productive tetrahydropterin binding.     

Kinetic analyses and structure-activity relationship studies of synthetic lysine acetylation catalysts

Lysine acylation of proteins is a crucial chemical reaction, both as a post-translational modification and as a method for bioconjugation. We previously developed a chemical catalyst, DSH, which activates a chemically stable thioester including acyl-CoA, allowing the site-selective lysine acylation of histones under physiological conditions. However, a more active catalyst is required for efficient lysine acylation in more complex biological milieu, such as in living cells, but there are no rational guidelines for developing efficient lysine acylation catalysts for use under physiological conditions as opposed to in organic solvents. We, herein, conducted a kinetic analysis of the ability of DSH and several derivatives to mediate lysine acetylation to better understand the structural elements essential for high acetylation activity under physiological conditions. Interestingly, the obtained trend in reactivity was different from that observed in organic solvents, suggesting that a different principle is necessary for designing chemical catalysts specifically for use under physiological conditions compared to catalysts for use in organic solvents. Based on the obtained information, we identified a new catalyst scaffold with high activity and structural flexibility for further modification to improve this catalyst system.     

The role of phadiatop in the screening of respiratory allergy

Phadiatop is a new in vitro screening test for respiratory allergy. This test, based on the RAST procedure, detects in serum, the presence of specific IgE to a mixture of common inhalent allergens. Among 70 patients (26 children and 44 adults) consulting for respiratory syndrome, Phadiatop was positive in 31 cases. There were a good correlation between this new test and skin tests (59% for adults and 92% for children), total IgE (70% for adults and 65% for children) and RAST (93% for adults and 96% for children). Phadiatop, with a specificity of 100%, a sensitivity of 82% (76% for adults and 92% for children) and an efficiency of 90% (86% for adults and 96% for children), is a more accurate test than total IgE and could be an excellent in vitro screening test for respiratory allergy.     

Stem cells in development of therapeutics for Parkinson's disease: a perspective

Using Parkinson's disease as a prototype of neurodegenerative diseases, we propose applications of human stem cells in the development of therapeutics for neurodegenerative diseases. First, in vitro differentiation of human stem cells offers a versatile model for dissecting molecular interactions underlying human dopamine (DA) neuron specification, which may form a foundation for instigating regeneration of DA neurons from progenitors that reside in the brain. Second, stem cells derived from diseased cells or through genetic modification can serve as a platform for unraveling biochemical processes that lead to the cellular pathogenesis of degeneration. This may in turn serve as a template for identifying or developing therapeutics for slowing, stopping, or reversing the disease process. And finally, stem cells, particularly those induced from patients' own cells, provide a reliable source of DA neurons for cell-based therapy.     

Affinity of corticosteroids for mineralocorticoid and glucocorticoid receptors of the rabbit kidney: effect of steroid substitution

Corticosteroid derivatives coupled in the C3, C7 or C17 position with a long aliphatic chain were synthesized in order to select a suitable ligand for the preparation of a biospecific affinity adsorbent for mineralocorticoid receptor purification. The affinity of these derivatives for mineralocorticoid receptors (MR) and glucocorticoid receptors (GR) was explored in rabbit kidney cytosol. In this model, aldosterone bound to a single class of receptors with high affinity (Kd 1 nM) and mineralocorticoid specificity. RU26988, a highly specific ligand for GR, did not compete for these sites. The C7 and C17 positions were found to be of crucial importance in the steroid's interaction with the mineralocorticoid receptors, since the linkage of a long side chain in these positions induced complete loss of affinity. Hence, deoxycorticosterone no longer bound to MR after 17 beta substitution with a 9-carbon aliphatic chain. This loss of affinity was not observed for glucocorticoids. The 17 beta nonylamide derivative of dexamethasone still competed for GR. Increasing the length of the C7 side of the spirolactone SC26304 suppressed its affinity for MR. Finally, C3 was an appropriate position for steroid substitution. The 3-nonylamide of carboxymethyloxime deoxycorticosterone bound to MR but not to GR, and therefore constitutes a suitable ligand for the preparation of a mineralocorticoid adsorbent.     

