scholarly journals Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1085 ◽  
Author(s):  
Patrick A. de Jonge ◽  
F. A. Bastiaan von Meijenfeldt ◽  
Laura E. van Rooijen ◽  
Stan J. J. Brouns ◽  
Bas E. Dutilh
Keyword(s):  
Tandem Repeats ◽  
Protein Domain ◽  
Carbohydrate Binding ◽  
Human Gut ◽  
The Third ◽  
Phage Tail ◽  
Protein Encoding ◽  
Insight Into ◽  
Tail Proteins

The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage.

Sebastian Moore’s Spiritual Vision and Christological Project

2018 ◽  
Vol 136 (3) ◽  
pp. 165-177
Author(s):  
Louis Roy OP
Keyword(s):  
Structural Components ◽  
The Third ◽  
Insight Into

This essay wants to examine the structural components and the viability of Sebastian Moore’s christological construction. The first section presents the origin of his insight into the redemptive role of Jesus. The second section reports his views on desire. In connection with desire, the third section details the experience that the followers of Jesus had of him, from the beginnings in Galilee, through his passion and death, ending with his appearances after his resurrection. The fourth justifies the validity of his Christology.

scholarly journals Architecturally complex O-glycopeptidases are customized for mucin recognition and hydrolysis

2021 ◽  
Vol 118 (10) ◽  
pp. e2019220118
Author(s):  
Benjamin Pluvinage ◽  
Elizabeth Ficko-Blean ◽  
Ilit Noach ◽  
Christopher Stuart ◽  
Nicole Thompson ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Peptide Bond ◽  
Molecular Organization ◽  
Dimensional Structure ◽  
Carbohydrate Binding ◽  
Functional Roles ◽  
Protein Substrates ◽  
Individual Domain ◽  
Insight Into

A challenge faced by peptidases is the recognition of highly diverse substrates. A feature of some peptidase families is the capacity to specifically use post-translationally added glycans present on their protein substrates as a recognition determinant. This is ultimately critical to enabling peptide bond hydrolysis. This class of enzyme is also frequently large and architecturally sophisticated. However, the molecular details underpinning glycan recognition by these O-glycopeptidases, the importance of these interactions, and the functional roles of their ancillary domains remain unclear. Here, using the Clostridium perfringens ZmpA, ZmpB, and ZmpC M60 peptidases as model proteins, we provide structural and functional insight into how these intricate proteins recognize glycans as part of catalytic and noncatalytic substrate recognition. Structural, kinetic, and mutagenic analyses support the key role of glycan recognition within the M60 domain catalytic site, though they point to ZmpA as an apparently inactive enzyme. Wider examination of the Zmp domain content reveals noncatalytic carbohydrate binding as a feature of these proteins. The complete three-dimensional structure of ZmpB provides rare insight into the overall molecular organization of a highly multimodular enzyme and reveals how the interplay of individual domain function may influence biological activity. O-glycopeptidases frequently occur in host-adapted microbes that inhabit or attack mucus layers. Therefore, we anticipate that these results will be fundamental to informing more detailed models of how the glycoproteins that are abundant in mucus are destroyed as part of pathogenic processes or liberated as energy sources during normal commensal lifestyles.

Septum formation in Aspergillus nidulans

1995 ◽  
Vol 73 (S1) ◽  
pp. 396-399 ◽  
Author(s):  
Michelle Momany ◽  
Jennifer L. Morrell ◽  
Steven D. Harris ◽  
John E. Hamer
Keyword(s):  
Aspergillus Nidulans ◽  
Antibody Production ◽  
Nuclear Division ◽  
Temperature Sensitive ◽  
Cellular Processes ◽  
The Third ◽  
Septum Formation ◽  
Chromosome Transmission ◽  
Insight Into

