Properties of non‐canonical GC base pairs and their relations with mechanochemical cleavage of DNA are analyzed. A hypothesis of the involvement of the transient GC wobble base pairs both in the mechanisms of the mechanochemical cleavage of DNA and epigenetic mechanisms involving of 5‐methylcytosine, is proposed. The hypothesis explains the increase in the frequency of the breaks of the sugar‐phosphate backbone of DNA after cytosines, the asymmetric character of these breaks, and an increase in break (...) frequency in CpG after cytosine methylation. As an alternative hypothesis, probable implication of GC+ Hoogsteen base pairs is considered, which now exemplify the best‐studied non‐canonical GC base pairs in the DNA double helix. Also see the video abstract here https://youtu.be/EUunVWL0ptw. (shrink)

Base pair mismatches in DNA arise from errors in DNA replication, recombination, and biochemical modification of bases. Mismatches are inherently transient. They are resolved passively by DNA replication, or actively by enzymatic removal and resynthesis of one of the bases. The first step in removal is recognition of strand discontinuity by one of the MutS proteins. Mismatches arising from errors in DNA replication are repaired in favor of the base on the template strand, but other mismatches trigger (...) base excision or nucleotide excision repair (NER), or non‐repair pathways such as hypermutation, cell cycle arrest, or apoptosis. We argue that MutL homologues play a key role in determining biologic outcome by recruiting and/or activating effector proteins in response to lesion recognition by MutS. We suggest that the process is regulated by conformational changes in MutL caused by cycles of ATP binding and hydrolysis, and by physiologic changes which influence effector availability. (shrink)

DNA helicases are a class of molecular motors that catalyze processive unwinding of double stranded DNA. In spite of much study, we know relatively little about the mechanisms by which these enzymes carry out the function for which they are named. Most current views are based on inferences from crystal structures. A prominent view is that the canonical ATPase motor exerts a force on the ssDNA resulting in “pulling” the duplex across a “pin” or “wedge” in the enzyme leading to (...) a mechanical separation of the two DNA strands. In such models, DNA base pair separation is tightly coupled to ssDNA translocation of the motors. However, recent studies of the Escherichia coli RecBCD helicase suggest an alternative model in which DNA base pair melting and ssDNA translocation occur separately. In this view, the enzyme‐DNA binding free energy is used to melt multiple DNA base pairs in an ATP‐independent manner, followed by ATP‐dependent translocation of the canonical motors along the newly formed ssDNA tracks. Repetition of these two steps results in processive DNA unwinding. We summarize recent evidence suggesting this mechanism for RecBCD helicase action. (shrink)

Despite advances in treatments over the last decades, a uniformly reliable and free of side effects therapy of human cancers remains to be achieved. During chromosome replication, a premature halt of two converging DNA replication forks would cause incomplete replication and a cytotoxic chromosome nondisjunction during mitosis. In contrast to normal cells, most cancer cells bear numerous DNA deletions. A homozygous deletion permanently marks a cell and its descendants. Here, we propose an approach to cancer therapy in which a pair (...) of sequence‐specific roadblocks is placed solely at two cancer‐confined deletion sites that are located ahead of two converging replication forks. We describe this method, termed “replication blocks specific for deletions” (RBSD), and another deletions‐based approach as well. RBSD can be expanded by placing pairs of replication roadblocks on several different chromosomes. The resulting simultaneous nondisjunctions of these chromosomes in cancer cells would further increase the cancer‐specific toxicity of RBSD. (shrink)

A recent paper by Rieper, Anders and Vedral (arxiv.org/abs/1006.4053: The Relevance Of Continuous Variable Entanglement In DNA) suggests that quantum entanglement among base pairs in the DNA double helix stabilizes the molecule. A summary of their paper is reported in MIT Technology Review (http://www.technologyreview.com/blog/arxiv/25375/) is below..

To decode the function and molecular recognition of several recently discovered cytosine derivatives in the human genome – 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine – a detailed understanding of their effects on the structural, chemical, and biophysical properties of DNA is essential. Here, we review recent literature in this area, with particular emphasis on features that have been proposed to enable the specific recognition of modified cytosine bases by DNA-binding proteins. These include electronic factors, modulation of base-pair stability, flexibility, and radical (...) changes in duplex conformation. We explore these proposals and assess whether or not they are supported by current biophysical data. This analysis is focused primarily on the properties of epigenetically modified DNA itself, which provides a basis for discussion of the mechanisms of recognition by different proteins. 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine have recently been discovered in mammalian DNA and appear to have essential regulatory roles. Here, we summarize recent investigations into their effects on the structural, chemical, and biophysical properties of DNA, an understanding of which is essential to decoding their behavior in the genome. (shrink)

Long DNA palindromes pose a threat to genome stability. This instability is primarily mediated by slippage on the lagging strand of the replication fork between short directly repeated sequences close to the ends of the palindrome. The role of the palindrome is likely to be the juxtaposition of the directly repeated sequences by intrastrand base‐pairing. This intra‐strand base‐pairing, if present on both strands, results in a cruciform structure. In bacteria, cruciform structures have proved difficult to detect in vivo, (...) suggesting that if they form, they are either not replicated or are destroyed. SbcCD, a recently discovered exonuclease of Escherichia coli, is responsible for preventing the replication of long palindromes. These observations lead to the proposal that cells may have evolved a post‐replicative mechanism for the elimination and/or repair of large DNA secondary structures. (shrink)

Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher‐order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC‐binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression and (...) regulation. This review aims to describe the current understanding of the dynamic nature of the cohesin‐DNA complex and its dependence on cohesin for genome maintenance. We discuss the current 3C technique and numerous bioinformatics pipelines used to comprehend structural genomics and epigenetics focusing on the analysis of Cohesin‐centred interactions. We also incorporate our present comprehension of Loop Extrusion (LE) and insights from stochastic modelling. (shrink)

The human genome consists of more than 3 billion base pairs built from four different nucleotides that hold the genetic information for the entire organism. The genome is commonly divided into coding and noncoding DNA sequences, with coding DNA sequences defined as those that can be transcribed into mRNA and translated into proteins, or genes. The genetic code determines the impact of a nucleotide change in a gene on the protein sequence and function, and it is essential to (...) understanding the genetic basis of many congenital diseases. The Human Genome Project has accelerated our understanding about the genome function. We now know that our genome consists of 20,000–25,000 genes that occupy only.. (shrink)

A number of novel gene detection techniques all revolve around the ligation of synthetic nucleic acid probes. In such ligase‐assisted gene detection reactions, specific DNA or RNA sequences are investigated by using them as guides for the covalent joining of pairs of probe molecules. The probes are designed to hybridize immediately next to each other on the target nucleic acid strand. Demonstration of ligated probes results in highly specific detection of and efficient distinction between similar sequence variants under standard (...) reaction conditions. Accordingly, the principle has been applied in automated genetic screening procedures. Ligation reactions are also integral to a number of amplification procedures and they will be of value in an expanding range of genetic analyses. (shrink)

Small tandem DNA duplications in the range of 15 to 300 base‐pairs play an important role in the aetiology of human disease and contribute to genome diversity. Here, we discuss different proposed mechanisms for their occurrence and argue that this type of structural variation mainly results from mutagenic repair of chromosomal breaks. This hypothesis is supported by both bioinformatical analysis of insertions occurring in the genome of different species and disease alleles, as well as by CRISPR/Cas9‐based experimental data (...) from different model systems. Recent work points to fill‐in synthesis at double‐stranded DNA breaks with complementary sequences, regulated by end‐joining mechanisms, to account for small tandem duplications. We will review the prevalence of small tandem duplications in the population, and we will speculate on the potential sources of DNA damage that could give rise to this mutational signature. With the development of novel algorithms to analyse sequencing data, small tandem duplications are now more frequently detected in the human genome and identified as oncogenic gain‐of‐function mutations. Understanding their origin could lead to optimized treatment regimens to prevent therapy‐induced activation of oncogenes and might expose novel vulnerabilities in cancer. (shrink)

Coarse-grain models are essential to understand the biological function of DNA molecules because the length and time scales of the sequence-dependent physical properties of DNA are often beyond the reach of experimental and all-atom computational methods. Simulating coarse-grain models of DNA, e.g. using Langevin dynamics, requires the parametrization of both potential and kinetic energy functions. Many studies have shown that the flexibility (i.e., potential energy) of a DNA molecule depends on its sequence. In contrast, little is known about the sequence-dependence (...) of DNA mass parameters required to model its kinetic energy. In this paper, an algebraic expression is derived for the kinetic energy as a function of linear and angular velocities of each DNA base parameterized by its mass, center of mass, and rotational inertia tensor. The parameters of this function are then approximated from a set of fine-grain molecular dynamics simulations representing all combinations of the four DNA base pairs AT, TA, GC, and CG, in different sequence contexts. Compatibility conditions associated with the assumption of each base being modeled as a rigid body were verified to be good approximations. The kinetic parameters were found to be significantly different between the four G, C, A, and T bases, and to not be dependent on the sequence context. This suggests that the effective kinetic parameters of a DNA base may depend only on the base itself, not on its neighbors. (shrink)

Some 60 years ago chemicals that intercalate between base pairs of duplex DNA were found to amplify frameshift mutagenesis. Surprisingly, the robust induction of frameshifts by intercalators still lacks a mechanistic model, leaving this classic phenomenon annoyingly intractable. A promising idea of asymmetric half‐intercalation‐stabilizing frameshift intermediates during DNA synthesis has never been developed into a model. Instead, researchers of frameshift mutagenesis embraced the powerful slipped‐mispairing concept that unexpectedly struggled with the role of intercalators in frameshifting. It is proposed (...) that the slipped mispairing and the half‐intercalation ideas are two sides of the same coin. Further, existing findings are reviewed to test predictions of the combined “half‐intercalation into the slipped‐mispairing intermediate” model against accumulated knowledge. The existence of potential endogenous intercalators and the phenomenon of “DNA bookmarks” reveal ample possibilities for natural frameshift mutagenisis in the cell. From this alarming perspective, it is discussed how the cell could prevent genome deterioration from frameshift mutagenesis. (shrink)

