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)

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..

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)

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)

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)

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)

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)

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)

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.

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)

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)

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)

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)

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.

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)

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)

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)

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)

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)

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)

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)

This manuscript provides an overview of forensic DNA data banks and their use, with some focus on existing programs established in the U.S., Canada, and the U.K. The intent is to provide a constructive analysis of both strengths and weaknesses in performance, and especially to suggest directions for improvement. Implementation of these suggestions will be crucial to allow DNA data banks to be most effective in advancing societal goals of enhancing public safety and collective security.

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)

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)

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)

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)

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)

Forensic data banks contain biological samples and DNA extracts as well as computerized databases of coded DNA profiles of convicted offenders, arrestees and crime scene samples. When used for investigative and law enforcement purposes, DNA data banks have been successful in providing key investigative leads in hundreds of criminal investigations. A number of these crimes would never have been resolved without use of such data banks. In addition, in some limited number of investigations, the exclusion of known suspects whose DNA (...) profiles are known to be in an offender database can save valuable investigative time.Despite the above benefits, in hundreds of cases DNA samples are never collected and administrative and laboratory logjams delay prompt database searches. Furthermore, hundreds of DNA database matches languish, without any followup by law enforcement or prosecutors. These prevent or delay DNA matches and therefore can leave the public in grave risk of potential harm from recidivistic offenders who otherwise could have been apprehended and convicted if the process functioned more effectively. (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)

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)

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)

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)

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)

Methylation of DNA plays an important role in the control of gene expression in higher eukaryotes. This is largely achieved by the packaging of methylated DNA into chromatin structures that are inaccessible to transcription factors and other proteins. Methylation involves the addition of a methyl group to the 5‐position of the cytosine base in DNA, a reaction catalysed by a DNA (cytosine‐5) methyltransferase. This reaction occurs in nuclear replication foci where the chromatin structure is loosened for replication, thereby allowing (...) access to methyltransferases. Partly as a result of their recognising the presence of a methylcytosine on the parental strand following replication, these large enzymes are able to maintain the distribution of methyl groups along the DNA of somatic cells and, thereby, maintain tissue‐specific patterns of gene expression. (shrink)

Although DNA profiling has been an important forensic research technique since the late 1980s, for a long time, it had not captured much attention from either academics or the public so far.In recent years, this neglect seems to have ended. Not only has wide-spread media coverage of events such as 9/11 and the 2004 tsunami brought about widespread knowledge of the usefulness of forensic DNA identification, the development of large databases containing DNA profiles of both suspected and convicted criminals has (...) in the last few years also triggered a discussion on the intrusiveness of these measures into a number of civil rights.Indeed, although the increasing use of DNA based techniques in the criminal justice system promises to offer some great benefits for a society that is permeated with risk-aversion, at the same time it also gives rise to some worrying ethical and social consequences.In this article, we confine ourselves to an analysis of the practice of DNA sample retention by government agencies that use these samples to derive digital storable DNA profiles. While this practice seems unnecessary for the purpose of criminal investigation, it carries some severe risks for genetic privacy rights which have hardly been explored so far. (shrink)

Transport of DNA across bacterial membranes involves complex DNA uptake systems. In Gram‐positive bacteria, the DNA uptake machinery shares fundamental similarities with type IV pili and type II secretion systems. Although dedicated pilus structures, such as type IV pili in Gram‐negative bacteria, are necessary for efficient DNA uptake, the role of similar structures in Gram‐positive bacteria is just beginning to emerge. Recently two essentially very different pilus structures composed of the same major pilin protein ComGC were proposed to be involved (...) in transformation of the Gram‐positive bacterium Streptococcus pneumoniae – one is a long, thin, type IV pilus‐like fiber with DNA binding capacity and the other one is a pilus structure that was thicker, much shorter and not able to bind DNA. Here we discuss how competence induced pili, either by pilus retraction or by a transient pilus‐related opening in the cell wall, may mediate DNA uptake in S. pneumoniae. (shrink)

There is growing evidence that mutations can arise in non‐dividing cells (both bacterial and mammalian) in the absence of chromosomal replication. The processes that are involved are still largely unknown but may include two separate mechanisms. In the first, DNA lesions resulting from the action of endogenous mutagens may give rise to RNA transcripts with miscoded bases. If these confer the ability to initiate DNA replication, the DNA lesions may have an opportunity to miscode during replication and thus could give (...) rise to apparently ‘adaptive’ mutations. A second mechanism is suggested by recent work in starved bacteria, showing that there is much more turnover of chromosomal DNA than has been previously thought. This could permit polymerase errors to lead to mutations in non‐dividing cells. Such cryptic DNA synthesis, which may essentially replace existing DNA rather than duplicating it, could, in principle, act as an additional source of variability on which selection may act, initially in the absence of cell division. In mammals such processes would undoubtedly have implications for germ cell mutagenesis and carcinogenesis. (shrink)