We are investigating septation in Aspergillus nidulans. We have shown that septum formation is dependent on the third nuclear division and actin is involved in this process. We have also characterized nine temperature-sensitive septation (sep) mutants. On the basis of our analysis we have divided these mutants into three phenotypic classes. We are uncovering the order of events in the septation pathway by analysis of double mutants constructed with different pairs of sep mutants. The sepB gene has been cloned and sequenced. Homology with the Saccharomyces cerevisiae CTF4 gene and the phenotype of the sepB mutant support a role in monitoring the fidelity of chromosome transmission. We are also investigating the role of the asp genes (Aspergillus septins). Three asp genes were identified by homology with the S. cerevisiae septins. aspB has been cloned, sequenced, and fused to a biotinylated tag for antibody production. Antibody production and localization studies are now underway. Because septation requires the integration of several cellular processes, our studies should give insight into the cell cycle, cell wall biosnythesis and development of A. nidulans. Key words: septation, cytokinesis, Aspergillus nidulans.

scholarly journals Models or metaphors?: Remarks on ‚tranference’ in philosophy and science

2013 ◽  
Vol 24 (4) ◽  
pp. 121-138
Author(s):  
Borislav Mikulic
Keyword(s):  
Language And Thought ◽  
The Third ◽  
Rational Discourse ◽  
Fourth Part ◽  
Recent Philosophy ◽  
Linguistic Functions ◽  
The Difference ◽  
Insight Into

Dealing with the presumed universality of metaphor and its role in the discourse of philosophy and science, the article discusses, in the first part, the theses on metaphor as ?all pervading means? of language and thought, raised by romantic and post-romantic philosophers of language, and its impact on the meta-discourse on philosophy and science in recent contemporary contributions by epistemologists of science and language philosophers. The aim of the article is to show, on one side, that this universalisation of metaphor has been operative in the recent philosophy rather as a tacit confusion of metaphors with models and analogies than as elaboration of the presumed constitutive role of the so-called genuin metaphor in the rational discourse. On this ground, the article tries to provide, in the second and the third part, additonal and different arguments than those raised by ?friends of metaphor? for locating the presumed ?irrationality? of metaphor so as to reexamine the relevance of the difference between the literality of the underlying linguistic functions and the emphatic assertion by metaphorical expressions. As a result, in the fourth part, a different model has been suggested for estimating metaphors as universal, legitimate, and epistemically innovative in the rational discourse of philosophy and science. Such a view allows for conceiving of the presumed ?all-pervading? character of transference in language and thought as based on the universality of linguistic functions and yet enables to consider metaphors as what they actually are - a particular, but peculiar, intralinguistic phenomenon without which no insight into the differential and material character of language and speech seems to be possible at all.

scholarly journals “Watching Eyes” Triggers Third-Party Punishment: The Role of Emotion Within the Eyes

2021 ◽  
Vol 12 ◽  
Author(s):  
Mingping Li ◽  
Chenyu Shangguan ◽  
Huqing Shi ◽  
Jiamei Lu
Keyword(s):  
Social Interaction ◽  
Dictator Game ◽  
Third Party ◽  
The Third ◽  
Direct Benefits ◽  
The Third Party ◽  
Positive Results ◽  
Insight Into ◽  
Behavioral Phenomenon

Third-party punishment refers to a behavioral phenomenon whereby people punish wrongdoers even if their sanction incurs personal costs but yields no direct benefits. Given the eye cues demonstrated ability to convey signals of being observed, its effect on third-party punishment, driven by virtue of its effects on others' perceptions, was investigated. In addition, emotional message featured in the eye region is crucial in social interaction, whether the emotion within the eyes serves this effect with varying degrees of influence has rarely considered. The present study aimed at exploring (a) the watching eyes effect on the third-party punishment and (b) whether this effect varies from negative eyes to positive eyes. By two experiments using a modified Third-Party Dictator Game, we displayed either eye images or control images above the question on whether to punish the dictators or not. There was no emotional diversity of eye cues in Experiment 1, and most participants tended to punish for unfair offer. However, the appearance of eye images increased the punishment relative to control images. In Experiment 2, the eye cues were subdivided into positive and negative. The effect of watching eyes on the third-party punishment was significantly stronger when the eyes were negative than positive. Results revealed that eye cues play a role in promoting the third-party punishment and offer a potential insight into the mixed findings, such that the emotion within the eyes, especially the negative expression in the eyes, may influence the watching eyes effect.