Gene transcription in eukaryotes is associated with conformational changes of a large area of chromatin adjacent to a gene. This rearrangement may involve the whole loop (topological domain) to which a given gene belongs.Regulatory events associated with activation or inactivation of transcription are found to act through relatively short nucleotide sequences, often located several thousand base pairs apart from gene. These sequences, termed enhancers may act independently on their distance from or orientation with respect to the gene.Both long‐range (...) conformational rearrangements of chromatin and any long distance effects of enhancers may be associated with elastic torsional strain in DNA, arising in transcriptionally active chromatin loops. Enhancer effects, in particular, may be associated with conformational transitions in DNA competing for the energy deposited in the elastic spring of the DNA. (shrink)

Chromosomal origins of DNA replication in higher eukaryotes differ significantly from those of E. coli (oriC) and the tumor virus, SV40 (ori sequence). Initiation events appear to occur throughout broad zones rather than at specific origin sequences. Analysis of four chromosomal origin regions reveals that they share common modular sequence elements. These include DNA unwinding elements, pyrimidine tracts that may serve as strong DNA polymerase‐primase start sites, scaffold associated regions, transcriptional regulatory sequences, and, possibly, initiator protein binding sites and inherently (...) destabilized regions. Based on the novel organization of chromosomal origin regions, we propose a model for initiation of DNA replication in higher eukaryotes. Unwinding of duplex DNA during initiation may be uncoupled, both temporally and spatially, from DNA synthesis, resulting in transient single‐stranded intermediates that function in lieu of conventional replication forks during chromosomal DNA replication. DNA synthesis begins subsequently at multiple sites Within the unwound regions rather than at specific origin sequences. (shrink)

Life on earth is bound together by a common heritage, centered around a molecule that is present in almost every living cell of every living creature. Deoxyribonucleic acid (DNA), composed of four base pairs, the nucleic acids thymine, adenine, cytosine, and guanine, encodes the data that directs, in conjunction with the environment, the development and metabolism of all nondependent living creatures. Except for some viruses that rely only on ribonucleic acid (RNA), all living things are built by the (...) interaction of DNA and RNA within cells and their environments. There is no worldwide consensus yet as to whether portions of the human genome should be granted intellectual property protection, as indeed they are in the United States and a number of other nations. DNA posed numerous challenges to the legal framework for patent protection and may suggest developing an entirely new social and legal category recognizing its uniqueness. (shrink)

Transient changes in DNA torsional tension are generated by environmental stimuli and transcriptional activity. In eukaryotic cells, these changes can only be accommodated by a chromatin structure that is flexible. This property of chromatin may be essential to the regulation of eukaryotic gene activity.

While its mechanism and biological significance are unknown, the utility of a short mitochondrial DNA sequence as a “barcode” providing accurate species identification has revolutionized the classification of organisms. Since highest accuracy was achieved with recently diverged species, hopes were raised that barcodes would throw light on the speciation process. Indeed, a failure of a maternally donated, rapidly mutating, mitochondrial genome to coadapt its gene products with those of a paternally donated nuclear genome could result in developmental failure, thus creating (...) a post-zygotic barrier leading to reproductive isolation and sympatric branching into independent species. However, the barcode itself encodes a highly conserved, species-invariant, protein, and the discriminatory power resides in the non-amino acid specific bases of synonymous codons. It is here shown how the latter could register changes in the oligonucleotide frequencies of nuclear DNA that, when they fail to match in pairing meiotic chromosomes, could reproductively isolate the parents so launching a primary divergence into two species. It is proposed that, while not itself contributing to speciation, the barcode sequence provides an index of the nuclear DNA oligonucleotide frequencies that drive speciation. (shrink)

Puffing of polytene chromosomes is associated with intense genetic activity. Genetic determinants of puffing in Drosophila can now be dissected by transplanting genes known to puff to other chromosomal locations by transposonmediated germ line transformation. Recent studies show that induction of a heat shock puff requires only about one hundred and fifty base pairs of DNA upstream of the gene, around the start of transcription, and not the protein coding sequence itself. Moreover, the size of the ‘ectopic’ puff (...) was found to be related to the size of the corresponding transcript. Similar work is now in progress with hormonally‐controlled puffs. (shrink)

In spite of the importance of point mutations for evolution and human diseases, their natural spectrum of incidence in different species is not known. Here I propose to determine these spectra by comparing consecutive sequence periods in stretches of repetitive DNA. The article presents the analysis of more than 51,000 such point mutations identified by this approach in the genomes of human, chimpanzee, rat, mouse, pufferfish, zebrafish, and sea squirt. I propose to explain the observed spectra by auto‐mutagenic mechanisms of (...) genome variation involving the inter‐conversions of nucleotides, single base‐pair inversions and their combinations. (shrink)

We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce (...) intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments. 10.1126/science.1151721. (shrink)

In human languages, a palindrome reads the same forward as backward (e.g., ‘madam’). In regulatory DNA, a palindrome is an inverted sequence repeat that allows a transcription factor to bind as a homodimer or as a heterodimer with another type of transcription factor. Regulatory palindromes are typically imperfect, that is, the repeated sequences differ in at least one base pair, but the functional significance of this asymmetry remains poorly understood. Here, we review the use of imperfect palindromes in Drosophila (...) photoreceptor differentiation and mammalian steroid receptor signaling. Moreover, we discuss mechanistic explanations for the predominance of imperfect palindromes over perfect palindromes in these two gene regulatory contexts. Lastly, we propose to elucidate whether specific imperfectly palindromic variants have specific regulatory functions in steroid receptor signaling and whether such variants can help predict transcriptional outcomes as well as the response of individual patients to drug treatments. (shrink)

Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have enabled the discovery of tens of thousands of SVs per human genome. These SVs primarily affect non‐coding DNA sequences, but the difficulties in interpreting their impact limit our understanding of human disease etiology. The functional annotation of non‐coding DNA sequences and methodologies to characterize their three‐dimensional (3D) organization (...) in the nucleus have greatly expanded our understanding of the basic mechanisms underlying gene regulation, thereby improving the interpretation of SVs for their pathogenic impact. Here, we discuss the various mechanisms by which SVs can result in altered gene regulation and how these mechanisms can result in rare genetic disorders. Beyond changing gene expression, SVs can produce novel gene‐intergenic fusion transcripts at the SV breakpoints. (shrink)

A recent phylogenetic survey of the New World orioles (genus Icterus; Omland et al. 1999) suggested that the Baltimore Oriole (I. galbula) and the Black-backed Oriole (I. abeillei) are sister taxa. That survey examined mitochondrial DNA (mtDNA) from a single representative of each species in the genus. Here, we examine mtDNA sequences from 15 Blackbacked and 20 Baltimore Orioles. The two species appear to be very recently diverged, with average sequence divergences for both cytochrome b (cyt b) and the control (...) region indicating a probable late Pleistocene split. Despite this very recent divergence, there is one fixed base-pair difference between the species in cyt b and another in the control region, suggesting that one or both species have undergone a bottleneck during or since speciation. This molecular evidence of recent divergence suggests that male plumage differences between Black-backed and Baltimore Orioles evolved very rapidly. (shrink)

The most striking region of structural differentiation of a eukaryotic chromosome is the kinetochore. This chromosomal domain plays an integral role in the stability and propagation of genetic material to the progeny cells during cell division. The DNA component of this structure, which we refer to as the centromere, has been localized to a small region of 220–250 base pairs within the chromosomes from the yeast Saccharomyces cerevisiae. The centromere DNA (CEN) is organized in a unique structure in (...) the cell nucleus and is required for chromosome stability during both mitotic and meiotic cell cycles. The centromeres from one chromosome can stabilize small circular minichromosomes or other yeast chromosomes. The centromeres may therefore interact with the same components of the segregation apparatus regardless of the chromosome in which they reside. The CEN DNA does not encode any regulatory RNAs or proteins, but rather is a cis‐acting element that provides genetic stability to adjacent DNA sequences. (shrink)

Human DNA can be cloned as yeast artificial chromosomes (YACs), each of which contains several hundred kilobases of human DNA. This DNA can be manipulated in the yeast host using homologous recombination and yeast selectable markers. In relatively few steps it is possible to make virtually any change in the cloned human DNA from single base pair changes to deletions and insertions. In order to study the function of the cloned DNA and the effects of the changes made in (...) the yeast, the human DNA must be transferred back into mammalian cells. Recent experiments indicate that large genes can be transferred from the yeast host to mammalian cells in tissue culture and that the genes are transferred intact and are expressed. Using the same methods it may soon be possible to transfer YAC DNA into the mouse germ line so that the expression and function of genes cloned in YACs can be studied in developing and adult mammalian animals. (shrink)

The molecular genetic age can be said to have begun with the letter in Nature in 1953 by Watson and Crick, describing the helical structure of DNA. Some outstanding scientific work preceded that discovery, including especially the recognition by Chargaff of base-pair complementarity, but no discovery quite captured the imagination of the biomedical world as a few understated words by Watson and Crick in their famous one-page paper: "It has not escaped our notice that the specific pairing we have (...) postulated immediately suggests a possible copying mechanism for the genetic material". The manner in which genetic material was passed on from generation to generation had been decoded.That discovery was... (shrink)

