N for AsN – O for StrOcture? A strand–loop–strand motif for prokaryotic O‐glycosylation

So far, it has not been possible to identify a general sequence motif for O-glycosylation in bacteria. In this issue, Charbonneau et al. (2012) demonstrate why O-glycosylation is mediated by a 13-residue strand-loop-strand motif which is part of a 19-residue imperfect repeat in the passenger domain of bacterial autotransporters. This motif provides a convenient 'glycosylation cassette' and raises intriguing questions about the structural regulation of the glycosylation pathway.     

A Framework for Decision-Making for Mass Distribution of Mectizan<Superscript>®</Superscript> in Areas Endemic for <Emphasis Type="Italic">Loa loa</Emphasis>

BACKGROUND: The occurrence of Loa loa encephalopathy following mass treatment of onchocerciasis with Mectizan(R) has adversely affected onchocerciasis control efforts in central Africa. Persons with very high densities of L. loa microfilaremia are at increased risk of encephalopathy, but little is known about the geographic distribution of these persons within central Africa. RAPLOA, a new technique that correlates the proportion of community members reporting a history of eyeworm with the prevalence of high-intensity L. loa microfilaremia in that community, may be useful for rapid assessment of areas at potential risk of treatment-related L. loa encephalopathy. Validation of RAPLOA is ongoing. The operational and risk-reduction advantages of RAPLOA over the current technique of village-by-village rapid epidemiologic assessment for onchocerciasis (REA) are unknown. METHODS: We developed a decision model to compare four strategies for minimizing sequelae of L. loa encephalopathy following mass treatment with Mectizan(R) in areas co-endemic for onchocerciasis and loiasis: REA; RAPLOA with threshold eyeworm prevalences of 40% and 20% (RAPLOA-40 and RAPLOA-20, respectively); and combined REA/RAPLOA-40. RESULTS: In the model, all four strategies significantly reduced risk of death and neurologic complications from L. loa encephalopathy, but RAPLOA-20 and REA resulted in half as many such cases as did RAPLOA-40 or combined REA/RAPLOA-40. CONCLUSION: RAPLOA is likely to be useful programmatically in reducing risk of L. loa encephalopathy following mass treatment with Mectizan(R). It also may be cost-saving. Before full-scale implementation, additional data are needed on geographic clustering of high-density L. loa microfilaremia and on RAPLOA's reliability and cost.     

Is there safety‐in‐numbers for prey?

The abundance of prey affects the rate of predation, but little consensus exists on whether this enhances or reduces per capita mortality. Studies of aggregating prey in marine habitats generally emphasise that the probability of predation of any individual is the reciprocal of the number of prey within a school. A field experiment tested the alternative hypotheses that predation by predatory fish on schooling prey (1) increased with an increase in the number of prey per school and that this caused (2) survival to be lower in schools with more individuals. The number of prey (juvenile Acanthochromis polyacanthus ) per school was manipulated in replicate treatments with natural densities of large predatory fish (open plots) and treatments without large predatory fish (exclusion cages). Large predatory fish preyed on juveniles in a density-dependent manner and this was the key source of density-dependent mortality in plots open to all predators. There was some suggestion that small predatory fish also prey on juveniles in a density-dependent manner, but this was weak and did not translate into density-dependent mortality of juveniles. It would appear that aggregation of prey may be a successful strategy against predation from some predators, but not always every predator, or all predators in combination.     

Nanostructured sensors for biomedical applications — a current perspective

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Making connections — strategies for single molecule fluorescence biophysics

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RNA epigenetics — chemical messages for posttranscriptional gene regulation

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Caveolin; different roles for insulin signal?

Caveolae, discovered by electron microscope in the 1950s, are membrane invaginations that accommodate various molecules that are involved in cellular signaling. Caveolin, a major protein component of caveolae identified in 1990s, has been known to inhibit the function of multiple caveolar proteins, such as kinases, which are involved in cell growth and proliferation, and thus considered to be a general growth signal inhibitor. Recent studies using transgenic mouse models have suggested that insulin signal may be exempted from this inhibition, which rather requires the presence of caveolin for proper signaling. Caveolin may stabilize insulin receptor protein or directly stimulate insulin receptors. Other studies have demonstrated that caveolae provide the TC10 complex with cellular microdomains for glucose transportation through Glut4. These findings suggest that caveolin plays an important role in insulin signal to maintain glucose metabolism in intact animals. However, the role of caveolin in insulin signal may differ from that in other transmembrane receptor signals.     