Relationship between thermodynamic driving force and one-way fluxes in reversible processes

Chemical reaction systems operating in nonequilibrium open-system states arise in a great number of contexts, including the study of living organisms, in which chemical reactions, in general, are far from equilibrium. Here we introduce a theorem that relates forward and reverse fluxes and free energy for any chemical process operating in a steady state. This relationship, which is a generalization of equilibrium conditions to the case of a chemical process occurring in a nonequilibrium steady state in dilute solution, provides a novel equivalent definition for chemical reaction free energy. In addition, it is shown that previously unrelated theories introduced by Ussing and Hodgkin and Huxley for transport of ions across membranes, Hill for catalytic cycle fluxes, and Crooks for entropy production in microscopically reversible systems, are united in a common framework based on this relationship.     

Screening for functional expression and overexpression of a family of diiron-containing interfacial membrane proteins using the univector recombination system

The large number of uncharacterized genes emerging from genome sequencing projects has resulted in a need for quick and reliable screening methods for protein expression parameters. We have utilized the univector plasmid recombination system (as previously reported) to develop a series of vectors for rapid screening for expression in Escherichia coli. A high level of recombinant protein expression is a requirement for purification of protein for structural determination and other purposes. In other applications, successful complementation of a missing enzyme activity in E. coli, as well as directed evolution studies and metabolic engineering, often require a much lower level of protein expression. In this report we describe the construction of a number of new pHOST vectors that can be screened for both low- and high-level expression. We isolated a mutant vector for MBP fusions that exhibited a more optimal level of expression for complementation of aerobic respiration in hemA(-) E. coli, our functional assay for the alternative oxidase. We then demonstrated the use of our system to rapidly screen for both optimal functional expression and optimal overexpression of the alternative oxidase as well as two other members of a family of membrane-bound diiron carboxylate proteins, the plastid terminal oxidase and 5-demethoxyquinone hydroxylase.     

Divergent functional properties of the ribosome-associated molecular chaperone Ssb compared with other Hsp70s.

Ssbs of Saccharomyces cerevisiae are ribosome-associated molecular chaperones, which can be cross-linked to nascent polypeptide chains. Because Ssbs are members of a divergent subclass of Hsp70s found thus far only in fungi, we asked if the structural requirements for in vivo function were similar to those of "classic" Hsp70s. An intact peptide-binding domain is essential and an alteration of a conserved residue in the peptide-binding cleft (V442) affects function. However, Ssb tolerates a number of alterations in the peptide-binding cleft, revealing a high degree of flexibility in its functional requirements. Because binding of Ssb to peptide substrates in vitro was undetectable, we assessed the importance of substrate binding using the chimera BAB, in which the peptide binding domain of Ssb is exchanged for the analogous domain of the more "classical" Hsp70, Ssa. BAB, which binds peptide substrates in vitro, can substitute for Ssb in vivo. Alteration of a residue in the peptide-binding cleft of BAB creates a protein with a reduced affinity for peptide and altered ribosome binding that is unable to substitute for Ssb in vivo. These results indicate that Ssb's ability to bind unfolded polypeptides is likely critical for its function. This binding accounts, in part, for its stable interaction with translating ribosomes, even although it has a low affinity for peptides that detectably bind to other Hsp70s in vitro. These unusual properties may allow Ssb to function efficiently as a chaperone for ribosome-bound nascent chains.     

Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli

Theoretical studies have predicted a trade-off between growth rate and yield in heterotrophic organisms. Here we test for the existence of this trade-off by analyzing the growth characteristics of 12 E. coli B populations that evolved for 20,000 generations under a constant selection regime. We performed three different tests. First, we analyzed changes in growth rate and yield over evolutionary time for each population. Second, we tested for a negative correlation between rate and yield across the 12 populations. Finally, we isolated clones from four selected populations and tested for a negative correlation between rate and yield within these populations. We did not find evidence for a trade-off based on the first two tests. However, we did observe a trade-off based on the within-population correlation of yield and rate. Our results indicate that, at least for the populations studied here, an analysis of the within-population diversity might be the most sensitive test for the existence of a trade-off. The observation of a trade-off within, but not between, populations suggests that the populations evolved different genetic solutions for growth in the selective environment, which in turn led to different physiological constraints.     

Regulation of zebrafish hatching by tetraspanin cd63

Tetraspanins cause the clustering of membrane proteins into a level of organisation essential for cellular function. Given the importance and complicated nature of this mechanism, we attempted a novel approach to identify the function of a single component in a biologically relevant context. A morpholino knockdown strategy was used to investigate the role of cd63, a membrane protein associated with intracellular transport and a melanoma marker, in embryonic zebrafish. By using three separate morpholinos targeting cd63, we were able to identify a specific phenotype. Strikingly, morphant fish failed to hatch due to the lack of secreted proteolytic enzymes required for chorion-softening. The morphology of the hatching gland at both the cellular and intracellular levels was disorganised, suggesting a role for cd63 in the functioning of this organ. This work identifies a specific role for cd63 in the zebrafish embryo and provides evidence for the suitability of zebrafish as a model system for the investigation of tetraspanin enriched microdomains.     

Re-entry programs, from an anti-unconventional ex-offender

The purpose of this article seeks to question the relationship of higher levels of educational attainment and the ability for successful reintegration into mainstream society for the formerly incarcerated. Specifically this article highlights societal negligence for individual success of the formerly incarcerated, opting for a corporatized exploitation of those in the reentry process premised on the socially constructed label “ex-con.” Research surrounding labeling and reentry suggests once individuals are released from prison the social stigma experienced in society is a recipe for failure and reoffending. One way this emerges is in the form of hiring policies in corporate occupations, prohibiting the hiring of individual s convicted of a felony. Critical criminology suggests the class structure is in place for those in power to stay in power and keep those who are inferior in inferior social positions. Using both points of view as a framework, with the idea of corporate monopoly as a lens, allows for an untraditional critical perspective of the reentry process as a capitalist, for-profit industry. Questioning the role and intentions of reentry initiatives provides a general discussion for increasing success rates of those in the reentry process and reducing capital costs spent for incarceration. The specific focus of this article presents my experience of the reentry process.     

Estimates of time and propensity for dental treatment among institutionalised elders

The oral health and concerns of elderly residents were surveyed in a stratified random selection of 41 long-term care facilities in Vancouver. The residents who could participate were examined and interviewed to determine their oral health and concerns about dental treatment. The need and time required for treatment were estimated in six groups to reflect the propensity for treatment in dentate and edentate subjects. The propensity for treatment was high in about one-third of the participants whereas it was unlikely that one-tenth of those examined would ever use a dental service. In general, there was a widespread need for a diagnostic service because so few had been examined by a dentist in the previous year. Prosthodontics accounted for most of the treatment in all of the propensity groups, with substantially more time required by the dentate residents. There was also a substantial need for management of mucosal pathoses and oral hygiene and, to a lesser extent, for dental restorations and endodontics. Overall, our estimates indicate a substantial need for dental treatment among residents of long-term care facilities, although the need is reduced by half if the propensity for treatment is considered.     

Possible genomic imprinting of three human obesity-related genetic loci

To detect potentially imprinted, obesity-related genetic loci, we performed genomewide parent-of-origin linkage analyses under an allele-sharing model for discrete traits and under a family regression model for obesity-related quantitative traits, using a European American sample of 1,297 individuals from 260 families, with 391 microsatellite markers. We also used two smaller, independent samples for replication (a sample of 370 German individuals from 89 families and a sample of 277 African American individuals from 52 families). For discrete-trait analysis, we found evidence for a maternal effect in chromosome region 10p12 across the three samples, with LOD scores of 5.69 (single-point) and 4.52 (multipoint) for the pooled sample. For quantitative-trait analysis, we found the strongest evidence for a maternal effect (single-point LOD of 2.85; multipoint LOD of 4.01 for body mass index [BMI] and 3.69 for waist circumference) in region 12q24 and for a paternal effect (single-point LOD of 4.79; multipoint LOD of 3.72 for BMI) in region 13q32, in the European American sample. The results suggest that parent-of-origin effects, perhaps including genomic imprinting, may play a role in human obesity.     