The direction and specificity of endolysosomal membrane trafficking is tightly regulated by various cytosolic and membrane‐bound factors, including soluble NSF attachment protein receptors (SNAREs), Rab GTPases, and phosphoinositides. Another trafficking regulatory factor is juxta‐organellar Ca2+, which is hypothesized to be released from the lumen of endolysosomes and to be present at higher concentrations near fusion/fission sites. The recent identification and characterization of several Ca2+ channel proteins from endolysosomal membranes has provided a unique opportunity to examine the roles of Ca2+ and (...) Ca2+ channels in the membrane trafficking of endolysosomes. SNAREs, Rab GTPases, and phosphoinositides have been reported to regulate plasma membrane ion channels, thereby suggesting that these trafficking regulators may also modulate endolysosomal dynamics by controlling Ca2+ flux across endolysosomal membranes. In this paper, we discuss the roles of phosphoinositides, Ca2+, and potential interactions between endolysosomal Ca2+ channels and phosphoinositides in endolysosomal dynamics. (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)

NEMO means Network Mobility which is the extension of Mipv6 and it is invented for accessing internet for the group of people when they are travelling in Vehicle as Network group. During handoff while exchanging Binding Updates between the Mobile Network Node, Correspondent Node and Home Agent, many security threats are present during those messages exchange. It may prone to several standard malicious attacks on the BU and Binding Acknowledgement. An efficient end-to-end security method is required to protect the BU (...) Exchange between MNN, HA and CN. In this paper, a secure architecture is proposed to provide authentication and confidentiality at each level of communication using a 3-Party Key Exchange called 3-PKE-NEMO with the help of Bilinear Pairing Theorem. Handoff delay is reduced without compromising security strength. The whole experimentation of this proposed work is carried out using NS2 simulation tool and authentication proof is given using BAN logic between all the nodes in NEMO. The proposed security architecture is compared with related existing solutions and found to be more secure. (shrink)

In vowel discrimination, commonly found discrimination patterns are directional asymmetries where discrimination is faster if differing vowels are presented in a certain sequence compared to the reversed sequence. Different models of speech sound processing try to account for these asymmetries based on either phonetic or phonological properties. In this study, we tested and compared two of those often-discussed models, namely the Featurally Underspecified Lexicon model and the Natural Referent Vowel framework. While most studies presented isolated vowels, we investigated a large (...) stimulus set of German vowels in a more naturalistic setting within minimal pairs. We conducted an mismatch negativity study in a passive and a reaction time study in an active oddball paradigm. In both data sets, we found directional asymmetries that can be explained by either phonological or phonetic theories. While behaviorally, the vowel discrimination was based on phonological properties, both tested models failed to explain the found neural patterns comprehensively. Therefore, we additionally examined the influence of a variety of articulatory, acoustical, and lexical factors but also the influence of factors beyond the well-known in depth via multiple regression analyses. The analyses revealed that the perceptual factor of perceived loudness has a greater impact than considered in the literature and should be taken stronger into consideration when analyzing preattentive natural vowel processing. (shrink)

The gain of a selective advantage in cancer as well as the establishment of complex traits during evolution require multiple genetic alterations, but how these mutations accumulate over time is currently unclear. There is increasing evidence that a mutator phenotype perpetuates the development of many human cancers. While in some cases the increased mutation rate is the result of a genetic disruption of DNA repair and replication or environmental exposures, other evidence suggests that endogenous DNA damage induced by AID/APOBEC cytidine (...) deaminases can result in transient localized hypermutation generating simultaneous, closely spaced (i.e. “clustered”) multiple mutations. Here, we discuss mechanisms that lead to mutation cluster formation, the biological consequences of their formation in cancer and evidence suggesting that APOBEC mutagenesis can also occur genome‐wide. This raises the possibility that dysregulation of these enzymes may enable rapid malignant transformation by increasing mutation rates without the loss of fitness associated with permanent mutators. (shrink)

Frequency selective surface -based intelligent spatial filters are capturing the eyes of the researchers by offering a dynamic behavior when exposed to the electromagnetic radiations. In this manuscript, a concept of creating complementary structures which stems from Babinet’s principle is illustrated. A hybrid complementary pair of FSS comprising double square loop FSS and double square slot FSS on either side of the dielectric substrate is proposed. DSLFSS offers band-pass behavior and can be placed as a superstrate, whereas DSSFSS behaves as (...) a band-stop intelligent spatial filter that blocks the radiations falling on it, thus making them applicable for use as a substrate. The technique utilized for analyzing DSLFSS and DSSFSS structures is based on the equivalent circuit modeling and transmission line methodology. The CPFSS structure offers the design simplicity, hence, suitable for placing them with the printed patch antenna radiators in wireless networking devices operating in sub-6 GHz 5G spectrum. DSLFSS offers band-pass behavior ranging from 2.99 to 5.56 GHz, whereas DSSFSS offers band-stop behavior ranging from 2.85 to 5.42 GHz covering all n77, n78, and n79 bands of FR1 spectrum of sub-6 GHz 5G range. The passband and the stopband offered by the two structures of CPFSS geometry are stable to oblique angles of incidence and the proposed design also offers polarization-independent behavior. The thickness of the dielectric region existing within the pair of designed structures is critical for the location of the passbands and the stopbands. The impact of the overall thickness of the dielectric substrate on the passbands and stopbands is also reported in this article. (shrink)