Roots presents articles on major discoveries that laid the basis for contemporary molecular and cellular biology. In this article, Norton D. Zinder reviews the first findings about the single‐stranded DNA‐containing bacteriophages and what is known today about the genetics and molecular biology of these phages.

Replication protein A (RPA), the major single‐stranded DNA‐binding protein in eukaryotic cells, is required for processing of single‐stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high‐affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. Single molecule (...) studies showed that while RPA binds ssDNA with high affinity, the RPA complex can rapidly diffuse along ssDNA and be displaced by other proteins that act on ssDNA. Finally, dynamic DNA binding allows RPA to prevent error‐prone repair of double‐stranded breaks and promote error‐free repair. Together, these findings suggest a new paradigm where RPA acts as a first responder at sites with ssDNA, thereby actively coordinating DNA repair and DNA synthesis. (shrink)

The genetic stability of living cells is continuously threatened by the presence of endogenous reactive oxygen species and other genotoxic molecules. Of particular threat are the thousands of DNA single-strand breaks that arise in each cell, each day, both directly from disintegration of damaged sugars and indirectly from the excision repair of damaged bases. If un-repaired, single-strand breaks can be converted into double-strand breaks during DNA replication, potentially resulting in chromosomal rearrangement and genetic deletion. Consequently, (...) cells have adopted multiple pathways to ensure the rapid and efficient removal of single-strand breaks. A general feature of these pathways appears to be the extensive employment of protein–protein interactions to stimulate both the individual component steps and the overall repair reaction. Our current understanding of DNA single-strand break repair is discussed, and testable models for the architectural coordination of this important process are presented. BioEssays 23:447–455, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

The primary impediment to formulating a general theory for adaptive evolution has been the unknown distribution of fitness effects for new beneficial mutations. By applying extreme value theory, Gillespie circumvented this issue in his mutational landscape model for the adaptation of DNA sequences, and Orr recently extended Gillespie's model, generating testable predictions regarding the course of adaptive evolution. Here we provide the first empirical examination of this model, using a single-stranded DNA bacteriophage related to phiX174, and find that our (...) data are consistent with Orr's predictions, provided that the model is adjusted to incorporate mutation bias. Orr's work suggests that there may be generalities in adaptive molecular evolution that transcend the biological details of a system, but we show that for the model to be useful as a predictive or inferential tool, some adjustments for the biology of the system will be necessary. (shrink)

Single‐stranded DNA binding proteins have been known for some time to be crucial in many DNA metabolic reactions in both prokaryotes and eukaryotes. Despite a wealth of studies on these proteins we still do not understand their biochemical mechanism of action. Recent studies of the Escherichia coli single stranded DNA binding protein (SSB) are beginning to provide some insight into how this and similar proteins might function.

In lieu of an abstract, here is a brief excerpt of the content:Beyond Ratzinger's Republic:Communio's Postliberal TurnSam Zeno Conedera S.J. and Vincent L. Strand S.J.Is the political future of the West a postliberal one? For the past decade, numerous prominent thinkers in America and Europe have been debating this question. Matters that not long ago were merely of historical interest, such as Pope Gelasius I's understanding of the relation between sacral authority and royal power, Thomas Aquinas's thought on monarchy (...) and Robert Bellarmine's theory of the pope's indirect authority in temporal matters are now increasingly studied for their potential answers to contemporary political questions. This development, which would have been nearly unimaginable just a decade earlier, unsurprisingly has been led by Catholics. We say "unsurprisingly" in view of the long pre-modern tradition of Catholic political thought, as well as the Church's long struggle against liberalism during the nineteenth and early twentieth centuries. Some of the current postliberal writers explicitly connect themselves to both of these aspects by using the term "integralist" to describe their position.1 [End Page 889]This "new integralism" represents a radical departure from the mainstream of Catholic political discourse of the last half century, which has largely sought rapprochement with Western liberalism. A group of writers, led by John Courtney Murray, George Weigel, Michael Novak, and Robert George, have held that the American constitutional order is rooted in the natural law tradition, and therefore is basically friendly to Catholic political thought. The Church's role in American life, they say, is upholding the natural law as a public moral philosophy, while embracing the non-establishment clause of the First Amendment as a matter of principle, in accordance with the teachings of the Second Vatican Council. This "Whig Thomism," which for decades represented the predominant outlook of conservative American Catholics, must now face the challenge of a different sort of Thomism represented by the integralists.2While the engagement between Whig Thomists and integralists has received most of the attention from scholars and journalists alike, another postliberal option has emerged in recent years. Its source is a group of Catholic thinkers associated with the Communio theological movement. Their political vision, which has no single name or label, has a complex and subtle relationship with the thought of earlier Communio writers, most of whom shared the Whig Thomist desire for reconciliation with Western liberalism. [End Page 890] The appearance of a Communio postliberalism therefore represents a significant development within this intellectual tradition. The most important representative of the earlier Communio perspective on political questions is Joseph Ratzinger / Pope Benedict XVI, who has recently been lauded as the "most important Catholic thinker of the twentieth century" on matters at the intersection of theology and politics.3In an article titled "Ratzinger's Republic" that appeared in these pages in 2020, we identified a significant tension in his thought about the Church's contribution to political life.4 Exploring Ratzinger's writings on natural law, we demonstrated that two currents are present. In accord with his fundamental theological commitments about nature and grace and about faith and reason, Ratzinger often questioned the effectiveness of arguments from natural law. He claimed that, since reason is historically conditioned, and therefore in the current order marked by sin, reason needs grace and faith to function properly. Yet, on other occasions, Ratzinger strongly endorsed arguments from natural law, highlighting its role as the foundation of a just democratic political order. We traced this ambivalence about natural law back to a dilemma at the heart of Ratzinger's political thought. On the one hand, in accord with his thinking about the relations of nature and grace and faith and reason, Ratzinger argued that the state needs the Church to supply moral values that the state cannot furnish on its own. On the other hand, he believed it belongs to the very nature of the Church to be separate from the state, and he endorsed nonconfessional, religiously pluralistic states.5 In light of these two commitments, Ratzinger argued that the contribution Christians are to make to the state is to supply moral values that were discerned under the influence of grace and divine revelation but... (shrink)

