Origins of hydrogenosomes and mitochondria

Complete genome sequences for many oxygen-respiring mitochondria, as well as for some bacteria, leave no doubt that mitochondria are descendants of alpha-proteobacteria, a finding for which the endosymbiont hypothesis can easily account. Yet a wealth of data indicate that mitochondria and hydrogenosomes - the ATP-producing organelles of many anaerobic protists - share a common ancestry, a finding that traditional formulations of the endosymbiont hypothesis less readily accommodates. Available evidence suggests that a more in-depth understanding of the origins of eukaryotes and their organelles will hinge upon data from the genomes of protists that synthesize ATP without the need for oxygen.     

Harvesting and predation of a sex- and age-structured population

We study a discrete-time system of equations for a structured ungulate population exploited by human harvesting or a dynamic predator. The population is divided into juveniles, and female and male adults. Harvesting is concentrated on adults (trophy hunting of males or population control measures on females), whereas predation occurs in juveniles. Though the model consists of four nonlinear equations, we find explicit expressions for the steady states. We use these explicit expressions to investigate harvesting rates that allow population persistence, rates that ensure population control, and optimal harvesting efforts. Several reductions of complexity allow for a detailed analysis of the dynamics of the model. Most notably, we find that even compensatory density dependence can lead to a period doubling bifurcation, that the model does not support consumer–resource cycles, and that an Allee effect can emerge from the interplay of stage-specific predation and density-dependent prey reproduction.     

Isolation and evaluation of oil-producing microalgae from subtropical coastal and brackish waters

Microalgae have been widely reported as a promising source of biofuels, mainly based on their high areal productivity of biomass and lipids as triacylglycerides and the possibility for cultivation on non-arable land. The isolation and selection of suitable strains that are robust and display high growth and lipid accumulation rates is an important prerequisite for their successful cultivation as a bioenergy source, a process that can be compared to the initial selection and domestication of agricultural crops. We developed standard protocols for the isolation and cultivation for a range of marine and brackish microalgae. By comparing growth rates and lipid productivity, we assessed the potential of subtropical coastal and brackish microalgae for the production of biodiesel and other oil-based bioproducts. This study identified Nannochloropsis sp., Dunaniella salina and new isolates of Chlorella sp. and Tetraselmis sp. as suitable candidates for a multiple-product algae crop. We conclude that subtropical coastal microalgae display a variety of fatty acid profiles that offer a wide scope for several oil-based bioproducts, including biodiesel and omega-3 fatty acids. A biorefinery approach for microalgae would make economical production more feasible but challenges remain for efficient harvesting and extraction processes for some species.     

Intermediates and the folding of proteins L and G

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G, which are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted beta-1 and beta-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding, and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third beta-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally, the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first-order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.     

Structural requirements and mechanism for heparin-dependent activation and tetramerization of human betaI- and betaII-tryptase

Tryptase, a tetrameric serine protease, is a main constituent of the secretory granules in human mast cells, where it is stored in complex with heparin or chondroitin sulfate proteoglycan. Human tryptase has been implicated in a variety of clinical conditions including asthma, but the mechanisms that lead to its tetramerization/activation have not been extensively investigated. Here we addressed the activation mechanisms for human betaI and betaII-tryptase, which differ in that betaI-tryptase is N-glycosylated at Asn102 whereas betaII-tryptase has a Lys residue at position 102, and consequently lacks the corresponding N-glycosylation. We found that both tryptases were dependent on heparin for activation/tetramerization, but whereas betaI-tryptase activation preferentially occurred at acidic pH, betaII-tryptase activation was less pH-dependent. Both betaI and betaII-tryptase bound strongly to heparin-Sepharose at acidic pH but with lower affinity at neutral pH. Further, while addition of heparin to betaI-tryptase predominantly resulted in formation of active tetrameric enzyme, betaII-tryptase showed a tendency to form inactive aggregates. betaI and betaII-tryptase were similar in that the minimal heparin size to induce activation was an octasaccharide and in that the interaction with heparin and structurally related polysaccharides was dependent on high anionic charge density rather than on specific structural motifs. Addition of decasaccharides to both betaI and betaII-tryptase resulted in the formation of active monomeric enzyme, whereas intact heparin promoted assembly of tetrameric enzyme. This, together with a bell-shaped dose response curve for heparin-induced activation, suggests that the mechanism for tetramerization involves bridging of individual tryptase monomers by heparin. Taken together, this study indicates a key role for heparin in the activation of human beta-tryptase.     

