The social and ethical issues of post-genomic human biobanks

Biobanking - the organized collection of biological samples and associated data - ranges in scope from small collections of samples in academic or hospital settings to large-scale national repositories. Biobanks raise many ethical concerns, to which authorities are responding by introducing specific regulations. Genomics research, which thrives on the sharing of samples and information, is affected by two prominent ethical questions: do ethical principles prevent or promote the sharing of stored biological resources? How does the advent of large-scale biobanking alter the way in which ethical issues are addressed?     

Towards a comprehensive understanding of the Si(100)-2×1 surface termination through hydrogen passivation using methylamine and methanol: a theoretical approach

Using density functional theory, we explored the termination process of Si (100)-2?×?1 reconstructed surface mechanistically through the dehydrogenation of small molecules, considering methyl amine and methanol as terminating reagents. At first, both the terminating reagents form two types of adduct through adsorption on the Si (100)-2?×?1 surface, one in chemisorption mode and the other via physisorption, from which the dehydrogenation process is initiated. By analyzing the activation barriers, it was observed that termination of the Si-surface through the dehydrogenation is kinetically almost equally feasible using either reagent. We further examined in detail the mechanism for each termination process by analyzing geometrical parameters and natural population analysis charges. From bonding evaluation, it is evident that hydrogen abstraction from adsorbates on the Si-surface is asymmetric in nature, where one hydrogen is abstracted as hydride by the electrophilic surface Si and the other hydrogen is abstracted as proton by the neucleophilic surface Si. Moreover, it was also observed that hydride transfer from adsorbate to the Si-surface occurs first followed by proton transfer. Overall, our theoretical interpretation provides a mechanistic understanding of the Si (100)-2?×?1 reconstructed surface termination by amine and alcohol that will further motivate researchers to design different types of decorated semiconductor devices.

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Graphical Abstract Surface termination process of Si(100)-2×1 through formation of non-polar Si–H bonds via dehydrogenation of methylamine and methanol as terminating reagents

     

Why Do We Expect Carotenoids to be Antioxidants in vivo?

The antioxidant properties of β-carotene, in addition to its proposed immunomodulatory effects, have often been cited as the factors underlying its role in preventing disease initiation and propagation, yet the strongest evidence for diet and cancer prevention is based on fruit and vegetable intake and not β-carotene or other dietary carotenoids, per se. In the light of the outcome of the ATBC trial, the Physicians Health Study and the premature termination of the CARET study, this review addresses the issue of the antioxidant properties of the carotenoids and poses the questions: do dietary carotenes and xanthophylls have a clear role in disease prevention and are their antioxidant properties relevant to this role? What. do we know about their mechanisms of action in vitro as free radical scavengers?     

On the Explanatory Roles of Natural Selection

Can selection explain why individuals have the traits they do? This question has generated significant controversy. I will argue that the debate encompasses two separable aspects, to detrimental effect: (1) the role of selection in explaining the origin and evolution of biological traits and (2) the implications this may have for explaining why individuals have the traits they do. (1) can be settled on the basis of evolutionary theory while (2) requires additional, extra-scientific assumptions. By making a distinction between traits affected by a single factor and traits affected by multiple factors I show that selection can, under certain conditions, help explain the origin of traits. Resolving the first aspect enables us to critically assess the various incompatible and independent philosophical commitments made within the second aspect of the debate.     

The NH2-terminal domain of Escherichia coli ribosomal protein L11. Its three-dimensional location and its role in the binding of release factors 1 and 2

Ribosomes from three previously described mutants of Escherichia coli lacking L11 ( AM68 , AM76 , and AM77 ) supported in vitro termination with release factor 1 very poorly, but with release factor 2 had a severalfold elevation in activity for this function compared with ribosomes from a control strain or from a mutant containing unmethylated L11. L11 exerts its effect on the binding of the factors into a functional ribosomal complex with the termination codon. Reconstitution of L11 back into the L11-lacking ribosomes restored them to the control phenotype. The NH2-terminal part of L11 (amino acids 1-64) seems critical in modulating release factor binding. This part of L11 has been localized with the use of fragment-specific antibodies on the three-dimensional model of the 50 S subunit in the region from where the L7/L12 stalk originates. IgG antibodies from an antiserum specific for this fragment but not a middle fragment of L11 (amino acids 65-102) strongly inhibited in vitro termination. The activities of the two factors were inhibited differentially by several anti-L11 preparations recognizing antigenic determinants in the NH2-terminal part of L11. In all but one case, release factor 1 was more sensitive. These studies indicate that there are significant differences in the binding domains for the two release factors which are affected by the NH2-terminal part of L11.     