Each volume in the Purdue University Press Series in the History of Philosophy examines the fundamental ideas of a single philosopher, presenting one basic text by the thinker in question, and supplementing this by “a very thorough and up-to-date commentary.” The format is most successful when a reasonably short classic work containing the subject’s most important claims can be found. We might expect it to work much less well with a thinker like Peirce, serious study of whose work cannot (...) avoid taking seriously a large number of different papers and lectures: good reasons can be found for regarding any selection of a basic text unsatisfactory. It is thus a pleasure to report that Douglas Anderson met this challenge with considerable success. The commentary is of very high quality; and his choice of texts, although initially surprising, works very well. (shrink)

In The Abuse of Casuistry Jonsen and Toulmin describe one view of moral reasoning as follows:Those who take a rhetorical view of moral reasoning… do not assume that moral reasoning relies for its force on single chains of unbreakable deductions which link present cases back to some common starting point. Rather, this strength comes from accumulating many parallel, complementary considerations, which have to do with the current circumstances of the human individuals and communities involved and lend strength to our (...) conclusions, not like links to a chain but like strands to a rope or roots to a tree.Whether or not all moral reasoning resembles “strands to a rope,” bioethics testimony certainly does. Bioethics testimony is eclectic, a composite of many loosely woven strands. Rarely, if ever, is bioethics testimony “a chain of unbreakable deductions.” Rarely is it “pure” ethics, much less pure normative ethics. (shrink)

In The Abuse of Casuistry Jonsen and Toulmin describe one view of moral reasoning as follows:Those who take a rhetorical view of moral reasoning… do not assume that moral reasoning relies for its force on single chains of unbreakable deductions which link present cases back to some common starting point. Rather, this strength comes from accumulating many parallel, complementary considerations, which have to do with the current circumstances of the human individuals and communities involved and lend strength to our (...) conclusions, not like links to a chain but like strands to a rope or roots to a tree.Whether or not all moral reasoning resembles “strands to a rope,” bioethics testimony certainly does. Bioethics testimony is eclectic, a composite of many loosely woven strands. Rarely, if ever, is bioethics testimony “a chain of unbreakable deductions.” Rarely is it “pure” ethics, much less pure normative ethics. (shrink)

Each volume in the Purdue University Press Series in the History of Philosophy examines the fundamental ideas of a single philosopher, presenting one basic text by the thinker in question, and supplementing this by “a very thorough and up-to-date commentary.” The format is most successful when a reasonably short classic work containing the subject’s most important claims can be found. We might expect it to work much less well with a thinker like Peirce, serious study of whose work cannot (...) avoid taking seriously a large number of different papers and lectures: good reasons can be found for regarding any selection of a basic text unsatisfactory. It is thus a pleasure to report that Douglas Anderson met this challenge with considerable success. The commentary is of very high quality; and his choice of texts, although initially surprising, works very well. (shrink)

The central dogma of molecular biology dictates that, with only a few exceptions, information proceeds from DNA to protein through an RNA intermediate. Examining the enigmatic steps from prebiotic to biological chemistry, we take another road suggesting that primordial peptides acted as template for the self-assembly of the first nucleic acids polymers. Arguing in favour of a sort of archaic “reverse translation” from proteins to RNA, our basic premise is a Hadean Earth where key biomolecules such as amino acids, polypeptides, (...) purines, pyrimidines, nucleosides and nucleotides were available under different prebiotically plausible conditions, including meteorites delivery, shallow ponds and hydrothermal vents scenarios. Supporting a protein-first scenario alternative to the RNA world hypothesis, we propose the primeval occurrence of short two-dimensional peptides termed “selective amino acid- and nucleotide-matching oligopeptides” (henceforward SANMAOs) that noncovalently bind at the same time the polymerized amino acids and the single nucleotides dispersed in the prebiotic milieu. In this theoretical paper, we describe the chemical features of this hypothetical oligopeptide, its biological plausibility and its virtues from an evolutionary perspective. We provide a theoretical example of SANMAO’s selective pairing between amino acids and nucleosides, simulating a poly-Glycine peptide that acts as a template to build a purinic chain corresponding to the glycine’s extant triplet codon GGG. Further, we discuss how SANMAO might have endorsed the formation of low-fidelity RNA’s polymerized strains, well before the appearance of the accurate genetic material’s transmission ensured by the current translation apparatus. (shrink)