In lieu of an abstract, here is a brief excerpt of the content:The Human Genome ProjectSharon J. Durfy (bio) and Amy E. Grotevant (bio)In recent years, scientists throughout the world have embarked upon a long-term biological investigation that promises to revolutionize the decisions people make about their lives and lifestyles, the way doctors practice medicine, how scientists study biology, and the way we think of ourselves as individuals and as a species. It is called the Human Genome Project, and its (...) ultimate goal is to map and determine the chemical sequence of the three billion nucleotide base pairs that comprise the human genome. The feat is expected to take about fifteen years (see General Surveys).These three billion base pairs include an estimated 50,000 to 100,000 genes. The rest of the genome—perhaps 95 percent of it—is nongenic sequences with unknown function, sometimes called "junk." Determining the order and organization of all this material has been likened to tearing six volumes of the Encyclopaedia Brittanica into pieces, then trying to put it all back together to read the information (Surveys: Hall 1990). The effort could be well worth it, many scientists say, because it is expected to yield major insights into many common and complex diseases, including cancer, cardiovascular disease, and Alzheimer's disease (Debate: Dulbecco 1986; Koshland 1989).The Human Genome Project is not without controversy, however (Debate: Davis 1990; Leder 1990; Rechsteiner 1990). Many scientists fear that funding for it will be diverted from other areas of research, rather than obtained from new funding sources. This has enlivened the debate about the relative value of "big" versus "small" science. Also, the value of undertaking a complete sequencing of the genome has been questioned, especially given the high proportion of non-genic sequences.Advocates of the effort converted many critics by making two alterations in the original plan. Plans were included to simultaneously determine the nucleotide sequence of the genomes of other organisms; this provides comparisons and points of reference for the human sequence (U.S.: NIH/DOE 1990). Second, in response to concerns about the high cost of developing technology to sequence the whole [End Page 347] genome, the focus moved from large-scale sequencing to mapping the genome, which would hasten the search for disease genes (U.S.: NIH/DOE 1990).The ideal map would be both genetic, locating DNA markers, or signposts, at closely spaced intervals along the chromosomes, and physical, indicating the exact distance between these markers (Map: McKusick 1991). Since 1973, Human Gene Mapping workshops (HGM) have been held at least every two years to locate, compare, and compile genetic markers. This information is published and is accessible through Genome Database at Johns Hopkins University (McKusick 1991). The most recent Human Genome Mapping workshop was held in August 1991, at which the Human Genome Organization (HUGO) began to assume increased responsibility for coordination of the international mapping effort (Surveys: Maddox 1991).Historical Background of the United States EffortThe first serious discussions about sequencing the entire human genome occurred at a workshop at the University of California at Santa Cruz in 1985 (U.S.: Sinsheimer 1989). A second workshop, organized by the U.S. Department of Energy (DOE) and held in March 1986, addressed the feasibility of an organized program (U.S.: DOE 1986). Shortly thereafter, DOE instituted its own genome project (U.S.: DOE 1987). Reports in early 1988 from both the National Research Council (NRC) of the National Academy of Sciences (NAS) and Congress' Office of Technology Assessment (OTA) (U.S.: NRC 1988; OTA 1988) served as catalysts, and in fiscal year 1988, the U.S. Congress officially launched the Human Genome Project by appropriating funds to both the Department of Energy and the National Institutes of Health (NIH).To avoid potential congressional "meddling" (U.S.: Roberts 1988), NIH and DOE drafted a memorandum of understanding for interagency coordination in October 1988 (U.S.: NIH/DOE 1990). The agencies then created both separate and joint committees, and working groups to administer the project. NIH established the Office of Human Genome Research in 1988 (directed by James D. Watson) to plan and coordinate NIH genome activities. That office has evolved into the National Center for Human Genome Research (NCHGR... (shrink)

Since their introduction about ten years ago the rapid methods for sequencing DNA based either on selective chemical degradation1 or primed enzymatic synthesis2 have been subject to a number of modifications and improvements.3, 4 Two recently published papers describe further advances in these technologies: a method for obtaining information about DNA sequences directly from uncloned mammalian genomic DNA5 and a possible first step towards the automation of DNA sequencing6.

Since the first draft of the human genome was published in 2001, DNA sequencing technology has advanced at a remarkable pace. Launched in 1990, the Human Genome Project sought to sequence all three billion base pairs of the haploid human genome, an endeavor that took more than a decade and cost nearly three billion dollars. The subsequent development of so-called “next generation” sequencing methods has raised the possibility that real-time, affordable genome sequencing will soon be widely available. Currently, (...) NGS methods can be used to sequence up to 60 billion base pairs per day. Whole-genome sequencing costs an estimated $5,000-10,000, with that number predicted to fall to $1000 in the near future.In the past few years, the availability of high-throughput NGS methods has led to a proliferation of potential and actual clinical applications for NGS. NGS therefore has the potential to usher in the long-awaited era of personalized medicine. (shrink)

This article presents a conceptual and methodological framework to study heritage-based tribalism in Big Data ecologies by combining approaches from the humanities, social and computing sciences. We use such a framework to examine how ideas of human origin and ancestry are deployed on Twitter for purposes of antagonistic ‘othering’. Our goal is to equip researchers with theory and analytical tools for investigating divisive online uses of the past in today’s networked societies. In particular, we apply notions of heritage, othering and (...) neo-tribalism, and both data-intensive and qualitative methods to the case of people’s engagements with the news of Cheddar Man’s DNA on Twitter. We show that heritage-based tribalism in Big Data ecologies is uniquely shaped as an assemblage by the coalescing of different forms of antagonistic othering. Those that co-occur most frequently are the ones that draw on ‘Views on Race’, ‘Trust in Experts’ and ‘Political Leaning’. The framings of the news that were most influential in triggering heritage-based tribalism were introduced by both right- and left-leaning newspaper outlets and by activist websites. We conclude that heritage-themed communications that rely on provocative narratives on social media tend to be labelled as political and not to be conducive to positive change in people’s attitudes towards issues such as racism. (shrink)