Tandem termination signals: myth or reality?

In two Escherichia coli genomes, laboratory strain K-12 and pathological strain O157:H7, tandem termination codons as a group are slightly over-represented as termination signals. Individually however, they span the range of representations, over, as expected, or under, in one or both of the strains. In vivo, tandem termination codons do not make more efficient signals. The second codon can act as a backstop where readthrough of the first has occurred, but not at the expected efficiency. UGAUGA remains an enigma, highly over-represented, but with the second UGA a relatively inefficient back up stop codon.     

A new function for nonsense-mediated mRNA-decay factors

mRNAs often contain premature-termination (nonsense) codons as a result of mutations and RNA splicing errors. These nonsense codons cause rapid decay of the mRNAs that contain them, a phenomenon called nonsense-mediated mRNA decay (NMD). This response is thought to be a quality-control mechanism that protects cells from truncated dominant-negative proteins. Surprisingly, recent evidence strongly suggests that the NMD factors UPF1, UPF2, UPF3B, RNPS1, Y14 and MAGOH also promote translation of normal mRNAs in mammalian cells. This, along with an earlier discovery that NMD factors appear to dictate efficient translation termination, suggests that NMD factors do not merely function in RNA surveillance. These findings lead to the interesting question of why NMD factors evolved; are they for RNA-quality control or to promote efficient translation initiation and termination?     

The influence of social cues on the reproductive endocrinology of male brown-headed cowbirds: field and laboratory studies

Captive male brown-headed cowbirds exposed to long days exhibit gonadal growth and have elevated plasma testosterone (T) levels. This photoperiodic response is enhanced if males are housed with female cowbirds: Photostimulated males with females increase plasma testosterone levels sooner than do individually housed photostimulated males. Peak plasma T levels are similar in both groups, although peak levels are maintained longer in males housed with females. The gonadal cycle is similarly affected; males in the presence of females have earlier gonadal recrudescence and maintain mature gonads longer than do photostimulated males without females. Plasma corticosterone levels increase in the unpaired males, suggesting that removal of social cues is stressful for these birds. Free-living paired males have significantly higher plasma testosterone levels than do unpaired/unknown males early in the season, when social relationships are being established; the levels are similar thereafter. There is no difference between the two groups in testicular maturation rates; nor do they differ in plasma corticosterone levels at any time of the season. These results suggest that social stimuli are important in modulating the secretion of testosterone in males early in the season when pairing occurs, and possibly late in the season as well, probably to prevent termination of breeding prior to that of females.     

Why termination tRNAs have not been found? Because they are hidden in the large ribosomal RNA

It is well known that protein synthesis in ribosomes on mRNA requires two kinds of tRNAs: initiation and elongation. The former initiates the process (formylmethionine tRNA in prokaryotes and special methionine tRNA in eukaryotes). The latter participates in the synthesis proper, recognizing the sense codons. The synthesis is assisted by special proteins: initiation, elongation, and termination factors. The termination factors are necessary to recognize stop codons (UAG, UGA, and UAA) and to release the complete protein chain from the elongation tRNA preceding a stop codon. No termination tRNA capable of recognizing stop codons by its anticodon is known. The termination factors are thought to do this. We discovered in the large ribosomal RNA two regions that, like tRNAs, contain the anticodon hairpin, but with triplets complementary to stop codons. By analogy, we called them termination tRNAs (Ter-tRNA1 and Ter-tRNA2), though they transport no amino acids, and suggested them to directly recognize stop codons. The termination factors only condition such a recognition, making it specific and reliable (of course, they fulfill the hydrolysis of the ester bond between the polypeptide and tRNA). A strong argument in favor of our hypothesis came from vertebrate mitochondria. They acquired two new stop codons, AGA and AGG (in the standard code, they are two out of six arginine codons). We revealed that the corresponding anticodons appear in Ter-tRNA1.     

Predictors of positive airway pressure therapy termination in the first year: analysis of big data from a German homecare provider

Background

There is a lack of robust data about factors predicting continuation (or termination) of positive airway pressure therapy (PAP) for sleep apnea. This analysis of big data from a German homecare provider describes patients treated with PAP, analyzes the therapy termination rate over the first year, and investigates predictive factors for therapy termination.

Methods

Data from a German homecare service provider were analyzed retrospectively. Patients who had started their first PAP therapy between September 2009 and April 2014 were eligible. Patient demographics, therapy start date, and the date of and reason for therapy termination were obtained. At 1?year, patients were classified as having compliance-related therapy termination or remaining on therapy. These groups were compared, and significant predictors of therapy termination determined.

