RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence‐specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross‐linking immuno‐precipitation (CLIP) and other recently developed high‐throughput methods provide comprehensive, genome‐wide maps of protein‐RNA interactions in the cell. Structural biology gives detailed insights (...) into molecular mechanisms and principles of RNA recognition by RBPs, but has so far focused on single RNA binding proteins and often on single RNA binding domains. The combination of high‐throughput methods and detailed structural biology studies is expected to greatly advance our understanding of the code for protein‐RNA recognition in gene regulation, as we review in this article. (shrink)

Here I discuss findings that suggest a universal mechanism for proteins (and RNA) to recognize and interact with various binding partners by selectively binding to different conformations that pre‐exist in the free protein's conformational ensemble. The tandem RNA recognition motif domains of splicing factor U2AF65 fluctuate in solution between a predominately closed conformation in which the RNA binding site of one of the domains is blocked, and a lowly populated open conformation in which both RNA binding pockets are (...) accessible. RNA binding to U2AF65 may thus occur through the weakly populated open conformation, and the binding interaction stabilizes the open conformation. The conformational diversity observed in U2AF65 might also facilitate binding to diverse RNA sequences as found in the polypyrimidine tracts that help define 3′ splice sites. Similar binding pathways in other systems have important consequences in biological regulation, molecular evolution, and information storage. (shrink)

High‐fidelity binding of transcription factors (TFs) to DNA target sites is fundamental for proper regulation of cellular processes, as well as for the maintenance of cell identity. Recognition of cognate binding motifs in the genome is attributed by and large to the DNA binding domains of TFs. As an additional mode of conferring binding specificity, noncoding RNAs (ncRNAs) have been proposed to assist associated TFs in finding their binding sites by interacting with either DNA or RNA in the vicinity (...) of their target loci. However, a well‐documented example of such a mechanism was lacking until we recently reported that a ncRNA made by Epstein‐Barr virus uses an RNA–RNA interaction with nascent transcripts generated from the viral genome to facilitate the recruitment of an interacting TF, PAX5, to viral DNA. This proof‐of‐principle finding suggests that cellular ncRNAs may likewise function in guiding interacting TFs to chromatin target sites. (shrink)

Retroviruses encode a small, basic nucleocapsid (NC) protein that is found complexed to genomic RNA within the viral particle. The NC protein appears to function not only in a histone‐like manner in packaging the RNA into the particle but also in specifically selecting the viral genomic RNA for packaging. A cysteine‐histidine (cys‐his) region, usually composed of 14 amino acids and reminiscent of the ‘zinc fingers’ of transcription factors, is the only highly conserved sequence element among the retroviral NC proteins. This (...) review discusses the biochemical properties of NC, and its possible role(s) in retroviral replication. We also speculate on how the biochemical properties may relate to its function in RNA recognition and packaging. (shrink)

In The Shock of Recognition, Lewis Pyenson uses a method called Historical Complementarity to identify the motif of non-figurative abstraction in modern art and science. He identifies the motif in Picasso's and Einstein's educational environments. He shows how this motif in domestic furnishing and in urban lighting set the stage for Picasso's and Einstein's professional success before 1914. He applies his method to intellectual life in Argentina, using it to address that nation's focus on an inventory (...) of the natural world until the 1940s, its adoption of non-figurative art and nuclear physics in the middle of the twentieth century, and attention to landscape painting and the wonder of nature at the end of the century. (shrink)

Deamination of adenosine in RNA to form inosine has wide ranging consequences on RNA function including amino acid substitution to give proteins not encoded in the genome. What determines which adenosines in an mRNA are subject to this modification reaction? The answer lies in an understanding of the mechanism and substrate recognition properties of adenosine deaminases that act on RNA (ADARs). Our recent publication of X‐ray crystal structures of the human ADAR2 deaminase domain bound to RNA editing substrates shed (...) considerable light on how the catalytic domains of these enzymes bind RNA and promote adenosine deamination. Here we review in detail the deaminase domain‐RNA contact surfaces and present models of how full length ADARs, bearing double stranded RNA‐binding domains (dsRBDs) and deaminase domains, could process naturally occurring substrate RNAs. (shrink)