Early Decreased Tumor Volume Following Fractionated GammaKnife Radiosurgery for Metastatic Melanoma and the Role of “Adaptive Radiosurgery”

Neurosurgery ◽  
2010 ◽  
Vol 67 (2) ◽  
pp. E512-E513 ◽  
Author(s):  
Gabriel Zada ◽  
Cheng Yu ◽  
Paul G. Pagnini ◽  
Alexander A. Khalessi ◽  
Vladimir Zelman ◽  
...  
Keyword(s):  
Metastatic Melanoma ◽  
Gamma Knife ◽  
Tumor Volume ◽  
Gamma Knife Radiosurgery ◽  
Optic Chiasm ◽  
Malignant Neoplasms ◽  
The Third ◽  
Insight Into ◽  
Repeat Imaging

Abstract OBJECTIVE We report a case in which fractionated gamma knife radiosurgery was used to treat a metastatic melanoma lesion. The tumor demonstrated a rapid response to radiosurgery with an observable reduction in tumor volume between the second and third treatments, requiring a favorable modification in the third fractionated treatment. CLINICAL PRESENTATION A 61-year-old woman presented with a frontal floor metastatic melanoma lesion that was located adjacent to the optic apparatus. INTERVENTION Gamma knife radiosurgery was administered in three fractionated treatments of 6.5 Gy to the 50% isodose line in each case. Repeat imaging for the purpose of planning demonstrated that tumor volume at the time of the third treatment, 9 days following the first treatment, had decreased by 31%, resulting in a 21% decrease in the dose administered to the optic chiasm. CONCLUSION A case of metastatic melanoma treated with fractionated GKRS is presented, in which a significant reduction in tumor volume was noted 9 days following the initial treatment. This case provides insight into the rate with which malignant neoplasms may respond to intermediate-dose hypofractionated GKRS, and lends support to the concept of “adaptive radiosurgery” as a means of optimizing radiation to an evolving target while minimizing collateral radiation to surrounding structures.

Plasminogen Activation In Vivo upon Intravenous Infusion of DDAVP

1992 ◽  
Vol 67 (01) ◽  
pp. 111-116 ◽  
Author(s):  
Marcel Levi ◽  
Jan Paul de Boer ◽  
Dorina Roem ◽  
Jan Wouter ten Cate ◽  
C Erik Hack
Keyword(s):  
Monoclonal Antibodies ◽  
Plasminogen Activator ◽  
Plasma Levels ◽  
Fold Increase ◽  
Fibrinolytic System ◽  
Plasminogen Activation ◽  
Plasminogen Activator Activity ◽  
Insight Into

SummaryInfusion of desamino-d-arginine vasopressin (DDAVP) results in an increase in plasma plasminogen activator activity. Whether this increase results in the generation of plasmin in vivo has never been established.A novel sensitive radioimmunoassay (RIA) for the measurement of the complex between plasmin and its main inhibitor α2 antiplasmin (PAP complex) was developed using monoclonal antibodies preferentially reacting with complexed and inactivated α2-antiplasmin and monoclonal antibodies against plasmin. The assay was validated in healthy volunteers and in patients with an activated fibrinolytic system.Infusion of DDAVP in a randomized placebo controlled crossover study resulted in all volunteers in a 6.6-fold increase in PAP complex, which was maximal between 15 and 30 min after the start of the infusion. Hereafter, plasma levels of PAP complex decreased with an apparent half-life of disappearance of about 120 min. Infusion of DDAVP did not induce generation of thrombin, as measured by plasma levels of prothrombin fragment F1+2 and thrombin-antithrombin III (TAT) complex.We conclude that the increase in plasminogen activator activity upon the infusion of DDAVP results in the in vivo generation of plasmin, in the absence of coagulation activation. Studying the DDAVP induced increase in PAP complex of patients with thromboembolic disease and a defective plasminogen activator response upon DDAVP may provide more insight into the role of the fibrinolytic system in the pathogenesis of thrombosis.