Predicting <Superscript>13</Superscript>C<Superscript>α</Superscript> chemical shifts for validation of protein structures

The ¹³C^α chemical shifts for 16,299 residues from 213 conformations of four proteins (experimentally determined by X-ray crystallography and Nuclear Magnetic Resonance methods) were computed by using a combination of approaches that includes, but is not limited to, the use of density functional theory. Initially, a validation test of this methodology was carried out by a detailed examination of the correlation between computed and observed ¹³C^α chemical shifts of 10,564 (of the 16,299) residues from 139 conformations of the human protein ubiquitin. The results of this validation test on ubiquitin show agreement with conclusions derived from computation of the chemical shifts at the ab initio Hartree–Fock level. Further, application of this methodology to 5,735 residues from 74 conformations of the three remaining proteins that differ in their number of amino acid residues, sequence and three-dimensional structure, together with a new scoring function, namely the conformationally averaged root-mean-square-deviation, enables us to: (a) offer a criterion for an accurate assessment of the quality of NMR-derived protein conformations; (b) examine whether X-ray or NMR-solved structures are better representations of the observed ¹³C^α chemical shifts in solution; (c) provide evidence indicating that the proposed methodology is more accurate than automated predictors for validation of protein structures; (d) shed light as to whether the agreement between computed and observed ¹³C^α chemical shifts is influenced by the identity of an amino acid residue or its location in the sequence; and (e) provide evidence confirming the presence of dynamics for proteins in solution, and hence showing that an ensemble of conformations is a better representation of the structure in solution than any single conformation. Electronic Supplementary Material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

trans-Cyclooctene — a stable,voracious dienophile for bioorthogonal labeling

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Can paleopathology provide evidence for “compassion”?

Paleopathological analyses of skeletal remains have provided significant information about diet and health in prehistoric populations. A number of individuals have been recovered whose remains show evidence of impairments that would have precluded "normal" functioning, resulting in a disability. The most famous example is Shanidar I; more recent discoveries include the Romito 2 dwarf from Italy and a boy with spina bifida from the Windover site in Florida. These finds have been interpreted by some writers as evidence for compassion and "moral decency" among the other members of the community, who would have had to support these nonproductive individuals. However, these interpretations are based on a number of implicit assumptions: about the number of nonproductive members normally present in any population, about the abilities of disabled individuals to contribute to society, about the treatment of disabled individuals by other members of the group, and about the "moral rightness" of facilitating the survival of a disabled individual under all circumstances. These assumptions are not justified by the evidence from the archeological record or by reference to ethnographic analogy. A tendency to focus on physical traits as the sole measure of productive ability, images of Rousseau's "noble savage" transported to the past, and unexamined beliefs about the disabled in modern societies have influenced these archeological interpretations. We are not justified in drawing conclusions either about the quality of life for disabled individuals in the past or about the motives or attitudes of the rest of the community from skeletal evidence of physical impairment.     

The microbial cell — functional unit for energy dependent multistep biocatalysis

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The evidence‐based group‐level symptom‐reduction model as the organizing principle for mental health care: time for change?

The content and organization of mental health care have been heavily influenced by the view that mental difficulties come as diagnosable disorders that can be treated by specialist practitioners who apply evidence‐based practice (EBP) guidelines of symptom reduction at the group level. However, the EBP symptom‐reduction model is under pressure, as it may be disconnected from what patients need, ignores evidence of the trans‐syndromal nature of mental difficulties, overestimates the contribution of the technical aspects of treatment compared to the relational and ritual components of care, and underestimates the lack of EBP group‐to‐individual generalizability. A growing body of knowledge indicates that mental illnesses are seldom “cured” and are better framed as vulnerabilities. Important gains in well‐being can be achieved when individuals learn to live with mental vulnerabilities through a slow process of strengthening resilience in the social and existential domains. In this paper, we examine what a mental health service would look like if the above factors were taken into account. The mental health service of the 21st century may be best conceived of as a small‐scale healing community fostering connectedness and strengthening resilience in learning to live with mental vulnerability, complemented by a limited number of regional facilities. Peer support, organized at the level of a recovery college, may form the backbone of the community. Treatments should be aimed at trans‐syndromal symptom reduction, tailored to serve the higher‐order process of existential recovery and social participation, and applied by professionals who have been trained to collaborate, embrace idiography and maximize effects mediated by therapeutic relationship and the healing effects of ritualized care interactions. Finally, integration with a public mental health system of e‐communities providing information, peer and citizen support and a range of user‐rated self‐management tools may help bridge the gap between the high prevalence of common mental disorder and the relatively low capacity of any mental health service.     

