scholarly journals Hot and crispy: CRISPR–Cas systems in the hyperthermophile Sulfolobus solfataricus

2013 ◽  
Vol 41 (6) ◽  
pp. 1422-1426 ◽  
Author(s):  
Jing Zhang ◽  
Malcolm F. White

The CRISPR (clustered regularly interspaced short palindromic repeats) and Cas (CRISPR-associated) genes are widely spread in bacteria and archaea, representing an intracellular defence system against invading viruses and plasmids. In the system, fragments from foreign DNA are captured and integrated into the host genome at the CRISPR locus. The locus is transcribed and the resulting RNAs are processed by Cas6 into small crRNAs (CRISPR RNAs) that guide a variety of effector complexes to degrade the invading genetic elements. Many bacteria and archaea have one major type of effector complex. However, Sulfolobus solfataricus strain P2 has six CRISPR loci with two families of repeats, four cas6 genes and three different types of effector complex. These features make S. solfataricus an important model for studying CRISPR–Cas systems. In the present article, we review our current understanding of crRNA biogenesis and its effector complexes, subtype I-A and subtype III-B, in S. solfataricus. We also discuss the differences in terms of mechanisms between the subtype III-B systems in S. solfataricus and Pyrococcus furiosus.

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Clare Rollie ◽  
Stefanie Schneider ◽  
Anna Sophie Brinkmann ◽  
Edward L Bolt ◽  
Malcolm F White

The adaptive prokaryotic immune system CRISPR-Cas provides RNA-mediated protection from invading genetic elements. The fundamental basis of the system is the ability to capture small pieces of foreign DNA for incorporation into the genome at the CRISPR locus, a process known as Adaptation, which is dependent on the Cas1 and Cas2 proteins. We demonstrate that Cas1 catalyses an efficient trans-esterification reaction on branched DNA substrates, which represents the reverse- or disintegration reaction. Cas1 from both Escherichia coli and Sulfolobus solfataricus display sequence specific activity, with a clear preference for the nucleotides flanking the integration site at the leader-repeat 1 boundary of the CRISPR locus. Cas2 is not required for this activity and does not influence the specificity. This suggests that the inherent sequence specificity of Cas1 is a major determinant of the adaptation process.


2017 ◽  
Vol 21 (4) ◽  
pp. 308-320 ◽  
Author(s):  
Mark Rubin

Hypothesizing after the results are known, or HARKing, occurs when researchers check their research results and then add or remove hypotheses on the basis of those results without acknowledging this process in their research report ( Kerr, 1998 ). In the present article, I discuss 3 forms of HARKing: (a) using current results to construct post hoc hypotheses that are then reported as if they were a priori hypotheses; (b) retrieving hypotheses from a post hoc literature search and reporting them as a priori hypotheses; and (c) failing to report a priori hypotheses that are unsupported by the current results. These 3 types of HARKing are often characterized as being bad for science and a potential cause of the current replication crisis. In the present article, I use insights from the philosophy of science to present a more nuanced view. Specifically, I identify the conditions under which each of these 3 types of HARKing is most and least likely to be bad for science. I conclude with a brief discussion about the ethics of each type of HARKing.


2009 ◽  
Vol 37 (3/4) ◽  
pp. 580-613 ◽  
Author(s):  
Kadri Tüür

The object of study in the present article is birds, more precisely the sounds of birds as they are represented in Estonian nature writing. The evolutionary and structural parallels of bird song with human language are reviewed. Human interpretation of bird sounds raises the question, whether it is possible to transmit or “translate” signals between the Umwelts of different species. The intentions of the sender of the signal may remain unknown, but the signification process within human Umwelt can still be traced and analysed. By approaching the excerpts of nature writing using semiotic methodology, I attempt to demonstrate how bird sounds can function as different types of signs, as outlined by Thomas A. Sebeok. It is argued that the zoosemiotic treatment of nature writing opens up a number of interesting perspectives that would otherwise remain beyond the scope of traditional literary analysis.


2010 ◽  
Vol 38 (4) ◽  
pp. 879-882 ◽  
Author(s):  
A.J. Venkatakrishnan ◽  
Emmanuel D. Levy ◽  
Sarah A. Teichmann

Homo-oligomeric protein complexes are functionally vital and highly abundant in living cells. In the present article, we review our current understanding of their geometry and evolution, including aspects of the symmetry of these complexes and their interaction interfaces. Also, we briefly discuss the pathway of their assembly in solution.


Author(s):  
Pranvera Breznica ◽  
Rozafa Koliqi ◽  
Arlinda Daka

Upon entering into the biological environments, the surface of the nanoparticles is immediately coated with proteins and form the so-called a protein corona due to which a nanoparticle changes its "synthetic" identity to a new "biological" identity. Different types of nanoparticles have different protein binding profiles, which is why they have different protein corona composition and therefore it cannot be said that there is a universal protein corona. The composition and amount of protein in the corona depends on the physical and chemical characteristics of the nanoparticles, the type of biological medium and the exposure time. Protein corona increases the diameter but also changes the composition of the surface of the nanoparticles and these changes affect biodistribution, efficacy, and toxicity of the nanoparticles.


Author(s):  
Joao Marcos Hohemberger ◽  
Carlos Perez Bergmann ◽  
Lavinel G. Ionescu

The present article is a brief review of the current understanding of mercury-induced Liquid Metal Embrittlement (LME), with particular emphasis on the corrosion and failure of aluminum cryogenic heat exchangers.