Conformational propensities and residual structures in unfolded peptides and proteins

Ample evidence gathered over the last ten years indicates that unfolded and naturally disordered proteins and peptides can show local order in that short segments can adopt turn or polyproline II-like conformations. These findings show that unfolded states cannot be described by the so-called random coil model which assumes that individual amino acid residues sample the entire sterically accessible parts of the Ramachandran with very similar probabilities. This article reviews the experimental evidence for the notion that amino acid residues have different propensities for polyproline II, β-strand, helical and turn conformations in water. These propensities are changed by interactions with nearest neighbours. We show that for a substantial number of residues the conformational propensities in the unfolded state correlate with values for helix propagation and the Chou-Fasman propensities for β-strands. Based on the presented results we hypothesize that the conformational distributions of a representative set of short peptides could be used for predicting structural distributions of disordered peptides and proteins in the future.     

Tikiguania and the antiquity of squamate reptiles (lizards and snakes)

Tikiguania estesi is widely accepted to be the earliest member of Squamata, the reptile group that includes lizards and snakes. It is based on a lower jaw from the Late Triassic of India, described as a primitive lizard related to agamids and chamaeleons. However, Tikiguania is almost indistinguishable from living agamids; a combined phylogenetic analysis of morphological and molecular data places it with draconines, a prominent component of the modern Asian herpetofauna. It is unlikely that living agamids have retained the Tikiguania morphotype unchanged for over 216 Myr; it is much more conceivable that Tikiguania is a Quaternary or Late Tertiary agamid that was preserved in sediments derived from the Triassic beds that have a broad superficial exposure. This removes the only fossil evidence for lizards in the Triassic. Studies that have employed Tikiguana for evolutionary, biogeographical and molecular dating inferences need to be reassessed.     

Rapid and selective oxygen-regulated protein tyrosine denitration and nitration in mitochondria

Growing evidence connects a cumulative formation of 3-nitrotyrosyl adducts in proteins as a marker for oxidative damage with the pathogenesis of various diseases and pathological conditions associated with oxidative stress. A physiological signaling role for protein nitration has also been suggested. Controlled "denitration" would be essential for such a contribution of protein nitration to cellular regulatory processes. Thus, we further characterized such a potentially controlled, reversible tyrosine nitration that occurs in respiring mitochondria during oxygen deprivation followed by reoxygenation, which we recently discovered. Mitochondria constitute cellular centers of protein nitration and are leading candidates for a "nitrative" regulation. Mitochondria are capable of completely eliminating 3-nitrotyrosyl adducts during 20 min of hypoxia-anoxia and undergoing a selective partial reduction after only 5 min. This denitration is independent of protein degradation but depends on the oxygen tension. Reoxygenation re-establishes protein tyrosine nitration patterns that are almost identical to the pattern that occurs before hypoxia-anoxia, with nitration levels that depend on the duration of hypoxia-anoxia. The identified mitochondrial targets of this process are critical for energy and antioxidant homeostasis and, therefore, cell and tissue viability. This cycle of protein nitration and denitration shows analogies to protein phosphorylation, and we demonstrate that the cycle meets most of the criteria for a cellular signaling mechanism. Taken together, our data reveal that protein tyrosine nitration in mitochondria can be controlled, is target-selective and rapid, and is dynamic enough to serve as a nitrative regulatory signaling process that likely affects cellular energy, redox homeostasis, and pathological conditions when these features become disturbed.     

Cloning and adoption: a reply to Levy and Lotz

In previous articles I discussed the ethics of human reproductive cloning, focusing on a possible future scenario in which reproductive cloning can be accomplished without an elevated risk of anomalies to the children who are created. I argued that in such a scenario it would be ethically permissible for infertile couples to use cloning as a way to have genetically related children and that such use should not be prohibited. In 'Reproductive Cloning and a (Kind of) Genetic Fallacy', Neil Levy and Mianna Lotz raise objections to my conclusions. They disagree with the view, for which I argued, that some couples can have defensible reasons for desiring genetically related children. They also offer several new arguments against reproductive cloning, including an argument that it would diminish the number of adoptions, thereby adversely affecting the welfare of children who need to be adopted. In this paper I point out that Levy and Lotz's criticisms misconstrue my arguments and that there are serious problems with their arguments for prohibiting infertile couples from using cloning, including their argument from adoption.     