RNA editing is a newly described genetic phenomenon. It encompasses widely different molecular mechanisms and events. According to the specific RNA modification, RNA editing can be broadly classified into six major types. Type II RNA editing occurs in plants and mammals; it consists predominantly in cytidine to uridine conversions resulting from deamination/transamination or transglycosylation, although in plants other mechanisms have not been excluded. Apolipoprotein B mRNA editing is the only well‐documented editing phenomenon in mammals. It is an intranuclear event that (...) occurs posttranscriptionally, coincident with splicing and polyadenylation. Recent observations indicate that the tissue‐ and sequence‐specific process is mediated by an enzyme that has separate domains for editing and sequence recognition. The presence of apolipoprotein B mRNA editing activity in tissues that do not produce the protein suggests that other RNAs may be edited and RNA editing may be a genetic phenomenon of general biological importance to the cell. (shrink)

The only RNA molecules known to be branched are circular structures with tails known as lariats that arise during nuclear pre‐mRNA splicing. Lariats accumulate within a large multicomponent particle called a spliceosome that forms upon the addition of unspliced mRNA to nuclear extracts. Recently an RNA molecule has been observed to catalyze branch formation. In this case a single intron of a yeast mitochondrial pre‐mRNA participates in a self‐splicing reaction that results in the accumulation of branched lariats that are processed (...) to correctly spliced exons.An enzyme highly specific for branch removal found in the same extracts that form branches during pre‐mRNA splicing can debranch RNA lariats to their linear forms without loss of nucleotides.The chemical synthesis of branched RNA has recently been achieved. High yields of sequence‐specific oligonucleotides are now available for the analysis of RNA splicing by techniques dependent on branch‐site recognition. (shrink)

AbstractmRNA stability is increasingly recognized as being essential for controlling the expression of a wide variety of transcripts during neuronal development and synaptic plasticity. In this context, the role of AU‐rich elements (ARE) contained within the 3′ untranslated region (UTR) of transcripts has now emerged as key because of their high incidence in a large number of cellular mRNAs. This important regulatory element is known to significantly modulate the longevity of mRNAs by interacting with available stabilizing or destabilizing RNA‐binding proteins (...) (RBP). Thus, in parallel with the emergence of ARE, RBP are also gaining recognition for their pivotal role in regulating expression of a variety of mRNAs. In the nervous system, the member of the Hu family of ARE‐binding proteins known as HuD, has recently been implicated in multiple aspects of neuronal function including the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. Through its ability to interact with ARE and stabilize multiple transcripts, HuD has now emerged as an important regulator of mRNA expression in neurons. The present review is designed to provide a comprehensive and updated view of HuD as an RBP in the nervous system. Additionally, we highlight the role of HuD in multiple aspects of a neuron's life from early differentiation to changes in mature neurons during learning paradigms and in response to injury and regeneration. Finally, we describe the current state of knowledge concerning the molecular and cellular events regulating the expression and activity of HuD in neurons. BioEssays 28: 822–833, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

Transcription factors (TFs) have to find their binding sites, which are distributed throughout the genome. Facilitated diffusion is currently the most widely accepted model for this search process. Based on this model the TF alternates between one‐dimensional sliding along the DNA, and three‐dimensional bulk diffusion. In this view, the non‐specific associations between the proteins and the DNA play a major role in the search dynamics. However, little is known about how the DNA properties around the motif contribute to the (...) search. Accumulating evidence showing that TF binding sites are embedded within a unique environment, specific to each TF, leads to the hypothesis that the search process is facilitated by favorable DNA features that help to improve the search efficiency. Here, we review the field and present the hypothesis that TF‐DNA recognition is dictated not only by the motif, but is also influenced by the environment in which the motif resides. (shrink)

The three‐dimensional structures adopted by RNA molecules are crucial to their biological functions. The nucleotides of an RNA molecule interact to form characteristic secondary‐structure mctifs. Tertiary interactions orient these secondary‐structure elements with respect to each other to form the functional RNA. Here we describe the basic structural elements with special emphasis on a novel tertiary motif, the pseudoknot.