The study of church growth has historically been divided into two strands of research: the Church Growth Movement and the Social Science approach. This article argues that Dunbar’s Social Brain Hypothesis represents a legitimate and fruitful third strand in the study of church growth, sharing features of both previous strands but identical with neither. We argue that five predictions derived from the Social Brain Hypothesis are accurately borne out in the empirical and practical church growth literature: that larger congregations (...) lead to lower active engagement from members; that single-leader congregations are limited to around 150 members; that congregations of 150 are further stratified into smaller functioning groups; that congregations expanding beyond 150 members undergo internal tensions and are forced to reorganise; and that congregations larger than 150 will require structural sub-divisions to retain active member involvement. While these assertions are reflected in the church growth literature and articulate the common sense assumptions of church growth experts, the Social Brain Hypothesis offers a coherent theoretical framework which unifies these observations and thereby represents a distinctive contribution to church growth studies. (shrink)

Within the sedimentation diagram of infective RNA preparations isolated from Tobacco Mosaic Virus, undegraded molecules form a sharp peak with a molecular weight corresponding to the total RNA content of the virus particle. Degradation kinetics by ribonuclease is of the linear, single-target type, indicating that the RNA is single-stranded. The intact RNA of a virus particle thus forms one big single-stranded molecule. Quantitative evaluation of the effect degradation by RNA-ase on the infectivity of the RNA shows that (...) the integrity of the entire molecule is required for its biological activity. (shrink)

Last year, we reported a new mechanism of DNA replication in mammals. It occurs inside mitochondria and entails the use of processed transcripts, termed bootlaces, which hybridize with the displaced parental strand as the replication fork advances. Here we discuss possible reasons why such an unusual mechanism of DNA replication might have evolved. The bootlace mechanism can minimize the occurrence and impact of single‐strand breaks that would otherwise threaten genome stability. Furthermore, by providing an implicit mismatch recognition (...) system, it should limit the occurrence of replication‐dependent deletions and insertions, and defend against invading elements. Such a mechanism may also limit attempts to manipulate the mammalian mitochondrial genome. (shrink)

Single‐stranded DNA‐protein complex (T‐complex) is proposed to mediate T‐DNA transfer from Agrobacterium to plant cells. A novel model for transfer is presented which incorporates features of both bacterial conjugation and viral infection. Specific protein components of the T‐complex, its ultrastructure and possible functions in the plant cell are discussed.

For twenty years, D. H. Mellor has promoted an influential defence of a view of time he first called the ‘tenseless’ view, but now associates with what he calls the ‘B-theory.’ It is his defence of this view, not the view itself, which is generally taken to be novel. It is organized around a forcefully presented attack on rival views which he claims to be a development of McTaggart's celebrated argument that the ‘A-series’ is contradictory. I will call this attack (...) ‘Mellor's McTaggart.’ Although it has received much critical attention, it has not been well understood. For one thing, it has changed over the years in a way that is little appreciated. Whereas Mellor's original version amounts to a dilemma each horn of which contains a single strand of argument, later statements of the first horn contain a second strand of argument unannounced. I shall be concerned to disentangle these strands. I shall also show them to have been largely anticipated by Gareth Evans. However, my main aim is not the clarification of Mellor's McTaggart, but its refutation. I shall show that there is a rival to Mellor's view of time against which the first horn of the dilemma begs the question both as originally presented, and as supplemented. This rival is a ‘Priorean’ version of the ‘presentist’ doctrine that only what is present exists. Although Prior himself gave McTaggart's own argument short shrift, in refuting Mellor's development of it I do not merely resurrect Prior's moves. Mellor's McTaggart introduces specifically semantic considerations. It focuses not as McTaggart did on presentness and futurity etc., but on the truth-values of tokens of propositions in which presentness and futurity etc. are ascribed. Consequently, its refutation requires an answer, from the perspective of a presentist metaphysics, to a question which came to the fore only after Prior's death. The question is this: How should semantic theory be developed in the light of the need for a theory of linguistic understanding? Though Evans flirted with the issue of how this question should be answered from a presentist perspective, the answer he articulates is wrong. I shall do no more than sketch the correct answer. That is all a refutation of Mellor's McTaggart requires. (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)

The RecA family proteins mediate homologous recombination, a ubiquitous mechanism for repairing DNA double‐strand breaks (DSBs) and stalled replication forks. Members of this family include bacterial RecA, archaeal RadA and Rad51, and eukaryotic Rad51 and Dmc1. These proteins bind to single‐stranded DNA at a DSB site to form a presynaptic nucleoprotein filament, align this presynaptic filament with homologous sequences in another double‐stranded DNA segment, promote DNA strand exchange and then dissociate. It was generally accepted that RecA family (...) proteins function throughout their catalytic cycles as right‐handed helical filaments with six protomers per helical turn. However, we recently reported that archaeal RadA proteins can also form an extended right‐handed filament with three monomers per helical turn and a left‐handed protein filament with four monomers per helical turn. Subsequent structural and functional analyses suggest that RecA family protein filaments, similar to the F1‐ATPase rotary motor, perform ATP‐dependent clockwise axial rotation during their catalytic cycles. This new hypothesis has opened a new avenue for understanding the molecular mechanism of RecA family proteins in homologous recombination. BioEssays 30:48–56, 2008. © 2007 Wiley Periodicals, Inc. (shrink)

