Strategies to Guide the Return of Genomic Research Findings: An Australian Perspective

In Australia, along with many other countries, limited guidance or other support strategies are currently available to researchers, institutional research ethics committees, and others responsible for making decisions about whether to return genomic findings with potential value to participants or their blood relatives. This lack of guidance results in onerous decision-making burdens—traversing technical, interpretative, and ethical dimensions—as well as uncertainty and inconsistencies for research participants. This article draws on a recent targeted consultation conducted by the Australian National Health and Medical Research Council to put forward strategies for supporting return of finding decision-making. In particular, we propose a pyramid of decision-making support: decision-making guidelines, technical and interpretative assistance, and ethical assistance for intractable “tough” cases. Each step of the pyramid involves an increasing level of regulatory involvement and applies to a smaller subsection of genomic research findings. Implementation of such strategies would facilitate a growing evidence base for return of finding decisions, thereby easing the financial, time, and moral burdens currently placed on researchers and other relevant decision-makers while also improving the quality of such decisions and, consequently, participant outcomes.     

A Clinical Service to Support the Return of Secondary Genomic Findings in Human Research

Human genome and exome sequencing are powerful research tools that can generate secondary findings beyond the scope of the research. Most secondary genomic findings are of low importance, but some (for a current estimate of 1%–3% of individuals) confer high risk of a serious disease that could be mitigated by timely medical intervention. The impact and scope of secondary findings in genome and exome sequencing will only increase in the future. There is considerable agreement that high-impact findings should be returned to participants, but many researchers performing genomic research studies do not have the background, skills, or resources to identify, verify, interpret, and return such variants. Here, we introduce a proposal for the formation of a secondary-genomic-findings service (SGFS) that would support researchers by enabling the return of clinically actionable sequencing results to research participants in a standardized manner. We describe a proposed structure for such a centralized service and evaluate the advantages and challenges of the approach. We suggest that such a service would be of greater benefit to all parties involved than present practice, which is highly variable. We encourage research centers to consider the adoption of a centralized SGFS.     

The Energy Return on Investment for Algal Biocrude: Results for a Research Production Facility

This study is an experimental determination of the energy return on investment (EROI) for algal biocrude production at a research facility at the University of Texas at Austin (UT). During the period of this assessment, algae were grown at several cultivation scales and processed using centrifugation for harvesting, electromechanical cell lysing, and a microporous hollow fiber membrane contactor for lipid separation. The separated algal lipids represent a biocrude product that could be refined into fuel and the post-extraction biomass could be converted to methane. To determine the EROI, a second-order analysis was conducted, which includes direct and indirect energy flows, but does not include energy expenses associated with capital investments. The EROI for the production process evaluated here was significantly less than 1, however, the majority of the energy consumption resulted from non-optimized growth conditions. While the experimental results do not represent an expected typical case EROI for algal fuels, the approach and end-to-end experimental determination of the different inputs and outputs provides a useful outline of the important parameters to consider in such an analysis. The Experimental Case results are the first known experimental energy balance for an integrated algal biocrude production facility, and as such, are expected to be helpful for setting research and development priorities. In addition to the Experimental Case (based on direct measurements), three analytical cases were considered in this work: (1) a Reduced (Inputs) Case, (2) a Highly Productive Case, and (3) a Literature Model. The Reduced (Inputs) Case and the Highly Productive Case speculate the energy use for a similar system in an improved, commercial-scale production setting. The Literature Model is populated with relevant data that have previously been reported in the literature. For the Experimental Case, Reduced Case, Highly Productive Case, and Literature Model, the estimated second-order EROI was 9.2?×?10^?4, 0.074, 0.22, and 0.35, respectively. These results were dominated by growth inputs (96%, 89%, 87%, and 61% of the total energy requirement, respectively). Furthermore, the EROI was adjusted using quality factors that were calculated according to the price of each input, yielding a quality-adjusted EROI that parallels a partial financial return on investment analysis. For the Experimental Case, the Reduced Case, and the Highly Productive Case, the quality-adjusted EROI was 9.2?×?10^?5, 0.013, and 0.36, respectively.     