The fate of cellular RNAs is largely dependent on their structural conformation, which determines the assembly of ribonucleoprotein (RNP) complexes. Consequently, RNA‐binding proteins (RBPs) play a pivotal role in the lifespan of RNAs. The advent of highly sensitive in cellulo approaches for studying RNPs reveals the presence of unprecedented RNA‐binding domains (RBDs). Likewise, the diversity of the RNA targets associated with a given RBP increases the code of RNA–protein interactions. Increasing evidence highlights the biological relevance of RNA conformation for (...) class='Hi'>recognition by specific RBPs and how this mutual interaction affects translation control. In particular, noncanonical RBDs present in proteins such as Gemin5, Roquin‐1, Staufen, and eIF3 eventually determine translation of selective targets. Collectively, recent studies on RBPs interacting with RNA in a structure‐dependent manner unveil new pathways for gene expression regulation, reinforcing the pivotal role of RNP complexes in genome decoding. (shrink)

The structures of spherical RNA plant tiruses, containing 180 copies of one protein subunit, are closely related to those of the animal RNA picornaviruses, which are built of 60 copies of each of three larger capsid proteins. Other spherical RNA and DNA viruses utilize the same structural motif as building units of the viral capsid. It is therefore probable that many of the simple RNA viruses, whether found in animals or plants, have had a common genetic origin. The original (...) gene may have coded for a protein that bound to specific molecules on the cell surface. (shrink)

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and non-coding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a re-examination. In (...) this review we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioural motifs of cooperative RNA consortia. In addition to molecular biological perspectives this may lead to a better understanding of genetic code evolution and dynamics. (shrink)

Contemporary Christian ethics encounters the challenge to communicate genuinely Christian normative orientations within the scientific debate in such a way as to render these orientations comprehensible, and to maintain or enhance their plausibility even for non-Christians. This essay, therefore, proceeds from a biblical motif, takes up certain themes from the Christian tradition (in particular the idea of social justice), and connects both with a compelling contemporary approach to ethics by secular moral philosophy, i.e. with Axel Honneth's reception of Hegel, (...) as based on Hegel's theory of recognition. As a first step, elements of an ethics of recognition are developed on the basis of an anthropological recourse to the conditions of intersubjective encounters. These conditions are then brought to bear on the idea of social justice, as developed in the social-Catholic tradition, and as systematically explored in the Pastoral Letter of the United States Conference of Catholic Bishops, Economic Justice For All (1986). Proceeding from this basis, aspects of a Christian ethics of community service with regard to long-term care can be defined. (shrink)

The immune system, to protect the body, must discriminate between the pathogenic and non-pathogenic microbes and respond to them in different ways. How the mucosal immune system manages to make this distinction is poorly understood. We suggest here that the distinction between pathogenic and non-pathogenic microbes is made by an integrated system rather than by single types of cells or single types of receptors; a systems biology approach is needed to understand immune recognition.

In lieu of an abstract, here is a brief excerpt of the content:Trauma, Recognition, and the Place of LanguageJuliet Mitchell (bio)Definitions of trauma abound within the psychoanalytic discipline. My own definition is going to be simple. A trauma, whether physical or psychical, must create a breach in a protective covering of such severity that it cannot be coped with by the usual mechanisms by which we deal with pain or loss. The severity of the breach is such that even (...) if the incident is expected, the experience cannot be foretold. We cannot thus make use of anxiety as a preparatory signal. The death of a sick relative, the amputation of a diseased limb may be consciously known about in advance, but if they are to be described as traumatic then the foreknowledge was useless. In trauma we are untimely ripped.Whether it is as childhood seduction, infantile abuse, shell shock, or war violence, or as a preoccupation with the place of neoteny and the trials of human birth, trauma is continually posited as the hypothetical “origin” of psychic states. However, although “trauma” is crucial to psychoanalytic theory, trauma in itself is not really the focus of its analysis. Freud proposed a “biological bedrock” on which psychic states were formed, but this bedrock was not the object of psychoanalytic inquiry. I suggest that what emerges as a motif in the many retheorizings of psychoanalysis time and again, as another “bedrock,” is trauma. One might call it an “experiential bedrock.” As with biology, it is crucial—but as the area of another mode of inquiry. Psychoanalysis is equipped to contribute to the understanding of the reaction to trauma, not to the trauma itself.In a colloquial context we tend to look from the perspective of the observer and label a range of difficult or tragic occurrences “traumatic.” Instead, I want to define trauma from the perspective of the person who experiences it. This means both that the same event will not always be traumatic for different people, and that the experience of different events, if they are experienced as trauma, will be the same whatever the event and whoever the sufferer. It was essentially for this reason that Freud eventually disagreed with the rich findings of Otto Rank, who proposed the trauma of birth as the origin of mankind’s neurosis. Trauma is the great equalizer. What differentiates us, since we were all born? Furthermore, what appears to be the trauma from the observer’s perspective may, from the viewpoint of the psychic response of the recipient, only be the catalyst that brings to the surface an experience which, were it not for this later event, might not in itself have been traumatic (or vice versa). Even so extreme an experience as the Holocaust may not breach the defenses of a particular individual. The catalytic event in the present triggers an earlier occurrence which becomes traumatic only by virtue of its retrospectively endowed meaning.Probably all animate matter can be traumatized; it would seem likely that the response to the breach in the human defensive system takes place at a generalizable psychosocial level. Recognition and language are interactional social processes; without another person neither a psyche nor language is possible. Object relations analysts, notably D. W. Winnicott, whom Max Hernandez addresses in his paper in this issue, have devoted their work to aspects of the psyche, Lacanians to language. To me the fields are interdependent and gain from being looked at together, both in their practice and in the theories that can [End Page 121] be applied to them. When we have a physical trauma it is common for an immediate aftereffect to be some uncertainty about words; even the ability to spell correctly can temporarily disappear. There are undoubtedly physiological explanations for this. But I shall argue that there are psychological parallels. Every patient whom I would regard as having had some relevant form of trauma had a specific relationship to language, and it is this that concerns me. In addition, Max Hernandez describes the breach in the defenses caused by the anal rape of a patient when he was a young boy. But neither the patient’s symptom nor his complaint on coming to a therapist for treatment pertains to... (shrink)