Results

Of 98,329 patients included in the analysis, 11,702 (12%) terminated PAP therapy within the first year (after mean 171?±?91?days). There was a U-shaped relationship between therapy termination and age; therapy termination was higher in the youngest (<?30?years, 15.5%) and oldest (≥ 80?years, 19.8%) patients, and lower in those aged 50–59?years (9.9%). Therapy termination was significantly more likely in females versus males (hazard ratio 1.48, 95% confidence interval 1.42–1.54), in those with public versus private insurance (1.75, 1.64–1.86) and in patients whose first device was automatically adjusting or fixed-level continuous positive airway pressure versus bilevel or adaptive servo-ventilation (1.28, 1.2–1.38).

Conclusions

This analysis of the largest dataset investigating PAP therapy termination identified a number of predictive factors. These can help health care providers chose the most appropriate PAP modality, identify specific patient phenotypes at higher risk of stopping PAP and target interventions to support ongoing therapy to these groups, as well as allow them to develop a risk stratification tool.

     

Why Termination tRNAs Have Not Been Found? Because They Are Hidden in the Large Ribosomal RNA (A Hypothesis)

It is well known that protein synthesis in ribosomes on mRNA requires two kinds of tRNAs: initiation and elongation. The former initiates the process (formylmethionine tRNA in prokaryotes and special methionine tRNA in eukaryotes). The latter participates in the synthesis proper, recognizing the sense codons. The synthesis is assisted by special proteins: initiation, elongation, and termination factors. The termination factors are necessary to recognize stop codons (UAG, UGA, and UAA) and to release the complete protein chain from the elongation tRNA preceding a stop codon. No termination tRNA capable of recognizing stop codons by its anticodon is known. The termination factors are thought to do this. We discovered in the large ribosomal RNA two regions that, like tRNAs, contain the anticodon hairpin, but with triplets complementary to stop codons. By analogy, we called them termination tRNAs (Ter-tRNA1 and Ter-tRNA2), though they transport no amino acids, and suggested them to directly recognize stop codons. The termination factors only condition such recognition to make it specific and reliable (of course, they fulfill the hydrolysis of the ester bond between the polypeptide and tRNA). A strong argument in favor of our hypothesis came from vertebrate mitochondria. They acquired two new stop codons, AGA and AGG (in the standard code, they are two out of six arginine codons). We revealed that the corresponding anticodons appear in Ter-tRNA1.     

A spectrum of modularity in multi‐functional gene circuits

A major challenge in systems biology is to understand the relationship between a circuit's structure and its function, but how is this relationship affected if the circuit must perform multiple distinct functions within the same organism? In particular, to what extent do multi‐functional circuits contain modules which reflect the different functions? Here, we computationally survey a range of bi‐functional circuits which show no simple structural modularity: They can switch between two qualitatively distinct functions, while both functions depend on all genes of the circuit. Our analysis reveals two distinct classes: hybrid circuits which overlay two simpler mono‐functional sub‐circuits within their circuitry, and emergent circuits, which do not. In this second class, the bi‐functionality emerges from more complex designs which are not fully decomposable into distinct modules and are consequently less intuitive to predict or understand. These non‐intuitive emergent circuits are just as robust as their hybrid counterparts, and we therefore suggest that the common bias toward studying modular systems may hinder our understanding of real biological circuits.     

A mechanism for stop codon recognition by the ribosome: a bioinformatic approach.

Protein synthesis in ribosomes requires two kinds of tRNAs: initiation and elongation. The former initiates the process (formylmethionine tRNA in prokaryotes and special methionine tRNA in eukaryotes). The latter participates in the synthesis proper, recognizing the sense codons. Synthesis is also assisted by special proteins: initiation, elongation, and termination factors. The termination factors are necessary to recognize stop codons (UAG, UGA, and UAA) and to release the complete protein chain from the elongation tRNA preceding a stop codon. No termination tRNA capable of recognizing stop codons by their anticodons is known. The termination factors are thought to do this. In the large ribosomal RNA, we found two sites that, like tRNAs, contain the anticodon hairpin but with triplets complementary to stop codons. One site is hairpin 69 from domain IV; the other site is hairpin 89, domain V. By analogy, we call them termination tRNAs: Ter-tRNA1 and Ter-tRNA2, respectively, even though they transport no amino acids, and suggest that they directly pair to stop codons. The termination factors only aid in this recognition, making it specific and reliable. A strong argument in favor of our hypothesis comes from vertebrate mitochondria. They are known to acquire two new stop codons, AGA and AGG. In the standard code, these are two out of six arginine codons. We revealed that the corresponding anticodons, UCU and CCU, have evolved in Ter-tRNA1 of these mitochondria.