Desmoplakin I and desmoplakin II. Purification and characterization

Desmoplakins I and II (DP1 and DP2), major cytoskeletal structural proteins concentrated in desmosomes, have been purified in milligram quantities from keratomed pig tongue epithelium. DP1 and DP2 extracted from purified desmosomes in 4 M urea were chromatographed on DEAE-cellulose and remained soluble after removal of urea during subsequent chromatography. The two proteins differed by only about 15% in molecular weight (Mr = 285,000 for DP1 and 225,000 for DP2 on sodium dodecyl sulfate-polyacrylamide gels) were found to have similar Svedberg constants, 6.7 S (DP1) and 6.4 S (DP2); nevertheless, separation was readily achieved by gel filtration, since DP1 has a Stokes radius (Rs) of 164 nm, but DP2 has a Rs = 90 nm. Calculated molecular mass was 462,000 daltons for DP1 and 242,000 daltons for DP2, suggesting that DP1 may be a dimer in solution and DP2 a monomer. Cross-linking by disuccinimidyl suberate of 125I-labeled DP1 or DP2 at nanomolar concentrations confirmed that DP1 is a dimer by doubling of its apparent Mr on sodium dodecyl sulfate gels and indicated that DP2, which failed to become cross-linked, is a monomer. DP1 in the presence of 8 M urea could not be cross-linked, indicating that urea dissociated the dimers. Calculated frictional ratios (f/f0 = 3 for DP1 and 2 for DP2) indicate that both proteins are highly asymmetric. Rotary shadowing of DP1 demonstrated flexible dumbbell-like extended shapes with a maximal length of about 180 nm with a central rod and coiled or folded end domains. DP2 showed variable extended shapes of maximal length of 78-93 nm. The increased length and Rs of desmoplakin I is probably accounted for by formation of tail-to-tail dimers. Two-dimensional peptide maps and amino acid analysis showed very similar profiles for the two proteins. Purified keratin filaments failed to bind DP1 or DP2, and prekeratins polymerized in vitro and sedimented failed to remove desmoplakins, suggesting that desmoplakins do not bind keratins directly. These studies provide a basis for functional and detailed structural studies with purified native desmosomal proteins.     

Research involving prisoners: consensus and controversies in international and European regulations

This article examines international and European regulations on research involving prisoners for consensus, differences, and their consequences, and offers a critical evaluation of the various approaches. Agreement exists that prisoners are at risk of coercion, which might interfere with their ability to provide voluntary informed consent to research. Controversy exists about the magnitude of this risk and the consequences that should follow from this risk. Two strategies are proposed for a method of protecting prisoners that does not lead to discrimination: first, more caution to assure non-coerced consent and second, restrictions on the type of research. Most regulations stress the importance of the principle of equivalence of healthcare in places of detention as part of an efficient protection against research risks and discrimination.
All the presented approaches have shortcomings. While 'over-use' of prisoners for research as compared to the general population is ethically unjustified, not granting prisoners access to studies beneficial to their own health because of over-strict regulations is equally unjustified. A middle solution should be preferred, one that grants a minimum of protection together with the lowest possible barriers. Research that does not entail a direct benefit for the individual detainee should be restricted to types of research that have a benefit for detainees as a group and that are of low risk. What will ultimately protect prisoners best, while producing the greatest benefit for them, is access to the same healthcare available to members of the community including research as a true option.     

Isolation and Characterization of Chromosome-Gain and Increase-in-Ploidy Mutants in Yeast

We have developed a colony papillation assay for monitoring the copy number of genetically marked chromosomes II and III in Saccharomyces cerevisiae. The unique feature of this assay is that it allows detection of a gain of the marked chromosomes even if there is a gain of the entire set of chromosomes (increase-in-ploidy). This assay was used to screen for chromosome-gain or increase-in-ploidy mutants. Five complementation groups have been defined for recessive mutations that confer an increase-in-ploidy (ipl) phenotype, which, in each case, cosegregates with a temperature-sensitive growth phenotype. Four new alleles of CDC31, which is required for spindle pole body duplication, were also recovered from this screen. Temperature-shift experiments with ipl1 cells show that they suffer severe nondisjunction at 37°. Similar experiments with ipl2 cells show that they gain entire sets of chromosomes and become arrested as unbudded cells at 37°. Molecular cloning and genetic mapping show that IPL1 is a newly identified gene, whereas IPL2 is allelic to BEM2, which is required for normal bud growth.     

Integration and Disruption Effects of Shape and Texture in Haptic Search

In a search task, where one has to search for the presence of a target among distractors, the target is sometimes easily found, whereas in other searches it is much harder to find. The performance in a search task is influenced by the identity of the target, the identity of the distractors and the differences between the two. In this study, these factors were manipulated by varying the target and distractors in shape (cube or sphere) and roughness (rough or smooth) in a haptic search task. Participants had to grasp a bundle of items and determine as fast as possible whether a predefined target was present or not. It was found that roughness and edges were relatively salient features and the search for the presence of these features was faster than for their absence. If the task was easy, the addition of these features could also disrupt performance, even if they were irrelevant for the search task. Another important finding was that the search for a target that differed in two properties from the distractors was faster than a task with only a single property difference, although this was only found if the two target properties were non-salient. This means that shape and texture can be effectively integrated. Finally, it was found that edges are more beneficial to a search task than disrupting, whereas for roughness this was the other way round.     