This article explains why intercultural communication always should be studied in context and how even though misunderstanding is normally at stake in intercultural communication, one can argue that the promotion of mutual understanding actually is of mutual interest for all of humanity. Studying in context means paying attention to circumstances around the uses of signs as well as to the roles and moods of the users of signs. Promoting mutual understanding means avoiding a state of mind that implies the depreciation (...) of the other. To be intercultural, a communication must not be infected by prejudices. Any real attempt at intercultural communication is a paradoxical procedure. It supposes that human beings who engage in it at one and the same time recognize the stranger as similar and as different. Also, it can lead to acceptance of the other and a better understanding of what communication is about as well as to rejection and obscurantism. In this paper, I argue that even though people always relate in various ways to common and different cultural backgrounds, they still have to relate to common issues that govern their ways, and that focusing on those common issues and studying the various communicative contexts and contents help promoting mutual understanding, as these activities highlight the implicit role of the value of respect in all interpersonal communication. Human beings cannot avoid evaluating situations, contexts, relations, peoples and cultures. How can we establish that mutual respect and open-mindedness are better than disdain and dogmatism? Well, precisely by affirming that human relations commonly build on the inevitability of communicating and contrasting values and norms. Meaning in interaction permanently transforms cultural elements and patterns into something new. Intercultural communication becomes more respectable when it acknowledges the variety of ways humans interact meaningfully and the plurality of their logic of action. It is good and reasonable to value understanding because this variety and this pluralism always have kept the social alive and more than ever in our modern globalized world contribute to the creativity and interactivity of modern life. The interest of pragmatics in user attitudes, its focus on practical rather than on alethic modalities, can contribute to a more nuanced approach to intercultural communication, where the different elements of meaning in interaction can be studied in various bundles rather than in a single strand. (shrink)

The concept of regulatory ‘checkpoints’ in the eukaryotic cycle has proved to be a fruitful one. Here, its applicability to the bacterial cell cycle is examined. A primitive DNA damage checkpoint operates in E. coli such that, after exposure to ultraviolet light, while excision repair occurs, chromosome replication continues very slowly with the production of discontinuous daughter strands. The slower the rate of excision of photoproducts, the greater the delay before the normal rate of DNA replication is restored, the additional (...) time for repair ensuring that normal survival is maintained. A model is proposed in which replication rate is controlled by the ratio of RecAcoated to uncoated single stranded regions of DNA in the replication fork. There are also two cell division inhibitors SulA (=SfiA) and SfiC under the control of the SOS system and sensitive to DNA damage, but they are irrelevant to the survival of wild‐type bacteria under normal conditions. In strains where SulA and SfiC do not operate, inhibition is not influenced by the rate of excision repair and so fails one of the criteria for a DNA damage checkpoint, namely the monitoring of the DNA for the level of residual damage. (shrink)

Diploid germ cells produce haploid gametes through meiosis, a unique type of cell division. Independent reassortment of parental chromosomes and their recombination leads to ample genetic variability among the gametes. Importantly, new mutations also occur during meiosis, at frequencies much higher than during the mitotic cell cycles. These meiotic mutations are associated with genetic recombination and depend on double‐strand breaks (DSBs) that initiate crossing over. Indeed, sequence variation among related strains is greater around recombination hotspots than elsewhere in the (...) genome, presumably resulting from recombination‐associated mutations. Significantly, enhanced mutagenicity in meiosis may lead to faster divergence during evolution, as germ‐line mutations are the ones that are transmitted to the progeny and thus have an evolutionary impact. The molecular basis for mutagenicity in meiosis may be related to the repair of meiotic DSBs by polymerases, or to the exposure of single‐strand DNA to mutagenic agents during its repair. (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)

India has been independent for 70 years now, and it is a good time to reflect on the political philosophy that underwrote the movement that gained that independence. When we do so, we discover the origins of a political vocabulary that is still in use today, although sadly not used with the same rigor and precision with which it was used then. We also find that those who recur to Indian political thought from the pre-independence period tend to return to (...) a single strand of that thought—the theorization of ahimsa by Mohandas K. Gandhi, as for instance in the recent essay on Indian political thought in The New York Times by Gopalkrishna Gandhi (Gandhi won’t leave India 2017). In this discussion, we hope to draw attention to some of the less well-known resources offered by pre-independence Indian philosophy and in particular the political thought of the Arya samaji Congressman, philosopher and political activist, Lajpat Rai. His political philosophy is important for understanding the theorization of and debates within the Indian independence movement; we think that it also suggests ways to think about contemporary political and revolutionary movements and merits consideration in current debates in political philosophy. (shrink)

The many genetic complementation groups of DNA excision‐repair defective mammalian cells indicate the considerable complexity of the excision repair process. The cloning of several repair genes is taking the field a step closer to mechanistic studies of the actions and interactions of repair proteins. Early biochemical studies of mammalian DNA repair in vitro are now at hand. Repair synthesis in damaged DNA can be monitored by following the incorporation of radiolabelled nucleotides. Synthesis is carried out by mammalian cell extracts and (...) is defective in extracts from cell lines derived from individuals with the excisionrepair disorder xeroderma pigmentosum. Biochemical complementation of the defective extracts can be used to purify repair proteins. Repair of damage caused by agents including ultraviolet irradiation, psoralens, and platinating compounds has been observed. Neutralising antibodies against the human single‐stranded DNA binding protein (HSSB) have demonstrated a requirement for this protein in DNA excision repair as well as in DNA replication. (shrink)