The ArgumentThis paper focuses on the opening of a discursive space: the emergence of informational and scriptural representations of life and their self-negating consequences for the construction of biological meaning. It probes the notion of writing and the book of life and shows how molecular biology's claims to a status of language and texuality undermines its own objective of control. These textual significations were historically contingent. The informational representations of heredity and life were not an outcome of the internal cognitive (...) momentum of molecular biology; they were not a logical necessity of the unravelling of the base-pairing of the DNA double-helix. They were transported into molecular biology still within the protein paradigm of the gene in the 1940s and permeated nearly every discipline in the life and social sciences. These information-based models, metaphors, linguistic, and semiotic tools which were central to the formulation of the genetic code were transported into molecular biology from cybernetics, information theory, electronic computing, and control and communication systems — technosciences that were deeply embedded with the military experiences of world war II and the Cold War. The information discourse thus became fixed in molecular biology not because it worked in the narrow epistemic sense (it did not), but because it positioned molecular biology within postwar discourse and culture, perhaps within the transition to a post-modern information-based society. (shrink)

Evolution and geometry generate complexity in similar ways. Evolution drives natural selection while geometry may capture the logic of this selection and express it visually, in terms of specific generic properties representing some kind of advantage. Geometry is ideally suited for expressing the logic of evolutionary selection for symmetry, which is found in the shape curves of vein systems and other natural objects such as leaves, cell membranes, or tunnel systems built by ants. The topology and geometry of symmetry is (...) controlled by numerical parameters, which act in analogy with a biological organism’s DNA. The introductory part of this paper reviews findings from experiments illustrating the critical role of two-dimensional (2D) design parameters, affine geometry and shape symmetry for visual or tactile shape sensation and perception-based decision making in populations of experts and non-experts. It will be shown that 2D fractal symmetry, referred to herein as the “symmetry of things in a thing”, results from principles very similar to those of affine projection. Results from experiments on aesthetic and visual preference judgments in response to 2D fractal trees with varying degrees of asymmetry are presented. In a first experiment (psychophysical scaling procedure), non-expert observers had to rate (on a scale from 0 to 10) the perceived beauty of a random series of 2D fractal trees with varying degrees of fractal symmetry. In a second experiment (two-alternative forced choice procedure), they had to express their preference for one of two shapes from the series. The shape pairs were presented successively in random order. Results show that the smallest possible fractal deviation from “symmetry of things in a thing” significantly reduces the perceived attractiveness of such shapes. The potential of future studies where different levels of complexity of fractal patterns are weighed against different degrees of symmetry is pointed out in the conclusion. (shrink)

A biological explanation for the dependence of genome-wide mutation-rate variation on local base context is now becoming clearer. The proportions of G + C relative to A + T—expressed as GC%—is a species-specific DNA character. The frequencies of these single bases correlate with frequencies of corresponding oligonucleotides that are more-sensitive indicators of species specificity. Thus, when k = 3 there are 64 possible trinucleotide sequences and a GC%-rich species has a high frequency of GC-rich 3-mers. Closely related species have (...) similar k-mer patterns. For distantly related species, even if happening to have the same GC% values, k-mer patterns are widely discordant. Conventionally, a base substitution mutation is viewed as a chemical 1-mer phenomenon. However, the selective difference by which the corresponding mutation is scored usually relates to context. Thus, an A to U codon mutation in sickle cell anemia, rather than attracting an anticodon in a structural loop of glutamate tRNA, pairs with the more complementary anticodon loop of valine tRNA. Likewise, a recent statistical analysis of genome-wide mutation-rate variation supports the view that a failure of discordant DNA loops to pair at meiosis can initiate and/or sustain the speciation process. Such disharmony among base patterns may have unknowingly been hinted at by geneticist William Bateson who invoked a music metaphor when considering speciation mechanisms. (shrink)

The advent of new technologies has rekindled some hopes that it will be possible to identify genetic variants that will help to explain why individuals are different with respect to complex traits. At least one leader in the development of “whole genome sequencing”—the Chinese company BGI—has been quite public about its commitment to using the technique to investigate the genetics of intelligence in general and high intelligence in particular. Because one needs large samples to detect the small effects associated with (...) small genetic differences in the sequence of those base pairs, to make headway with the new sequencing technologies, one also needs to enlist much larger numbers of study participants than geneticists have enrolled before. In an effort to increase the size of a sample, one team of researchers approached the Center for Talented Youth at Johns Hopkins University. They wanted to gain access to records concerning participants in CTY's ongoing Study of Exceptional Talent, and they wanted to approach those individuals to see if they would be willing to share samples of their DNA.We agreed that CTY's dilemma about whether to give the researchers access to those records raised larger questions about the ethics of research into the genetics of intelligence, and we decided to hold a workshop at The Hastings Center that could examine those questions. Our purpose was to create what, borrowing from Sarah Richardson, we came to call a “transformative conversation” about research into the genetics of general cognitive ability—a conversation that would take a wide and long view and would involve a diverse group of stakeholders, including both people who have been highly critical of the research and people who engage in it. This collection of essays, which grew out of that workshop, is intended to provide an introduction to and exploration of this complex and important area. (shrink)