Temperature-activity relationship for the intestinal Na<Superscript>+</Superscript>-K<Superscript>+</Superscript>-ATPase of<Emphasis Type="Italic"> Sparus aurata</Emphasis>. A role for the phospholipid microenvironment?

The temperature dependence for Na(+)-K(+)-ATPase has been examined in the proximal-distal axis of the intestine of gilthead seabream (Sparus aurata), i.e. pyloric caeca (PC), anterior intestine (AI) and posterior intestine (PI). Data derived from the Arrhenius plots showed differences in terms of temperature discontinuity points ( Td) (13.29 degrees C, 16.39 degrees C and 17.48 degrees C for PC, AI and PI, respectively) and activation energy ratios (Ea(2)/Ea(1)) obtained at both sides of Td (2.38, 1.98 and 1.78, for PC, AI and PI, respectively). The analyses of polar lipids showed differences in the levels of certain fatty acids among intestinal regions. The content of each fatty acid and different fatty acid ratios were correlated with the corresponding Td and Ea(2)/Ea(1) values. Regression analyses revealed the existence of strong negative correlations between docosahexaenoic acid (22:6n-3, DHA) or the DHA/monoenes ratio and Td. No obvious relationships were observed for other polyunsaturated fatty acids (PUFA) nor saturated fatty acids. The results obtained in the present study indicate that the heterogeneous values of Td displayed by the Na(+)-K(+)-ATPase along the intestinal tract could be related to a modulatory role of certain fatty acid within the lipid microenvironment of the enzyme.     

PI3-kinase is essential for ADP-stimulated integrin α<Subscript>IIb</Subscript>β<Subscript>3</Subscript>-mediated platelet calcium oscillation,implications for P2Y receptor pathways in integrin α<Subscript>IIb</Subscript>β<Subscript>3</Subscript>-initiated signaling cross-talks

Summary Phosphatidylinositol 3-kinase (PI3K) pathway is important for platelet activation. Recent studies showed that PI3K and oscillative calcium could cross talk to each other and positively regulate integrin α _IIbβ₃-mediated outside-in signaling. However, the mechanism of this feedback regulation remains to be further characterized. Here we found that treatments of both PI3K inhibitor wortmannin and P2Y1 inhibitor A3P5P could inhibit granular secretion in platelets. Additionally, when RGD-substrate adherent platelets were treated with the ADP scavenger apyrase to deplete the granular-released ADP, their attachments in engaging with substrates became looser and the frequency of calcium oscillation decreased. Since it is known that ADP stimulates the PI3K and calcium signal primarily through P2Y12 and P2Y1 receptors respectively, our data indicated that integrin α_IIbβ₃ downstream PI3K and calcium activation might be not completely coupled to integrin associated signaling complex, but in part through feedback stimulation by granular released ADP. Our data indicates the important roles of PI3K and granular released ADP in coordinating the feedback regulations in integrin α_IIbβ₃-mediated platelet activation.     

Is metabolic rate a universal ‘pacemaker’ for biological processes?

A common, long‐held belief is that metabolic rate drives the rates of various biological, ecological and evolutionary processes. Although this metabolic pacemaker view (as assumed by the recent, influential ‘metabolic theory of ecology’) may be true in at least some situations (e.g. those involving moderate temperature effects or physiological processes closely linked to metabolism, such as heartbeat and breathing rate), it suffers from several major limitations, including: (i) it is supported chiefly by indirect, correlational evidence (e.g. similarities between the body‐size and temperature scaling of metabolic rate and that of other biological processes, which are not always observed) – direct, mechanistic or experimental support is scarce and much needed; (ii) it is contradicted by abundant evidence showing that various intrinsic and extrinsic factors (e.g. hormonal action and temperature changes) can dissociate the rates of metabolism, growth, development and other biological processes; (iii) there are many examples where metabolic rate appears to respond to, rather than drive the rates of various other biological processes (e.g. ontogenetic growth, food intake and locomotor activity); (iv) there are additional examples where metabolic rate appears to be unrelated to the rate of a biological process (e.g. ageing, circadian rhythms, and molecular evolution); and (v) the theoretical foundation for the metabolic pacemaker view focuses only on the energetic control of biological processes, while ignoring the importance of informational control, as mediated by various genetic, cellular, and neuroendocrine regulatory systems. I argue that a comprehensive understanding of the pace of life must include how biological activities depend on both energy and information and their environmentally sensitive interaction. This conclusion is supported by extensive evidence showing that hormones and other regulatory factors and signalling systems coordinate the processes of growth, metabolism and food intake in adaptive ways that are responsive to an organism's internal and external conditions. Metabolic rate does not merely dictate growth rate, but is coadjusted with it. Energy and information use are intimately intertwined in living systems: biological signalling pathways both control and respond to the energetic state of an organism. This review also reveals that we have much to learn about the temporal structure of the pace of life. Are its component processes highly integrated and synchronized, or are they loosely connected and often discordant? And what causes the level of coordination that we see? These questions are of great theoretical and practical importance.     