The Streptococcus pyogenes CRISPR‐Cas system has gained widespread application as a genome editing and gene regulation tool as simultaneous cellular delivery of the Cas9 protein and guide RNAs enables recognition of specific DNA sequences. The recent discovery that Cas9 can also bind and cleave RNA in an RNA‐programmable manner indicates the potential utility of this system as a universal nucleic acid‐recognition technology. RNA‐targeted Cas9 (RCas9) could allow identification and manipulation of RNA substrates in live cells, empowering the study (...) of cellular gene expression, and could ultimately spawn patient‐ and disease‐specific diagnostic and therapeutic tools. Here we describe the development of RCas9 and compare it to previous methods for RNA targeting, including engineered RNA‐binding proteins and other types of CRISPR‐Cas systems. We discuss potential uses ranging from live imaging of transcriptional dynamics to patient‐specific therapies and applications in synthetic biology. (shrink)

Sorting of membrane proteins is generally mediated by cytosolic coats, which create a scaffold to form coated buds and vesicles and to selectively concentrate cargo by interacting with cytosolic signals. The classical paradigm is the interaction between clathrin coats and associated adaptor proteins, which cluster receptors with characteristic tyrosine and dileucine motifs during endocytosis. Clathrin in association with different sets of adaptors is found in addition at the trans-Golgi network and endosomes. Sequences similar to internalization signals also direct lysosomal and (...) basolateral sorting, which implicates related clathrin-adaptor coats in the respective sorting pathways. This review concentrates on the recognition of sorting signals by clathrin-associated adaptor proteins, an area of significant recent progress due to new methodological and conceptual approaches. BioEssays 21:558–567, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

Many innate immune response proteins recognize foreign nucleic acids from invading pathogens to initiate antiviral signaling. These proteins mostly rely on structural characteristics of the nucleic acids rather than their specific sequences to distinguish self and nonself. One feature utilized by RNA sensors is the extended stretch of double‐stranded RNA (dsRNA) base pairs. However, the criteria for recognizing nonself dsRNAs are rather lenient, and hairpin structure of self‐RNAs can also trigger an immune response. Consequently, aberrant activation of RNA sensors has (...) been reported in numerous human diseases. Yet, in most cases, the activating antigens remain unknown. Recent studies have developed sequencing techniques tailored to specifically capture dsRNAs and identified that various noncoding elements in the nuclear and the mitochondrial genome can generate dsRNAs. Here, the identity of endogenous dsRNAs, their recognition by dsRNA sensors, and their implications in the pathogenesis of human diseases ranging from inflammatory to degenerative are presented. (shrink)

This book is a comprehensive study of the Odyssey's plot, which shows how the motifs of disguise and recognition are used to articulate the central values of Homeric society. The story of Odysseus' homecoming is discussed in relation to family dynamics, heroic competition, the social institutions of marriage and hospitality, gender relations, and the enduring power of song.