Poly(ADP‐ribosyl)ation is a post‐translational modification occurring in the nucleus. The most abundant and best‐characterized enzyme catalyzing this reaction, poly(ADP‐ribose) polymerase 1 (PARP1), participates in fundamental nuclear events. The enzyme functions as molecular “nick sensor”. It binds with high affinity to DNA single‐strand breaks resulting in the initiation of its catalytic activity. Activated PARP1 promotes base excision repair. In addition, PARP1 modifies several transcription factors and thereby precludes their binding to DNA. We propose that a major function of PARP1 (...) includes the silencing of transcription preventing expression of damaged genes. Concomitant stimulation of DNA repair suggests that PARP1 acts as a switch between transcription and DNA repair. Another PARP‐type enzyme, tankyrase, is involved in the regulation of telomere elongation. Tankyrase modifies a telomere‐associated protein and thereby prevents it masking telomeric repeats providing access of telomerase for telomere elongation. Therefore, poly(ADP‐ribosyl)ation reactions may act as molecular switches in DNA metabolism. BioEssays 23:543–548, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Now much revised since its first appearance in 1941, this book, despite its brevity, is notable for its scope and rigor. It provides a single strand of simple techniques for the central business of modern logic. Basic formal concepts are explained, the paraphrasing of words into symbols is treated at some length, and a testing procedure is given for truth-function logic along with a complete proof procedure for the logic of quantifiers. Fully one third of this revised edition (...) is new, and presents a nearly complete turnover in crucial techniques of testing and proving, some change of notation, and some updating of terminology. The study is intended primarily as a convenient encapsulation of minimum essentials, but concludes by giving brief glimpses of further matters. (shrink)

DNA joining enzymes play an essential role in the maintenance of genomic integrity and stability. Three mammalian genes encoding DNA ligases, LIG1, LIG3 and LIG4, have been identified. Since DNA ligase II appears to be derived from DNA ligase III by a proteolytic mechanism, the three LIG genes can account for the four biochemically distinct DNA ligase activities, DNA ligases I, II, III and IV, that have been purified from mammalian cell extracts. It is probable that the specific cellular roles (...) of these enzymes are determined by the proteins with which they interact. The specific involvement of DNA ligase I in DNA replication is mediated by the non‐catalytic amino‐terminal domain of this enzyme. Furthermore, DNA ligase I participates in DNA base excision repair as a component of a multiprotein complex. Two forms of DNA ligase III are produced by an alternative splicing mechanism. The ubiqitously expressed DNA ligase III‐α forms a complex with the DNA single‐strand break repair protein XRCC1. In contrast, DNA ligase III‐β, which does not interact with XRCC1, is only expressed in male meiotic germ cells, suggesting a role for this isoform in meiotic recombination. At present, there is very little information about the cellular functions of DNA ligase IV. (shrink)

In the organelles of plants and mammals, recent evidence suggests that genomic instability stems in large part from template switching events taking place during DNA replication. Although more than one mechanism may be responsible for this, some similarities exist between the different proposed models. These can be separated into two main categories, depending on whether they involve a single‐strand‐switching or a reciprocal‐strand‐switching event. Single‐strand‐switching events lead to intermediates containing Y junctions, whereas reciprocal‐strand‐switching creates Holliday (...) junctions. Common features in all the described models include replication stress, fork stalling and the presence of inverted repeats, but no single element appears to be required in all cases. We review the field, and examine the ideas that several mechanisms may take place in any given genome, and that the presence of palindromes or inverted repeats in certain regions may favor specific rearrangements. (shrink)

Replication protein A (RPA) is the main eukaryotic single‐stranded DNA (ssDNA) binding protein, having essential roles in all DNA metabolic reactions involving ssDNA. RPA binds ssDNA with high affinity, thereby preventing the formation of secondary structures and protecting ssDNA from the action of nucleases, and directly interacts with other DNA processing proteins. Here, we discuss recent results supporting the idea that one function of RPA is to prevent annealing between short repeats that can lead to chromosome rearrangements by microhomology‐mediated (...) end joining or the formation of hairpin structures that are substrates for structure‐selective nucleases. We suggest that replication fork catastrophe caused by depletion of RPA could result from cleavage of secondary structures by nucleases, and that failure to cleave hairpin structures formed at DNA ends could lead to gene amplification. These studies highlight the important role RPA plays in maintaining genome integrity. (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)

In addition to their function in transport of water, ions, small metabolites, and growth factors in normal plant tissue, the plasmodesmata presumably serve as routes for cell‐to‐cell movement of plant viruses in infected tissue. Virus cell‐to‐cell spread through plasmodesmata is an active process mediated by specialized virus encoded movement proteins; however, the mechanism by which these proteins operate is not clear. We incorporate recent information on the biochemical properties of plant virus movement proteins and their interaction with plasmodesmata in a (...) model for transport of nucleic acids through plasmodesmatal channels. We propose that only single stranded (ss) nucleic acids can be transported efficiently through plasmodesmata, and that movement proteins function as molecular chaperones for ss nucleic acids to form unfolded movement protein‐ss nucleic acid complexes. These complexes are targeted to plasmodesmata. Plasmodesmatal permeability is then increased following interaction with movement protein and the entire movement complex or its nucleic acid component is translocated across the plasmodesmatal channel. (shrink)