A ‘Jurist-linguistic’ Reading of the wuḍūʾ Verse (Q. 5:6)

2010 ◽  
Vol 12 (1-2) ◽  
pp. 313-282
Author(s):  
ʿAbd al-ʿAzīz Mūsā
Keyword(s):  
The Third

This article sheds light on the role of grammar in understanding legislative texts, with reference to the wuḍūʾ verse (Q. 5:6). The first section deals with the issue of washing the elbows along with the feet as part of ritual ablution, and lists the various interpretations of the preposition ilā in the aya, and discusses the grammatical theory used by different fuqahāʾ to support their arguments. The second section tackles how much of the head should be rubbed in ritual ablution, with regard to the use of the preposition bi- in the phrase bi-ruʾūsikum, while the third focuses on the two readings of the phrase arjulakum/arjulikum (‘your feet’) and on passing legislative judgement on whether the feet be washed or just rubbed. The study concludes that lugha and fiqh theory are of mutual importance and together help to clarify legislative judgements, and, on this basis, that jurists should not pass any legislative judgement without referring to language.

On Metaphysics and the Political: A Polemics of Reading Baudelaire in the 1930s

2019 ◽  
Vol 58 (2) ◽  
pp. 249-259
Author(s):  
Joseph Acquisto
Keyword(s):  
Twentieth Century ◽  
Political Crisis ◽  
The Political ◽  
Modern Poetry ◽  
Progressive Politics ◽  
The World ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

This essay examines a polemic between two Baudelaire critics of the 1930s, Jean Cassou and Benjamin Fondane, which centered on the relationship of poetry to progressive politics and metaphysics. I argue that a return to Baudelaire's poetry can yield insight into what seems like an impasse in Cassou and Fondane. Baudelaire provides the possibility of realigning metaphysics and politics so that poetry has the potential to become the space in which we can begin to think the two of them together, as opposed to seeing them in unresolvable tension. Or rather, the tension that Baudelaire animates between the two allows us a new way of thinking about the role of esthetics in moments of political crisis. We can in some ways see Baudelaire as responding, avant la lettre, to two of his early twentieth-century readers who correctly perceived his work as the space that breathes a new urgency into the questions of how modern poetry relates to the world from which it springs and in which it intervenes.

No fear of George Kingsley Zipf

10.1558/37291 ◽  
2018 ◽  
Vol 2 (2) ◽  
pp. 242-263
Author(s):  
Stefano Rastelli ◽  
Kook-Hee Gil
Keyword(s):  
Minimalist Program ◽  
Classroom Research ◽  
Language Design ◽  
Efficient Computation ◽  
Generative Linguistics ◽  
The Third ◽  
Factor Effect ◽  
Language Classroom ◽  
Recent Developments ◽  
Insight Into

This paper offers a new insight into GenSLA classroom research in light of recent developments in the Minimalist Program (MP). Recent research in GenSLA has shown how generative linguistics and acquisition studies can inform the language classroom, mostly focusing on what linguistic aspects of target properties should be integrated as a part of the classroom input. Based on insights from Chomsky’s ‘three factors for language design’ – which bring together the Faculty of Language, input and general principles of economy and efficient computation (the third factor effect) for language development – we put forward a theoretical rationale for how classroom research can offer a unique environment to test the learnability in L2 through the statistical enhancement of the input to which learners are exposed.

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