Religion and Identity: The Role of Ideological,Social, and Spiritual Contexts

Existing research demonstrates a positive relation between religion and identity among adolescents. A conceptual framework is presented suggesting that religion provides a distinct setting for identity exploration and commitment through offering ideological, social, and spiritual contexts. It is then suggested that the religious context promotes a sense of identity that transcends the self and promotes a concern for the social good and that religious institutions provide unique settings for adolescent identity formation. In addition to the potential developmental benefits of religion, negative consequences on identity development are considered. Finally, recommendations for empirical study are suggested.     

Reserpine and chlorpromazine,their use in alcoholic and geriatric patients

Although reserpine and chlorpromazine had tranquilizing effect on a number of geriatric and alcoholic patients in a state hospital, several complicating results were noted, some with a bearing on the patients' health and others that might affect the assignment of personnel. Lipoprotein studies carried out on patients receiving reserpine seemed to indicate that a reduction in the blood levels of the denser lipoprotein molecules took place during therapy. Several elderly patients receiving chlorpromazine died of diseases that were not as sharply manifest by symptoms as they might be expected to be. Hence the need for closer observation than a limited staff could afford seemed a matter for consideration. Another consideration of the same order was the possible need for increased personnel for psychotherapy in light of the more receptive condition of the patients.     

Mitochondrial genetics and obesity: evolutionary adaptation and contemporary disease susceptibility

Obesity is a leading risk factor for a variety of metabolic diseases including cardiovascular disease, diabetes, and cancer. Although in its simplest terms, obesity may be thought of as a consequence of excessive caloric intake and sedentary lifestyle, it is also evident that individual propensity for weight gain can vary. The etiology of individual susceptibility to obesity seems to be complex—involving a combination of environmental–genetic interactions. Herein, we suggest that the mitochondrion plays a major role in influencing individual susceptibility to this disease via mitochondrial–nuclear interaction processes and that environmentally influenced selection events for mitochondrial function that conveyed increased reproductive and survival success during the global establishment of human populations during prehistoric times can influence individual susceptibility to weight gain and obesity.     

Pastoral dairy marketing and household wealth interactions and their implications for calves and humans in Ethiopia

Surveys of pastoral households in a semi-nomadic Borana community during 1987–1988 were used to test the hypothesis that poorer families living closest to a market town would be most affected by the enhanced opportunity to sell dairy products, which would intensify competition between people and calves for milk and have negative implications for calf management. These poorer families indeed reported the highest rates of milk offtake per cow, and the milk increment was probably sold to purchase more grain for human consumption at the expense of milk intake for the calf. Consequently, this strategy may increase the susceptibility of malnourished calves to disease, especially those from lower-producing dams. Benefits of improved human energy intake from grain and retention of livestock capital must be weighed against risks of calf death and possible malnutrition of people from milk restriction when assessing dairy marketing trade-offs that are most acute for the poor. Opportunity to sell dairy products at favorable terms of trade helps the poorest people survive, and their risks could be mitigated by policies that facilitate grain marketing in the rangelands and interventions that improve calf feeding management, diversify human diets, and create alternative opportunities for women to generate income. The households postulated to be most at risk were identified from a complex, but logical, interaction among factors of distance to market, household wealth, and the quality of milking cows held. This indicates that targeting such needy groups for development assistance may require a more detailed and interdisciplinary analysis of production systems than is commonly practiced.     

Adequate and economic factory transformability and the effects on logistical performance

Objective-oriented factory planning is a prerequisite for the economic operation of a factory. As intensive discussions in the literature as well as practical findings in factories over the years show, transformability and logistics are among the key objectives of a factory. It is striking, however, that both objectives have not so far been related to each other. Based on these findings, a method for evaluating the actual as well as the target transformability of a factory has been developed. It allows the user to assess whether the factory possesses adequate and economic transformability. In order to make the method more manageable for users in practice, a software tool is presented, and a benchmarking has been derived from the data collected by evaluating factory transformability. In addition, it has been found that transformability can influence logistics. A procedure will be presented that allows major means of adjustment to be found that improve the logistics objectives of a factory by using transformability. Finally, the outlook for future developments is discussed.