High cell density media for <Emphasis Type="Italic">Escherichia coli</Emphasis> are generally designed for aerobic cultivations – consequences for large-scale bioprocesses and shake flask cultures

Background  

For the cultivation of Escherichia coli in bioreactors trace element solutions are generally designed for optimal growth under aerobic conditions. They do normally not contain selenium and nickel. Molybdenum is only contained in few of them. These elements are part of the formate hydrogen lyase (FHL) complex which is induced under anaerobic conditions. As it is generally known that oxygen limitation appears in shake flask cultures and locally in large-scale bioreactors, function of the FHL complex may influence the process behaviour. Formate has been described to accumulate in large-scale cultures and may have toxic effects on E. coli.     

Augmentin<Superscript>®</Superscript> as an alternative antibiotic for growth suppression of <Emphasis Type="Italic">Agrobacterium</Emphasis> for tomato (<Emphasis Type="Italic">Lycopersicon esculentum</Emphasis>) transformation

Augmentin^® was used as an alternative antibiotic for suppressing Agrobacterium tumefaciens during tomato (Lycopersicon esculentum) transformation. The efficiency of Augmentin compared with Timentin^® to suppress the growth of Agrobacterium was at concentrations of 300 and 100 mg l^–1, respectively. In addition, the high concentration up to 500 mg l^–1 of both antibiotics showed no significant toxicity to shoot regeneration. The overgrowth of Agrobacterium was observed on tomato shoots regenerated on medium containing cefotaxime even at high concentration up to 500 mg l^–1. Moreover, shoot regeneration from medium containing cefotaxime was lower than the one from medium containing Timentin and Augmentin. However, we found that Timentin was more stable than Augmentin when stored as a mixed stock solution and kept at –20°C freezer. In order to increase the efficiency of Augmentin, we recommended the use of Augmentin at a concentration of 300 mg l^–1 with fresh preparation prior to use. Therefore, Augmentin can be used as another antibiotic for suppression of bacterial growth with comparative efficiency as Timetin for tomato transformation.     

Mitochondrial‐targeted catalase is good for the old mouse proteome,but not for the young: ‘reverse’ antagonistic pleiotropy?

Reactive oxygen species (ROS) are highly reactive oxygen‐containing molecules associated with aging and a broad spectrum of pathologies. We have previously shown that transgenic expression of the antioxidant enzyme catalase targeted to the mitochondria (mCAT) in mice reduces ROS, attenuates age‐related disease, and increases lifespan. However, it has been increasingly recognized that ROS also has beneficial roles in signaling, hormesis, stress response, and immunity. We therefore hypothesized that mCAT might be beneficial only when ROS approaches pathological levels in older age and might not be advantageous at a younger age when basal ROS is low. We analyzed abundance and turnover of the global proteome in hearts and livers of young (4 month) and old (20 month) mCAT and wild‐type (WT) mice. In old hearts and livers of WT mice, protein half‐lives were reduced compared to young, while in mCAT mice the reverse was observed; the longest half‐lives were seen in old mCAT mice and the shortest in young mCAT. Protein abundance of old mCAT hearts recapitulated a more youthful proteomic expression profile (P‐value < 0.01). However, young mCAT mice partially phenocopied the older wild‐type proteome (P‐value < 0.01). Age strongly interacts with mCAT, consistent with antagonistic pleiotropy in the reverse of the typical direction. These findings underscore the contrasting roles of ROS in young vs. old mice and indicate the need for better understanding of the interaction between dose and age in assessing the efficacy of therapeutic interventions in aging, including mitochondrial antioxidants.