GRAbB: Selective Assembly of Genomic Regions,a New Niche for Genomic Research

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).

This is a PLOS Computational Biology Software paper

     

The Hydrolysis Mechanism of Formamide Revisited: Comparison Between ab initio, Semiempirical and DFT Results

The hydrolysis of amides is a model reaction to study peptide hydrolysis. This process has been previously considered in the literature at the ab initio level. In this work, we revisit different reaction mechanisms (water-assisted, non-assisted, neutral and acid-catalyzed) with various theoretical methods : semiempirical, ab initio and Density Functional. The ab initio calculations are carried out at a computational level which is substantially higher than in previous studies. We describe the structure of the transition states and discuss the influence of the catalyst. We also compute the activation free energies for these processes at the Density Functional Theory level. Comparison of the methods allows to outline the main trends of these theoretical approaches which may be useful to design new computational strategies for investigating biological reaction mechanisms through the use of combined Quantum Mechanics/Molecular Mechanics methods.     

Between Europe and the Balkans: Mapping Slovenia and Croatia's “Return to Europe” in the 1990s

This essay traces the ongoing discursive processes through which two former Yugoslav states — Croatia and Slovenia — framed their so-called “exit from the Balkans” and “return to Europe” throughout the 1990s. Applying Maria Todorova's framework of “Balkanism” to these two cases, the essay examines how leaders sought recognition as belonging to Europe, or Central Europe, by defining their respective national identities in opposition to Balkan or Yugoslav ones. What distinguishes Balkanism from other critical traditions such as Orientalism is that the Balkans are located in a distinctively liminal position: at the same time part of Europe as well as its antithetical periphery, the “other” within. This in-between position can often lead to contradictory identity constructions, whereby an insistence on concretizing one's Europeanness coincides with a certain awareness that this European status is never ontologically secure. The essay concludes by considering ways in which the Balkans can be re-imagined, reassembling diverse fragments of Balkan identity into a site for positive engagement and critique.     

Question 8: Bridging the Gap Between In Silico and In Vitro Approaches to Minimal Cells

In this short paper we argue for the relevance and value of theoretical models in the field of origins of life, but also claim that both theoreticians and experimentalists should make an effort to come together and interact more closely to obtain more fruitful and significant results. As an example, we present our own modeling approach to protocell dynamics, including some simulation results, to show that it is possible to develop computational tools that start bridging that traditional gap between theory and experiments. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

The White Ceiling Heuristic and the Underestimation of Asian-American Income

The belief that ethnic majorities dominate ethnic minorities informs research on intergroup processes. This belief can lead to the social heuristic that the ethnic majority sets an upper limit that minority groups cannot surpass, but this possibility has not received much attention. In three studies of perceived income, we examined how this heuristic, which we term the White ceiling heuristic leads people to inaccurately estimate the income of a minority group that surpasses the majority. We found that Asian Americans, whose median income has surpassed White median income for nearly three decades, are still perceived as making less than Whites, with the least accurate estimations being made by people who strongly believe that Whites are privileged. In contrast, income estimates for other minorities were fairly accurate. Thus, perceptions of minorities are shaped both by stereotype content and a heuristic.     

trans-Translation: The Main Participants and the Role in Cell Life

trans-Translation is the unique process of synthesizing a single polypeptide chain from both mRNA and the coding region of transport–messenger RNA (tmRNA). It is necessary for cell vital activity in the changing environment. New data on the main participants of trans-translation, conditions under which it occurs, and its role in the cell are reviewed. The possible role of tmRNA in translation quality control is discussed.     