Male × female interaction for a pre-copulatory trait, but not a post-copulatory trait, among cosmopolitan populations of Drosophila melanogaster

Sexual coevolution occurs when changes in the phenotype of one sex select for changes in the other sex. We can identify the "footprint" of this coevolution by mating males and females from different populations and testing for a male-female genotype interaction for a trait associated with male (or female) performance. Here we mated male Drosophila melanogaster from five different continents with females from their own and different continents to test for a male-female interaction for mating speed, a pre-copulatory trait, and female reproductive investment, a post-copulatory trait. We found a strong male-female interaction for mating speed, consistent with previous studies using different populations, suggesting that the potential for sexual coevolution for this trait is present in this species. In contrast, we did not detect a male-female interaction for female reproductive investment. Although a male-female interaction for mating speed is compatible with the hypothesis of ongoing sexual coevolution, the nature of our experimental design is unable to exclude alternate explanations. Thus, the evolutionary mechanisms promoting male-female genotype interactions for pre-copulatory mating traits in D. melanogaster warrant further investigation.     

Which objectively assessed limitations in health status, activities of daily living, or in psychological and social spheres are decisive for referral to a nursing home or to a home for the aged

Which type of limitation is most decisive for a positive indication for a residential home or a somatic or psycho-geriatric nursing home, and to what extent do data on living situation (independent, adapted or intramural) and the social situation (alone or living together) influence this qualification? To obtain an answer to this question three experiments with an integrated, objective and independent assessment-for-care system were set up in the Netherlands. We studied one of them, in the town of Meppel, started in 1996. The study population consisted of all older people living in and around Meppel who had a positive indication for either a residential home, or a somatic or psycho-geriatric nursing home (N = 206 in 1998). Differences in limitations were computed by means of analysis of variance and the types of limitation and their impact on the type of allocated institutions were computed by logistic regression. The limitations only partially explain the types of indication. Indication for a residential home is based on physical limitations. When these increase they become a contra-indication for a residential home and a somatic nursing home indication is given. Mental limitations primarily yield indications for psycho-geriatric nursing homes. Social limitations have a higher incidence among persons with an indication for a somatic nursing home but cannot fully explain this indication. Persons with a residential home indication were significantly more often from an adapted living situation background. The living situation -alone or together-does not have an impact on the indication. We may not conclude that the assessment took place objectively, for, based on the registration it is impossible to conclude for what criteria a person was indicated for a specific type of institution. The objective of assessment, the allocation and distribution of collectively financed care in residential homes and nursing homes based on verifiable assessment methodology could not be realised.     

How large a managed area is needed to protect a threatened animal species? Combining simple dispersal and population models

The size and shape of the managed area for a threatened species to have a stable or growing population is a central issue for conservation management, for example for kiwi, Apteryx sp. Combining geometric probability results for retention of juveniles to breed in the protected area with a standard matrix population model allows the creation of an explicit relationship between the minimum area needed and how far juveniles of the species disperse to establish breeding territories. For a given set of demographic parameters for the population, and a rectangular protected area, there is a quadratic relationship between area and dispersal distance. Extensions for a circular protected area, and for a probability distribution on dispersal distance, are considered. The results are applied to kiwi, using established population parameters, giving results that match closely those from a previously published simulation. This approach can provide simple tools, readily implemented in a spreadsheet, for assessment of the size and shape of protected areas needed in conservation management of animals that disperse before breeding.