The remarkable lectures that Hegel gave in Berlin in the 1820s generated an exciting intellectual atmosphere which lasted for decades. From the 1830s, many students flocked to Berlin to study with people who had studied with Hegel, and both his original students, such as Feuerbach and Bauer, and later arrivals including Kierkegaard, Engels, Bakunin, and Marx, evolved into leading nineteenth-century thinkers. Jon Stewart's panoramic study of Hegel's deep influence upon the nineteenth century in turn reveals what that century contributed to (...) the wider history of philosophy. It shows how Hegel's notions of 'alienation' and 'recognition' became the central motifs for the era's thinking; how these concepts spilled over into other fields – like religion, politics, literature, and drama; and how they created a cultural phenomenon so rich and pervasive that it can truly be called 'Hegel's century.' This book is required reading for historians of ideas as well as of philosophy. (shrink)

Bivalent chromatin with active H3K4me3 and repressive H3K27me3 was initially identified in embryonic stem cells (ESCs) to poise expression of developmental genes upon lineage commitment. Since then, many more different bivalent modifications have been demonstrated in both ESCs and fully differentiated cells. Bivalency not only spatiotemporally controls gene transcription but also acts to fine‐tune the level of transcription during development. Although increasing number of studies demonstrated the functional significance of bivalent chromatin, the molecular connection of bivalent chromatin and transcriptional regulation (...) remains largely elusive. Recently, we showed Spindlin1/C11orf84 complex prefers to recognize the non‐canonical histone H3K4me3K9me3 bivalent mark, which is required for timely ribosomal RNA transcription. Here, we hypothesize the recognition of K4me3 and K9me3 at the same histone tail by Spindlin1/C11orf84 complex may serve as a general mechanism of conversion from a repressed to an active chromatin structure for transcriptional activation. (shrink)

Type-scenes have been studied and analysed for over seventy years. This paper presents a more detailed analysis of one type-scene, the 'recognition scene', than has previously been attempted, with the aim of moving towards a better-structured understanding of the 'syntax' of type-scenes generally. The structure of the recognition scene is dissected into motifs and 'moves', all of which are tabulated; this is the core of the analysis. The ensuing points of clarification elaborate on the definitions and assumptions built (...) into the analysis. Following this is an assessment of the 'syntax' and quantifiable elements of the recognition scene. The discussion closes with a general assessment of the more literary face of recognition scenes, discussing them in the context of the plan of the second half of the Odyssey. (shrink)

Chromatin structure and dynamics regulate key cellular processes such as DNA replication, transcription, repair, remodeling, and gene expression, wherein different protein factors interact with the nucleosomes. In these events, DNA and RNA polymerases, chromatin remodeling enzymes and transcription factors interact with nucleosomes, either in a DNA‐sequence‐specific manner and/or by recognizing different structural features on the nucleosome. The molecular details of the recognition of a nucleosome by different viral proteins, remodeling enzymes, histone post‐translational modifiers, and RNA polymerase II, have been (...) explored in the recent past. The present review puts forth critical insights into the basic mechanisms of nucleosome recognition by the various protein factors and the role of distinct surface epitopes on a nucleosome. These determinants of the underlying specificity include features such as the acidic patch, arginine anchor, histone post‐translational modifications, core DNA, DNA lesions, and linker DNA. (shrink)

Moving from the pages of Cahiers and Discours sur l' esthétique , where Paul Valéry clarifies the energetic value of aesthetics that rises from pleasure, the essay aims to promote a radical reconfiguration of conceptual domain of aesthetics. The sensation, in the surprising and gratifying form of pleasure, becomes expression of the efficiency of the link between emotional device and perceptive recognition: the thick and harmonizing synthesis that's peculiar to aesthetic.

Inspiracija ili provokacija za ovaj clanak dosla je od onih teoreticara dobrobiti zivotinja i envajarmentalistickih filozofa koji su doveli u pitanje opravdanost nase - stvarne ali i simbolicke - prakse jedenja mesa i, odatle stavili na kusnju celokupnu nasu mesozdresku i, uopste, prozdrljivu kulturu. Autor priloga taj motiv - motiv jedenja, gutanja, zdranja - nastoji da propita na tragu onih njegovih manifestovanja, izlaganja, nalaza ili dalekoseznijih tematizacija koji su se vise ili manje usputno odigravali u nekim tekstovima pojedinih stozernih mislilaca (...) moderne i savremene filozofske tradicije. Sugerise se da je pronicanje figure prozdiranja, sagledane iz perspektive njenog neprimetnog i vremenom gotovo obrednog prerastanja u samorazumljivi gest teorije - i niukoliko ne samo teorije - jedan u najmanju ruku instruktivan i inspirativan aktuelni momenat samosvesti celokupnog misljenja, odnosno vid njegove kriticke rekonstrukcije i dekonstrukcije. (shrink)