Structures of multisubunit RNA polymerases strongly differ from the many known structures of single subunit DNA and RNA polymerases. However, in functional complexes of these diverse enzymes, nucleic acids take a similar course through the active center. This finding allows superposition of diverse polymerases and reveals features that are functionally equivalent. The entering DNA duplex is bent by almost 90° with respect to the exiting template–product duplex. At the point of bending, a dramatic twist between subsequent DNA template bases aligns (...) the “coding“ base with the binding site for the incoming nucleoside triphosphate (NTP). The NTP enters through an opening that is found in all polymerases, and, in most cases, binds between an α‐helix and two catalytic metal ions. Subsequent phosphodiester bond formation adds a new base pair to the exiting template–product duplex, which is always bound from the minor groove side. All polymerases may undergo “induced fit” upon nucleic acid binding, but the underlying conformational changes differ. BioEssays 24:724–729, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Two recent papers1,2 report extensive nuclear DNA sequence from a 38,000‐year‐old Neandertal fossil, comparing it to modern humans and estimating when it diverged from, and whether it contributed to, our gene pool. Based on 65,250 and over a million base‐pairs of sequence across the genome, respectively, the groups arrived at slightly different interpretations. The data are an exciting and interesting new contribution, but are not surprising, and a sense of history and question helps put them in perspective. BioEssays (...) 29: 105–110, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

In addition to double‐ and single‐strand DNA breaks and isolated base modifications, ionizing radiation induces clustered DNA damage, which contains two or more lesions closely spaced within about two helical turns on opposite DNA strands. Post‐irradiation repair of single‐base lesions is routinely performed by base excision repair and a DNA strand break is involved as an intermediate. Simultaneous processing of lesions on opposite DNA strands may generate double‐strand DNA breaks and enhance nonhomologous end joining, which frequently results (...) in the formation of deletions. Recent studies support the possibility that the mechanism of base excision repair contributes to genome stability by diminishing the formation of double‐strand DNA breaks during processing of clustered lesions. BioEssays 23:745–749, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

DNA methylation can be considered a component of epigenetic memory with a critical role during embryo development, and which undergoes dramatic reprogramming after fertilization. Though it has been a focus of research for many years, the reprogramming mechanism is still not fully understood. Recent results suggest that absence of maintenance at DNA replication is a major factor, and that there is an unexpected role for TET3-mediated oxidation of 5mC to 5hmC in guarding against de novo methylation. Base-resolution and genome-wide (...) profiling methods are enabling more comprehensive assessments of the extent to which ART might impair DNA methylation reprogramming, and which sequence elements are most vulnerable. Indeed, as we also review here, studies showing the effect of culture media, ovarian stimulation or embryo transfer on the methylation pattern of embryos emphasize the need to face ART-associated defects and search for strategies to mitigate adverse effects on the health of ART-derived children. DNA methylation, critical for embryo development, suffers significant changes after fertilization, including demethylation, remethylation and TET3-mediated oxidation of 5 mC to 5 hmC. In addition to infertility and environmental insults, ART could impact DNA methylation and ART related consequences in the offspring have been reported. (shrink)

Transient global amnesia is a benign memory disorder with etiologies that have been debated for a long time. The prevalence of stressful events before a TGA attack makes it hard to overlook these precipitating factors, given that stress has the potential to organically effect the brain. Cortical spreading depression was proposed as a possible cause decades ago. Being a regional phenomenon, CSD seems to affect every aspect of the micro-mechanism in maintaining the homeostasis of the central nervous system. Corresponding (...) evidence regarding hemodynamic and morphological changes from TGA and CSD have been accumulated separately, but the resemblance between the two has not been systematically explored so far, which is surprising especially considering that CSD had been confirmed to cause secondary damage in the human brain. Thus, by deeply delving into the anatomic and electrophysiological properties of the CNS, the CSD-TGA model may render insights into the basic pathophysiology behind the façade of the enigmatic clinical presentation. (shrink)

Advances in DNA technology and the discovery of DNA polymorphisms have permitted the creation of DNA databases of individuals for the purpose of criminal investigation.Many ethical and legal problems arise in the preparation of a DNA database, and these problems are especially important when one analyses the legal regulations on the subject.In this paper three main groups of possibilities, three systems, are analysed in relation to databases. The first system is based on a general analysis of the population; the second (...) one is based on the taking of samples for a particular list of crimes, and a third is based only on the specific analysis of each case. The advantages and disadvantages of each system are compared and controversial issues are then examined. We found the second system to be the best choice for Spain and other European countries with a similar tradition when we weighed the rights of an individual against the public's interest in the prosecution of a crime. (shrink)

Students’ learning engagement is recognized as one of the main components of effective instruction and a necessary prerequisite for learning, but students’ learning engagement in flipped classroom poses some pedagogical challenges. This study aimed to promote students’ learning engagement via the flipped classroom approach. Design-based research was adopted in this study to conduct an experiment involving three iterations in a Modern Educational Technology course in a Chinese university. The participants included 36 third-year pre-service teacher undergraduates. Classroom observations and a learning (...) engagement questionnaire were used to measure the effectiveness of the flipped instruction in terms of students’ learning engagement. Data analysis applied descriptive statistics, ANOVA, and paired samples t tests. The results showed that after three rounds of iterative experiments, students’ learning engagement significantly improved. Several principles are provided as guidelines for instructors to implement flipped classroom approach to promote students’ learning engagement. (shrink)