A Genomic Comparison of Faster-Sex, Faster-X, and Faster-Male Evolution Between Drosophila melanogaster and Drosophila pseudoobscura

A genomic comparison of Drosophila melanogaster and Drosophila pseudoobscura provides a unique opportunity to investigate factors involved in sequence divergence. The chromosomal arrangements of these species include an autosomal segment in D. melanogaster which is homologous to part of the X chromosome in D. pseudoobscura. Using orthologues to calculate rates of nonsynonymous (d_N) substitutions, we found genes on the X chromosome to be significantly more diverged than those on the autosomes, but it is not true for segment 3L-XR which is autosomal in D. melanogaster (3L) and X-linked in D. pseudoobscura (XR). We also found that the median d_N values for genes having reproductive functions in either the male, the female, or both sexes are higher than those for sequences without reproductive function and even higher for sequences involved in male-specific function. These estimates of divergence for male sex-related sequences are most likely underestimates, as the very rapidly evolving reproductive genes would tend to lose homology sooner and thus not be included in the comparison of orthologues. We also noticed a high proportion of male reproductive genes among the othologous genes with the highest rates of d_N. Reproductive genes with and without an orthologue in D. pseudoobscura were compared among D. melanogaster, D. simulans, and D. yakuba and it was found that there were in fact higher rates of divergence in the group without a D. pseudoobscura orthologue. These results, from widely separated taxa, bolster the thesis that sexual system genes experience accelerated rates of change in comparison to nonsexual genes in evolution and speciation. [Reviewing Editor: Dr. Willie J. Swanson]     

The Use of Albino Adult Hair and Blond Prepubertal Hair Yields Equivalent Results in an In Vitro Hair Perforation Test to Differentiate Between Different Dermatophytic Fungi

An in vitro hair perforation test is used to differentiate isolates of Trichophyton mentagrophytes and Trichophyton rubrum complexes because morphological criteria are insufficient. Here, we performed in vitro hair perforation tests using blond prepubertal hair and albino adult hair to determine whether they differentiate between fungal species. We tested 43 well-characterized dermatophyte strains, Arthroderma spp. [n = 4], Epidermophyton floccosum [n = 1], Microsporum spp. [n = 8], and Trichophyton spp. [n = 30], and examined hair perforation at 3–30 days postinoculation (p.i.). The perforation times were not significantly different between the two hair types (P > 0.05). The T. mentagrophytes complex strains perforated hair 4–5 days p.i., whereas T. rubrum complex strains perforated hair 13–30 days p.i., except for Trichophyton violaceum, which perforated hair after 6–7 days. Thus, the hair perforation test is highly sensitive (100 %) and specific (100 %) for differentiating T. mentagrophytes from T. rubrum complexes 5 days p.i. At 14 and 30 days, the sensitivity and negative predictive value of the test remained unchanged (100 %), but the specificity was reduced (64.3 and 14.3 %, respectively). Consistent with previous reports, we observed “perforating organs” of zoophilic Microsporum canis and geophilic Microsporum gypseum at 4 and 3 days, respectively. This paper offers a “low-cost” and “low-tech” alternative to differentiating dermatophyte species where standard morphological techniques fail and/or where molecular techniques are not a viable option.     

The Relationship Between Census Results and Breeding Populations of some Marshland Passerines

Censuses employing the mapping method, ancillary to an intensive population study of Reed Buntings, Sedge Warblers and Reed Warblers, revealed some limitations of the technique, which requires modification if the aim of the census work is an absolute estimation of the breeding population.     

The Privatisation of Home and Hope: Return, Reforms and the Foreign Intervention in Bosnia-Herzegovina

Contextualising the foreign-imposed return policies in early post-war Bosnia-Herzegovina, this article argues that the return of the displaced – however important it was to many Bosnians – ultimately functioned as the self-perpetuating lynchpin of an externally generated framework for post-war reconstruction, often out of tune with the hopes of its intended beneficiaries. Rather than following conventional anthropological cultural relativist arguments, I propose a critique of the foreign intervention that places it in its social, political and economic context, drawing attention to patterns of longing and belonging in Bosnia-Herzegovina. I contrast the groundings and implications of intervention policies with the experiences and yearnings of displaced Bosnians and show that, while it was legitimised as the implementation of an ostensibly ideologically neutral human rights discourse, the foreign emphasis on property and safety rights over other concerns channelled the reconstruction of Bosnia-Herzegovina into a peculiar, normative trajectory of postsocialist neoliberalisation.     