Abstractc‐Rel is a proto‐oncogene first identified as the cellular counterpart of the v‐Rel oncogene derived from the avian reticuloendotheliosis retrovirus (REV‐T). It was subsequently discovered that c‐Rel belongs to the NF‐κB/Rel transcription factor family whose members share a common DNA recognition motif and similar signaling pathways. Despite the similarities, however, each NF‐κB/Rel member possesses unique properties with regard to tissue expression pattern, response to receptor signals and target gene specificity. These differences are fairly evident from the non‐redundant phenotypes (...) exhibited by individual NF‐κB/Rel knockout mice. Hence the work described in this review will compare and contrast the various physiological functions of c‐Rel to those of other NF‐κB members, particularly with respect to the regulation of proliferation, survival and effector functions in multiple hematopoietic and immunological cell types. The study of c‐Rel knockout mice in several disease models will also be discussed as they reveal an important role for c‐Rel in response to allergens, auto‐antigens, allo‐antigens and pathogenic infection. BioEssays 25:767–780, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Degradation of eukaryotic RNAs that contain premature termination codons (PTC) during nonsense‐mediated mRNA decay (NMD) is initiated by RNA decapping or endonucleolytic cleavage driven by conserved factors. Models for NMD mechanisms, including recognition of PTCs or the timing and role of protein phosphorylation for RNA degradation are challenged by new results. For example, the depletion of the SMG5/7 heterodimer, thought to activate RNA degradation by decapping, leads to a phenotype showing a defect of endonucleolytic activity of NMD complexes. This (...) phenotype is not correlated to a decreased binding of the endonuclease SMG6 with the core NMD factor UPF1, suggesting that it is the result of an imbalance between active (e.g., in polysomes) and inactive (e.g., in RNA‐protein condensates) states of NMD complexes. Such imbalance between multiple complexes is not restricted to NMD and should be taken into account when establishing causal links between gene function perturbation and observed phenotypes. (shrink)

One popular recombinant DNA tool is the EcoRI endonuclease, which cleaves DNA at GAATTC sites and serves as a paradigm for sequence specific DNA‐enzyme interactions. The recently revised X‐ray crystal structure of an EcoRI‐DNA complex reveals EcoRI employs novel DNA recognition motifs, a four α‐helix bundle and two extended chains, which project into the major groove to contact substrate purines and pyrimidines. Interestingly, pyrimidine contacts had been predicted based on genetic and biochemical studies. Current work focuses on the EcoRI (...) active site structure, enzyme and substrate conformational changes during catalysis, and host‐restriction system interactions. (shrink)

Abstract The quasispecies theory is a helpful concept in the explanation of RNA virus evolution and behaviour, with a relevant impact on methods used to fight viral diseases. It has undergone some adaptations to integrate new empirical data, especially the non-deterministic nature of mutagenesis, and the variety of behavioural motifs in cooperation, competition, communication, innovation, integration, and exaptation. Also, the consortial structure of quasispecies with complementary roles of memory genomes of minority populations better fits the empirical data than did the (...) original concept of a master sequence and its mutant spectra. The high productivity of quasispecies variants generates unique sequences that never existed before and will never exist again. In the present essay, we underline that such sequences represent really new ontological entities, not just error copies of previous ones. Their primary unique property, the incredible variant production, is suggested here as quasispecies productivity, which replaces the error-replication narrative to better fit into a new relationship between mankind and living nature in the twenty-first century. (shrink)

A science is an intellectual activity defined by its mechanisms that prevent its scientists from always reaching the conclusions that they set out to reach. Such mechanisms are needed because, if scientists are given full control over what hypotheses they select, what data they discard, and what results they publish, they can communicate any conclusion that they desire. Synthesis, by setting a grand challenge, forces scientists across uncharted territory where they encounter and solve unscripted problems. When theory is inadequate, the (...) synthesis fails, and fails in a way that cannot be ignored. Therefore, synthesis drives discovery and paradigm change in ways that simple hypothesis testing cannot. Here, we describe the discoveries that emerged when synthetic biologists were challenged to create an alternative genetic system that has different molecular structures than DNA and RNA. In pursuit of this particular “grand challenge,” synthesis forced the recognition that the community did not know as much about the double helix as it had constructively assumed. In general, a field of science having access to synthesis as a research strategy can create knowledge even if its practitioners do not fit the ideal of a dispassionate, advocacy-free scientist. (shrink)