I consider how we might begin to redress a cognitive model for thought experimental and other imagery-based scientific reasoning from an embodied cognition viewpoint. The paper gravitates on clarifying tour issues: (i) the danger of understanding the genuine novelty of thought-experimental reasoning and other imagery-based reasoning as a product of ‘quasi-perceiving’ new phenomenology with the ‘mind’s eye’ (as asserted by quasi-pictorialist theories of imagery); (ii) the erroneous choice of units of analysis that assume equivalence of external reports of visual imagery (...) with those internal structures that govern imagery-based reasoning, which are, as I will argue, largely linked to motor processes; (iii) the establishment of thought experimentation as imagery-based reasoning by providing evidence for the psychological necessity of imagistic simulation in thought experiments; (iv) a cognitive model for how learning via thought experimentation and other imagery-based reasoning takes place. The study was underpinned by constructivist assumptions. Case methodology was adopted, the case being a pair of final year A-level physics students. Data was collected through non-participant observation over two sessions of collaborative problem-solving. The tasks drew upon Newtonian mechanics. (shrink)

Many proposals for logic-based formalisations of argumentation consider an argument as a pair (Φ,α), where the support Φ is understood as a minimal consistent subset of a given knowledge base which has to entail the claim α. In case the arguments are given in the full language of classical propositional logic reasoning in such frameworks becomes a computationally costly task. For instance, the problem of deciding whether there exists a support for a given claim has been shown to be (...) -complete. In order to better understand the sources of complexity (and to identify tractable fragments), we focus on arguments given over formulæ in which the allowed connectives are taken from certain sets of Boolean functions. We provide a complexity classification for four different decision problems (existence of a support, checking the validity of an argument, relevance and dispensability) with respect to all possible sets of Boolean functions. Moreover, we make use of a general schema to enumerate all arguments to show that certain restricted fragments permit polynomial delay. Finally, we give a classification also in terms of counting complexity. (shrink)

According to Scheck, Newfeld, and Dwyer (2000), there have been innumerable individuals wrongly convicted of a crime and sentenced to life imprisonment or to death based upon faulty evidence. The historical development of DNA evidence as a tool in the investigative process during the past 25 years is explained/analyzed, and the role of eyewitness evidence in the wrongful conviction of innocent individuals. This paper culminates in the Anthony Capozzi case study where eyewitness testimony wrongfully imprisoned a man before the advent (...) of DNA technology and which ultimately freed him years after the crime. The methodology used is the examination of journal articles, books, and newspaper articles on the phenomenon of wrongful convictions. (shrink)

In this paper we explore shifts in how the law and ethics allow European law enforcement officers to use forensic genetic technologies. We do so by reviewing three technologies, ‘traditional’ (STR-based) forensic DNA profiling, forensic DNA phenotyping and the searching of genetic genealogy databases. In particular, we discuss changes in how ethical boundaries have been placed around what is seen as an appropriate use of genetic technologies in European criminal justice systems. While the ‘type’ of DNA that law enforcement officers (...) are permitted to analyse offers a useful ethical reference point, for newer forensic genomic technologies, ethical scrutiny, we argue, would also look at the specific purpose or use of the technology. (shrink)

Being based on the observation that a conjugate pair of representations, or dual logic, is a necessity under the presence of chaos, a new interpretation of quantum theory is proposed as describingproto-chaos. This chaos has to be a result of basic nonlinearity in the dynamic structure, of which, however, the nonchaotic phase seems to lie ourside the reach of experimental technique, thus the term proto-chaos. Nevertheless, assuming no extra degrees of freedom, the interpretation clarifies a number of riddles posed hitherto (...) and throws some light on the overall hierarchical structure of our understanding and description of nature. (shrink)

The topology of DNA duplexes changes during replication and also after deproteinization in vitro. Here we describe these changes and then discuss for the first time how the distribution of superhelical stress affects the DNA topology of replication intermediates, taking into account the progression of replication forks. The high processivity of Topo IV to relax the left‐handed (+) supercoiling that transiently accumulates ahead of the forks is not essential, since DNA gyrase and swiveling of the forks cooperate with Topo IV (...) to accomplish this task in vivo. We conclude that despite Topo IV has a lower processivity to unlink the right‐handed (+) crossings of pre‐catenanes and fully replicated catenanes, this is indeed its main role in vivo. This would explain why in the absence of Topo IV replication goes‐on, but fully replicated sister duplexes remain heavily catenated. (shrink)

The government of Bangladesh approved the human organ transplantation law in 1999 and updated it in 2018. This legislation approved both living‐related donor and posthumous organ transplantation. The law only allows family members to legally donate organs to their relatives. The main focus of this study was to explore how Bangladeshis make donation decisions on familial organs for transplantation. My ethnographic fieldwork with forty participants (physicians and nurses, a healthcare administrator, organ donors, recipients, and their relatives) disclosed that the organ (...) donation decision was family‐based. An assessment of the relationship between religion, culture, and biomedicine leads to the conclusion that deciding on donating organs to relatives is primarily family‐based and is perceived to be steeped in Islamic ethical principles and religious cultural tradition. The family‐based consent and motivation for donor‐recipient pair organ transplantation strengthen an altruistic environment for the family and act as the moral and legal authority that ensures ethical healthcare outcomes for Bangladeshis. (shrink)