The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used to obtain the nucleotide sequences; In the first one, chunks of equal length are considered. In the second approach, the whole RNA genome is divided into parts by adenine or the most frequent nucleotide as a “space”. Rank–frequency distributions are studied in both (...) cases. The defined nucleotide sequences are signs comparable to a certain extent to syllables or words as seen from the nature of their rank–frequency distributions. Within the first approach, the Pólya and the negative hypergeometric distribution yield the best fit. For the distributions obtained within the second approach, we have calculated a set of parameters, including entropy, mean sequence length, and its dispersion. The calculated parameters became the basis for the classification of viruses. We observed that proximity of viruses on planes spanned on various pairs of parameters corresponds to related species. In certain cases, such a proximity is observed for unrelated species as well calling thus for the expansion of the set of parameters used in the classification. We also observed that the fifth most frequent nucleotide sequences obtained within the second approach are of different nature in case of human coronaviruses. We expect that our findings will be useful as a supplementary tool in the classification of diseases caused by RNA viruses with respect to severity and contagiousness. (shrink)

DNA helicases catalyze the disruption of the hydrogen bonds that hold the two strands of double‐stranded DNA together. This energy‐requiring unwinding reaction results in the formation of the single‐stranded DNA required as a template or reaction intermediate in DNA replication, repair and recombination. A combination of biochemical and genetic studies have been used to probe and define the roles of the multiple DNA helicases found in E. coli. This work and similar efforts in eukaryotic cells, although far from complete, (...) have established that DNA helicases are essential components of the machinery that interacts with the DNA molecule. (shrink)

Traditionally, plant viruses are viewed as harmful, undesirable pathogens. However, their genomes can provide several useful ‘designer functions’ or ‘sequence modules’ with which to tailor future gene vectors for plant or general biotechnology.The majority (77 %) of known plant viruses have single‐stranded RNA of the messenger (protein coding) sense as their genetic material. Over the past 4 years, improved in vitro transcription systems and the construction of partial of fulllength DNA copies of several plant RNA viruses have enhanced our (...) ability to manipulate and study their genomes, particularly in the context of their pathogenic interactions with host plants.Recently, two forms of genetically engineered protection against plant virus infections have been reported. In both, a virus‐related ‘interfering’ molecule was stably introduced into plants via the DNA‐transfer mechanism of Agro‐bacterium tumefaciens. To date, the choice of ‘interfering’ molecule has been guided by empirical field‐observations and each is effective against only a narrow range of closely‐related viruses. As yet, we do not fully understand the molecular mechanism(s) responsible for the observed protection.The ability to manipulate the plant–pathogen relationship is a powerful tool to increase our knowledge and improve future strategies for uncoventional cropprotection by genetic engineering techniques. (shrink)

Divergent evolution can explain how many proteins containing structurally similar domains, which perform a variety of related functions, have evolved from a relatively small number of modules or protein domains. However, it cannot explain how protein domains with similar, but distinguishable, functions and similar, but distinguishable, structures have evolved. Examples of this are the RNA‐binding proteins containing the RNA‐binding domain (RBD), and a newly established protein group, the cold‐shock domain (CSD) protein family. Both protein domains contain conserved RNP motifs on (...) similar single‐stranded nucleic acid‐binding surfaces. Apart from the RNP motifs, which have a similar function, the two families show little similarity in topology or amino acid sequence. This can be considered an interesting example of convergent evolution at the molecular level. Previously, a β‐sheet surface was found to interact with RNA in non‐homologous proteins from yeast, phage and man, revealing that this mode of RNA binding may be a widely recurring theme. (shrink)

The RecA family proteins mediate homologous recombination, a ubiquitous mechanism for repairing DNA double‐strand breaks (DSBs) and stalled replication forks. Members of this family include bacterial RecA, archaeal RadA and Rad51, and eukaryotic Rad51 and Dmc1. These proteins bind to single‐stranded DNA at a DSB site to form a presynaptic nucleoprotein filament, align this presynaptic filament with homologous sequences in another double‐stranded DNA segment, promote DNA strand exchange and then dissociate. It was generally accepted that RecA family (...) proteins function throughout their catalytic cycles as right‐handed helical filaments with six protomers per helical turn. However, we recently reported that archaeal RadA proteins can also form an extended right‐handed filament with three monomers per helical turn and a left‐handed protein filament with four monomers per helical turn. Subsequent structural and functional analyses suggest that RecA family protein filaments, similar to the F1‐ATPase rotary motor, perform ATP‐dependent clockwise axial rotation during their catalytic cycles. This new hypothesis has opened a new avenue for understanding the molecular mechanism of RecA family proteins in homologous recombination. BioEssays 30:48–56, 2008. © 2007 Wiley Periodicals, Inc. (shrink)