Knowing how introns originated should greatly enhance our understanding of the information we carry in our DNA. Gilbert’s suggestion that introns initially arose to facilitate recombination still stands, though not for the reason he gave. Reanney’s alternative, that evolution, from the early “RNA world” to today’s DNA-based world, would require the ability to detect and correct errors by recombination, now seems more likely. Consistent with this, introns are richer than exons in the potential to extrude the stem-loop structures needed for (...) the homology search that can lead to heteroduplex formation and the recognition of base mismatches. In nucleic acid sequences that were unable concomitantly to encode sufficient stem-loop potential, protein-encoding potential was constrained to arise as segments (exons) interrupted by segments rich in stem-loop potential (introns). Thus, sequences with properties that we now deem intronic are likely to have preceded the emergence of exons. (shrink)

Large deletions and genomic re‐arrangements are increasingly recognized as common products of double‐strand break repair at Clustered Regularly Interspaced, Short Palindromic Repeats ‐ CRISPR associated protein 9 (CRISPR/Cas9) on‐target sites. Together with well‐known off‐target editing products from Cas9 target misrecognition, these are important limitations, that need to be addressed. Rigorous assessment of Cas9‐editing is necessary to ensure validity of observed phenotypes in Cas9‐edited cell‐lines and model organisms. Here the mechanisms of Cas9 specificity, and strategies to assess and mitigate unwanted effects (...) of Cas9 editing are reviewed; covering guide‐RNA design, RNA modifications, Cas9 modifications, control of Cas9 activity; computational prediction for off‐targets, and experimental methods for detecting Cas9 cleavage. Although recognition of the prevalence of on‐ and off‐target effects of Cas9 editing has increased in recent years, broader uptake across the gene editing community will be important in determining the specificity of Cas9 across diverse applications and organisms. (shrink)

This article presents three brief case studies of the way Romans talked about and expressed contempt. It examines aspects of discourses about contempt that are characteristic both of Roman literature and of modern concepts. The focus is on the relationship of hierarchy, recognition, and (active and passive) contempt in the Latin vocabulary and in two literary motifs taken from invective and historiography, two genres in which expressions of contempt are particularly frequent and prominent.

The most enigmatic feature of polytene chromosomes is their banding pattern, the genetic organization of which has been a very attractive puzzle for many years. Recent genome‐wide protein mapping efforts have produced a wealth of data for the chromosome proteins of Drosophila cells. Based on their specific protein composition, the chromosomes comprise two types of bands, as well as interbands. These differ in terms of time of replication and specific types of proteins. The interbands are characterized by their association with (...) “active” chromatin proteins, nucleosome remodeling, and origin recognition complexes, and so they have three functions: acting as binding sites for RNA pol II, initiation of replication and nucleosome remodeling of short fragments of DNA. The borders and organization of the same band and interband regions are largely identical, irrespective of the cell type studied. This demonstrates that the banding pattern is a universal principle of the organization of interphase polytene and non‐polytene chromosomes.Editor's suggested further reading in BioEssaysCaught in the act: Rapid, symbiont‐driven evolution AbstractFunction and evolution of sex determination mechanisms, genes and pathways in insects Abstract. (shrink)

Introductory essay to the collection "I that is We, We that is I" (ed. by Italo Testa and Luigi Ruggiu, Brill Books, 2016). In this book an international group of philosophers explore the many facets of Hegel’s formula which expresses the recognitive and social structures of human life. The book offers a guiding thread for the reconstruction of crucial motifs of contemporary thought such as the socio-ontological paradigm; the action-theoretical model in moral and social philosophy; the question of naturalism; and (...) the reassessment of the relevance of work and power for our understanding of human life. This collection addresses the shortcomings of Kantian and constructivist normative approaches to social practices and practical rationality it involves. It sheds new light on Hegel’s take on metaphysics and puts into question some presuppositions of the post-metaphysical interpretative paradigm. (shrink)