Investigations of Genome Relationships Between Leymus, Psathyrostachys and Hordeum Inferred by Genomic DNA:DNA in situ Hybridization

Genome relationships between the genera Leymus Hochst., PsathyrostachysNevski and Hordeum L. (Poaceae, Triticeae) were investigatedby fluorescent in situ hybridization using both total genomicDNA and cloned DNA sequences as probes. In hybrids between speciesof Hordeum and Leymus there was a clear differentiation betweenthe H genomes of Hordeum species and the genomes of Leymus speciesafter probing with genomic Hordeum or Leymus DNA. Chromosomesof species of Leymus and Psathyrostachys were also differentiatedby subtelomeric heterochromatic segments or by negative bandsalong their length. The number and location of 18S-5·8S-26SrRNA genes varied between the investigated genera. Unusually,L. angustus and P. stoloniformis rDNA sites were localized onboth ends of some chromosomes. Interphase nuclei of the Hordeumx Leymus hybrids had groups of chromosomes from both parentalgenomes in discrete, non-intermixed domains.Copyright 1994,1999 Academic Press Taxonomy, evolution, molecular evolution, repetitive DNA, rDNA sites, in situ hybridization, Triticeae, Leymus, Hordeum, Psathyrostachys     

Attitudes of Genetics Professionals Toward the Return of Incidental Results from Exome and Whole-Genome Sequencing

Professional recommendations for the return of results from exome and whole-genome sequencing (ES/WGS) have been controversial. The lack of clear guidance about whether and, if so, how to return ES/WGS incidental results limits the extent to which individuals and families might benefit from ES/WGS. The perspectives of genetics professionals, particularly those at the forefront of using ES/WGS in clinics, are largely unknown. Data on stakeholder perspectives could help clarify how to weigh expert positions and recommendations. We conducted an online survey of 9,857 genetics professionals to learn their attitudes on the return of incidental results from ES/WGS and the recent American College of Medical Genetic and Genomics Recommendations for Reporting of Incidental Findings in Clinical Exome and Genome Sequencing. Of the 847 respondents, 760 completed the survey. The overwhelming majority of respondents thought that incidental ES/WGS results should be offered to adult patients (85%), healthy adults (75%), and the parents of a child with a medical condition (74%). The majority thought that incidental results about adult-onset conditions (62%) and carrier status (62%) should be offered to the parents of a child with a medical condition. About half thought that offered results should not be limited to those deemed clinically actionable. The vast majority (81%) thought that individual preferences should guide return. Genetics professionals’ perspectives on the return of ES/WGS results differed substantially from current recommendations, underscoring the need to establish clear purpose for recommendations on the return of incidental ES/WGS results as professional societies grapple with developing and updating recommendations.     

Drug Transfer Across the Blood-Brain Barrier: Correlation Between In Vitro and In Vivo Models

To assess the drug transport across the blood-brain barrier (BBB), we compared the maximal brain extraction values at time 0 [E(0) values] obtained using either in vitro or in vivo methods. The in vitro BBB model consisted of a coculture of brain capillary endothelial cells growing on one side of a filter and astrocytes on the other. The in vivo model used intracarotid injection in anesthetized rats. Eleven compounds were tested. They were selected because they exhibit quantitatively different brain extraction rates: very low for inulin and sucrose, low for oxicam-related nonsteroidal antiinflammatory drugs and diclofenac, and high for propranolol and diazepam. As these compounds are apparently transferred by a passive diffusion mechanism, two others, glucose and leucine, were added that cross the BBB by a known carrier-mediated process. The in vivo and in vitro E(0) values showed a strong correlation as indicated by the Spearman's correlation coefficient (r = 0.88, p less than 0.01). The relative ease with which such cocultures can be produced in large quantities could facilitate the screening of new centrally acting drugs.