A hypothesis for the control of eukaryotic DNA replication at the chromosomal level is proposed. The specific regulatory problem arises from the subdivision of the genome into thousands of individually replicating units, each of which must be duplicated a single time during S‐phase. The hypothesis is based on the finding of direct repeats at replication origins. Such repeats can adopt, beyond the full‐length double helical structure, another configuration exposing two single‐stranded loops that provide suitable templates for the initiation (...) of DNA replication. Any further initiation at the same origin is excluded as the single strandedness is eliminated by the replication process. Restoration of the initiable loop structure is proposed to occur by DNA‐protein rearrangements involved in chromosome condensation and duplication of the chromosomal protein backbone during mitosis. A possible role of the maturation promoting factor (MPF) is suggested. (shrink)

The recombinational repair of chromosomal double‐strand breaks (DSBs) is of critical importance to all organisms, who devote considerable genetic resources to ensuring such repair is accomplished. In Saccharomyces cerevisiae, DSB‐mediated recombination can be initiated synchronously by the conditional expression of two site‐specific endonucleases, HO or I‐Scel. DNA undergoing recombination can then be extracted at intervals and analyzed. Recombination initiated by meiotic‐specific DSBs can be followed in a similar fashion. This type of ‘in vivo biochemistry’ has been used to describe (...) several discrete steps in two different homologous recombination pathways: gene conversion and single‐strand annealing. The roles of specific proteins during recombination can be established by examining DNA in strains deleted for the corresponding gene. These same approaches are now becoming available for the study of recombination in both higher plants and animals. Physical monitoring can also be used to analyze nonhomologous recombination events, whose mechanisms appear to be conserved from yeast to mammals. (shrink)

Eukaryotic genomes harbor a large number of homologous repeat sequences that are capable of recombining. Their potential to disrupt genome stability highlights the need to understand how homologous recombination processes are coordinated. The Saccharomyces cerevisiae Rad1–Rad10 endonuclease performs an essential role in recombination between repeated sequences, by processing 3′ single‐stranded intermediates formed during single‐strand annealing and gene conversion events. Several recent studies have focused on factors involved in Rad1–Rad10‐dependent removal of 3′ nonhomologous tails during homologous recombination, including (...) Msh2–Msh3, Slx4, and the newly identified Saw1 protein. Together, this new work provides a model for how Rad1–Rad10‐dependent end processing is coordinated: Msh2–Msh3 stabilizes and prepares double‐strand/single‐strand junctions for Rad1–Rad10 cleavage, Saw1 recruits Rad1–Rad10 to 3′ tails, and Slx4 mediates crosstalk between the DNA damage checkpoint machinery and Rad1–Rad10. (shrink)

The "relational mind" approach to the inner content of consciousness is developed in terms of various control structures and processing strategies and their possible neurobiological identifications in brain sites. This leads naturally to a division of consciousness into a passive and an active part. A global control structure for the "single strand" aspect of consciousness is proposed as the thalamo-nucleus reticularis thalami-cortex coupled system, which is related to experimental data on the electrical stimulation of awareness. Local control, in (...) terms of excitatory transfer from pre-processing sites to posterior working memory regions, is supported by data on subliminal perception timing and disambiguation of poorly defined percepts. The inner content of consciousness is understood as arising from the resulting relational features between inputs and stored pre-processing and episodic memories. Strong analogies are drawn between emergent properties of the model and suggested properties of "raw feels", supporting the thesis that working memories are the initial sites for the emergence of phenomenal awareness, and the frontal lobes for its further adumbration in terms of higher cognitive processing, including the creation of self. (shrink)

The universally recognized backbone of molecular biology describes the flow of genetic information from deoxyribonucleic acid (DNA) to ribonucleic acid (RNA) to protein or gene product, that is, DNA is transcribed into another nucleic acid (RNA), which is single stranded, next some types of RNA are in turn translated into proteins. Translation of nucleic acids to proteins is literally a translation from the genomic language to the metabolic language. Codons formed of a sequence of three nucleic acids summon a (...) specific amino acid. Translation from codons to proteins, that is, protein synthesis, takes place by specialized machinery comprising mRNA, ribosomes, and free amino acids. Inferring the structure of DNA opened the door for tremendous advances in understanding the role of genes in creating life, directing replication, and ongoing metabolic processes responsible for maintaining life at both the cellular and organism level. (shrink)

The majority of human, animal and plant viral pathogens possess genomes composed of RNA. The strategies evolved for expression and replication of viral RNA genomes can differ significantly from those utilized for expression and replication of host‐cell genetic material. Consequently, knowledge of the molecular details of these strategies can lead to a clearer understanding of the origin, evolution and control of viral pathogens. We describe recent progress in identifying important structural and functional domains of the RNA genomes and associated replicative (...) enzymes for two very different viruses: vesicular stomatitis virus, which possesses a single‐stranded RNA genome of negative polarity, and wound tumor virus, which contains a genome composed of 12 discrete segments of double‐stranded RNA. (shrink)

Targeted gene alteration (TGA) is a strategy for correcting single base mutations in the DNA of human cells that cause inherited disorders. TGA aims to reverse a phenotype by repairing the mutant base within the chromosome itself, avoiding the introduction of exogenous genes. The process of how to accurately repair a genetic mutation is elucidated through the use of single‐stranded DNA oligonucleotides (ODNs) that can enter the cell and migrate to the nucleus. These specifically designed ODNs hybridize to (...) the target sequence and act as a beacon for nucleotide exchange. The key to this reaction is the frequency with which the base is corrected; this will determine whether the approach becomes clinically relevant or not. Over the course of the last five years, workers have been uncovering the role played by the cells in regulating the gene repair process. In this essay, we discuss how the impact of the cell on TGA has evolved through the years and illustrate ways that inherent cellular pathways could be used to enhance TGA activity. We also describe the cost to cell metabolism and survival when certain processes are altered to achieve a higher frequency of repair. (shrink)