Metazoan genomes contain thousands of protein‐coding and non‐coding RNA genes, most of which are differentially expressed, i.e., at different locations, at different times during development, or in response to environmental signals. Differential gene expression is achieved through complex regulatory networks that are controlled in part by two types of trans‐regulators: transcription factors (TFs) and microRNAs (miRNAs). TFs bind to cis‐regulatory DNA elements that are often located in or near their target genes, while miRNAs hybridize to cis‐regulatory RNA elements mostly located (...) in the 3′ untranslated region of their target mRNAs. Here, we describe how these trans‐regulators interact with each other in the context of gene regulatory networks to coordinate gene expression at the genome‐scale level, and discuss future challenges of integrating these networks with other types of functional networks. (shrink)

Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops are the basic players. We thus redefine quasispecies as RNA quasispecies consortia (...) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competence-not error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs. (shrink)

Recent work on gene concepts has been influenced by recognition of the extent to which RNA transcripts from a given DNA sequence yield different products in different cellular environments. These transcripts are altered in many ways and yield many products based, somehow, on the sequence of nucleotides in the DNA. I focus on alternative splicing of RNA transcripts (which often yields distinct proteins from the same raw transcript) and on 'gene sharing', in which a single gene produces distinct proteins (...) with the exact same amino acid sequence. These are instances of molecular pleiotropy, in which distinct molecules are derived from a single putative gene. In such cases the cellular and external environments play major roles in determining which protein is produced. Where there is molecular pleiotropy, alternative gene concepts are naturally deployed; molecular epigenesis (revision of sequence-based information by altering molecular conformations or by action of non-informational molecules) plays a major role in orderly development. These results show that gene concepts in molecular biology do, and should, have both structural and functional components. They also show the need for a plurality of gene concepts and reveal fundamental difficulties in stabilizing gene concepts solely by reference to nucleotide sequence. (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)

Abstract3′ untranslated regions (3′ UTRs) of mRNAs have many functions, including mRNA processing and transport, translational regulation, and mRNA degradation and stability. These different functions require cis‐elements in 3′ UTRs that can be either sequence motifs or RNA structures. Here we review the role of secondary structures in the functioning of 3′ UTRs and discuss some of the trans‐acting factors that interact with these secondary structures in eukaryotic organisms. We propose potential participation of 3′‐UTR secondary structures in cytoplasmic polyadenylation in (...) the model organism Drosophila melanogaster. Because the secondary structures of 3′ UTRs are essential for post‐transcriptional regulation of gene expression, their disruption leads to a wide range of disorders, including cancer and cardiovascular diseases. Trans‐acting factors, such as STAU1 and nucleolin, which interact with 3′‐UTR secondary structures of target transcripts, influence the pathogenesis of neurodegenerative diseases and tumor metastasis, suggesting that they are possible therapeutic targets. (shrink)

Local differences in chromatin organisation may profoundly affect the activity of eukaryotic genomes. Regulation at the level of DNA packaging requires the targeting of structural proteins and histone‐modifying enzymes to specific sites and their stable or dynamic interaction with the nucleosomal fiber. The “chromodomain”, a domain shared by many regulators of chromatin structure, has long been suspected to serve as a module mediating chromatin interactions in a variety of different protein contexts. However, recent functional analyses of a number of different (...) chromodomains revealed an unexpected diversity of interaction targets, including histones, DNA and even RNA. The chromodomains of today seem to have evolved from a common ancestral fold to fulfill various functions in different molecular contexts. Combining information gained from recent functional and structural studies of chromodomains with a bioinformatic classification of their structure could lead to the definition of sequence motifs with predictive quality for chromodomain function. BioEssays 26:133–140, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Eukaryotic gene expression is extensively controlled at the level of mRNA stability and the mechanisms underlying this regulation are markedly different from their archaeal and bacterial counterparts. We propose that two such mechanisms, nonsense‐mediated decay (NMD) and motif‐specific transcript destabilization by CCCH‐type zinc finger RNA‐binding proteins, originated as a part of cellular defense against RNA pathogens. These branches of the mRNA turnover pathway might have been used by primeval eukaryotes alongside RNA interference to distinguish their own messages from those (...) of RNA viruses and retrotransposable elements. We further hypothesize that the subsequent advent of “professional” innate and adaptive immunity systems allowed NMD and the motif‐triggered mechanisms to be efficiently repurposed for regulation of endogenous cellular transcripts. This scenario explains the rapid emergence of archetypical mRNA destabilization pathways in eukaryotes and argues that other aspects of post‐transcriptional gene regulation in this lineage might have been derived through a similar exaptation route. -/- . (shrink)