2020 ◽  
Vol 38 (4) ◽  
pp. 246-263
Author(s):  
Claire Loven

Based on Article 34 European Convention on Human Rights, individual applications must be directed against one of the Convention States. Originally ‘horizontal’ cases therefore must be ‘verticalised’ in order to be admissible. This means that a private actor who had first brought a procedure against another private actor before the domestic courts, must complain about State (in)action in his application to the European Court of Human Rights. Recently, some scholars and judges have raised procedural issues that may arise in these cases, but generally, these ‘verticalised’ cases have remained underexplored. To unravel verticalised cases before the ECtHR and to better understand procedural issues that may arise from them, this article provides a deeper understanding of the origins of verticalised cases and the Court’s approach to them. It is explained that verticalised cases before the ECtHR can be very different in nature. These differences are rooted in the different types of horizontal conflicts that may arise on the domestic level, the different relations between private actors they may concern, and the different Convention rights that may be at stake. The wide variety of verticalized cases is also reflected in the Court’s approach to them, as is the second main topic that the present article explores.


Author(s):  
Siv Skard ◽  
Sveinung Jørgensen ◽  
Lars Jacob Tynes Pedersen

AbstractSustainable products offered in today’s marketplace are labelled with product-related green attributes (i.e. green core attributes) or non-product-related green attributes (i.e. green peripheral attributes). The current research investigates consumers’ inferences about a product’s functional quality when its core attributes are green (e.g. the ingredients) and when its peripheral attributes are green (e.g. the product packaging). Four experimental studies and an internal meta-analysis show that there is a sustainability liability effect in strength-dependent categories (for both core and peripheral attributes), and a sustainability asset effect in gentleness-dependent categories (for core attributes only). Our research contributes to the current understanding of how consumers make inferences about product quality when contemplating different types of green attributes. The findings have implications for how strength-dependent and gentleness-dependent products should be labelled as green.


2014 ◽  
Vol 8 (2) ◽  
Author(s):  
Simone Elisabeth Lang

AbstractIn describing the position of the narrator, research in literary studies generally follows Gérard Genette’s pioneering theory of narrative in distinguishing between the homo- and heterodiegetic type of narrator. This categorization is not sufficient to allow the position of the narrator to be described properly. The different ways in which the terms are used in literary studies reveal a shortcoming in the distinction behind them. Even in Genette’s work, there is a contradiction between the definition and the names of the two categories: Genette defines homo- and heterodiegesis with reference to the narrator’s presence in the narrated story, whereas he elsewhere states that the diegesis (in the sense of FrenchThe present article aims to do just that, starting from a theoretical standpoint. Thus, the different types of narrator that are possible are sketched in outline, and then explained with the help of examples.I begin by exposing the problems that result from using the terms in Genette’s manner (1), in order then to develop a list of possible narratorial standpoints based on the one hand on the involvement of the narratorial instance in the narrated world and on the other on its involvement in the story. By establishing separation of the two aspects as a ground rule in this way, a number of misunderstandings that are due to the varied ways in which the terminology has been used to date can be overcome.There follows a description of those cases that are unambiguously hetero- and homodiegetic (2), after which the problematic cases are considered (3), yielding the different types of homodiegetic narration that are possible. This latter set of distinctions will, like the others, shed light on the contours of the different narratorial positions and thus be capable of being put profitably into practice in textual interpretation. Accordingly, what is suggested is a way of using the terms that is first unambiguous and second beneficial to the interpretation of works, thus doing justice to the heuristic importance of narratology (see Kindt/Müller 2003; Stanzel 2002, 19).Thus, whereas the concept of diegesis provides the foundation for a distinction based on an ontological criterion that divides homo- and heterodiegesis from each other, the relationship between story and narrator is used to describe various types of homodiegetic narration. In the process, there come to light two types that are distinguished from each other by involvement in events (›homodiegetic, in the story‹ and ›homodiegetic, not in the story‹ narrators). If the narrator is not involved in events, the question arises of whether it would in principle have been possible for him to be involved in events, which is the norm with ›homodiegetic, not in the story‹ narrators, or whether a physical impossibility is the reason for his lack of involvement in the story. A special case of the ›homodiegetic, not in the story‹ narrator can be derived from this: peridiegetic narration: whereas narratorial instances of the ›homodiegetic, in the story‹ and ›homodiegetic, not in the story‹ types could in principle have been involved in the action and those of the ›homodiegetic, in the story‹ type actually were, peridiegetic narrators are marked by the fact that they cannot have been involved in the events.In summary, it will be shown that the concept of homodiegesis – in particular in the form in which it has previously been used, where links with the action and appearance in the story were not kept distinct – is in effect an umbrella term that brings together a number of possible forms. There is a prominent distinction between the ›homodiegetic, in the story‹ and the ›homodiegetic, not in the story‹ types of narrator (these types are represented in the present article by the old lawyer in Leo Perutz’s »The Beaming Moon« and the narrator who is a friend of Nathanael in E. T. A. Hoffmann’s »Sandman« respectively). The different degrees of homodiegetic narrator, which have often been mentioned in previous research and are defined by the strength of the character’s presence in the narrated world (from an uninvolved witness to an autodiegetic protagonist), are also to be situated between these two poles.It will also be shown in the process that the case of the narrator who is, for reasons of physical difference, not involved in events (the peridiegetic narrator) should be treated as a form of homodiegesis (for instance the schoolmaster in Theodor Storm’s


2011 ◽  
Vol 39 (3) ◽  
pp. 707-718 ◽  
Author(s):  
René A.W. Frank

Ionotropic receptors, including the NMDAR (N-methyl-D-aspartate receptor) mediate fast neurotransmission, neurodevelopment, neuronal excitability and learning. In the present article, the structure and function of the NMDAR is reviewed with the aim to condense our current understanding and highlight frontiers where important questions regarding the biology of this receptor remain unanswered. In the second part of the present review, new biochemical and genetic approaches for the investigation of ion channel receptor complexes will be discussed.


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