Now much revised since its first appearance in 1941, this book, despite its brevity, is notable for its scope and rigor. It provides a single strand of simple techniques for the central business of modern logic. Basic formal concepts are explained, the paraphrasing of words into symbols is treated at some length, and a testing procedure is given for truth-function logic along with a complete proof procedure for the logic of quantifiers. Fully one third of this revised edition (...) is new, and presents a nearly complete turnover in crucial techniques of testing and proving, some change of notation, and some updating of terminology. The study is intended primarily as a convenient encapsulation of minimum essentials, but concludes by giving brief glimpses of further matters. (shrink)

Intensive research and development of electrophoresis methodology and instrumentation during past decades has resulted in unique methods widely implemented in bioanalysis. While two‐dimensional electrophoresis and denaturing polyacrylamide gel electrophoresis in sodium dodecylsulfate are still the most frequently used electrophoretic methods applied to analyses of proteins, new miniaturized capillary and microfluidic versions of electromigrational methods have been developed. High‐throughput electrophoretic instruments with hundreds of capillaries for parallel separations and laser‐induced fluorescence detection of labeled DNA strands have been of key importance for (...) the scientific and commercial success of the Human Genome Project. Another powerful method, capillary isoelectric focusing with pressurized and pH‐driven mobilization, provides efficient separations and on‐line sensitive detection of proteins, bacteria and viruses. Electrophoretic microfluidic devices can integrate single‐cell injection, cell lysis, separation of its components and fluorescence or mass spectrometry detection. These miniaturized devices also proved the capability of single‐molecule detection. (shrink)

The Indian Buddhist philosopher Vasubandhu is known for his critical contribution to Buddhist Abhidharma thought, his turn to the Mahayana tradition, and his concise, influential Yogacara-Vijñanavada texts. _Paving the Great Way_ reveals another dimension of his legacy: his integration of several seemingly incompatible intellectual and scriptural traditions, with far-ranging consequences for the development of Buddhist epistemology and the theorization of tantra. Most scholars read Vasubandhu's texts in isolation and separate his intellectual development into distinct phases. Featuring close studies of Vasubandhu's (...) _Abhidharmakosabhasya_, _Vyakhyayukti_, _Vimsatika_, and _Trisvabhavanirdesa_, among other works, this book identifies recurrent treatments of causality and scriptural interpretation that unify distinct strands of thought under a single, coherent Buddhist philosophy. In Vasubandhu's hands, the Buddha's rejection of the self as a false construction provides a framework through which to clarify problematic philosophical issues, such as the nature of moral agency and subjectivity under a broadly causal worldview. Recognizing this continuity of purpose across Vasubandhu's diverse corpus recasts the interests of the philosopher and his truly innovative vision, which influenced Buddhist thought for a millennium and continues to resonate with today's philosophical issues. An appendix includes extensive English-language translations of the major texts discussed. (shrink)

In recent years there has been increasing interest in scientific understanding as an epistemic success term that is distinct from scientific knowledge (see, for example, De Regt, Leonelli and Eigner 2009). Although this literature is diverse, three dominant strands can be found that have rather deeper roots in the philosophy of science: understanding as unification (Friedman 1974; Kitcher 1981); understanding through mechanistic thinking as in certain types of causal modelling (Salmon 1998; Woodward 2003); and a kind of contextualist pluralist approach (...) to understanding (De Regt and Dieks 2005; De Regt 2009; 2014), which is in some ways similar to the account offered by Nelson Goodman (1968, 1978) and Catherine Elgin (1997, 2004). Proponents of these views often see them as complimentary or at least not contradictory. However, they have not yet to been brought neatly together in a single account. This is what I propose to do. At the heart of my approach is the thought that we should treat the characteristic content of understanding as pictorial, in contrast to the characteristic content of knowledge, which is propositional. By virtue of the distinctive ways in which they present their content, epistemically efficacious pictures exemplify, unify, show mechanical (and other) causal relations, allow for multiple readings and facilitate the contextualisation of their content, while still having determinate content. In other words, features of pictorial content facilitate cognitive and evaluative procedures that are characteristic of understanding and have already been identified as such in the literature. That understanding should be treated as something like “getting the picture” is supported, albeit weakly, by multiple remarks, more or less well-developed, linking understanding to picturing that can also be found in the literature on scientific understanding, as we shall see. (shrink)

"My interest in [Max] Scheler's critique of Kant runs back nearly a decade.... The more I read of Scheler, the more I began to see the value of a project dealing with his critique of Kant in Der Formalismus in der Ethik und die Materiale Wetethik, which would possess the virtue of focusing in a single project three important strands of philosophical interest: phenomenology, Kantianism, and ethics.... "The study is divided into six chapters and two appendices. Each of the (...) chapters constituting the body of the work contains a brief analysis of the Kantian position or discussion of the basic questions at issue in it, an exposition of Scheler's critique of the Kantian position and its presuppositions, and a detailed appraisal of Scheler's critique." -- from the introduction by the author. (shrink)