The Urfold: Structural Similarity Just above the Superfold Level?

Mapping Intimacies ◽

10.1101/728030 ◽

2019 ◽

Author(s):

Cameron Mura ◽

Stella Veretnik ◽

Philip E. Bourne

Keyword(s):

Structural Analysis ◽

Structural Similarity ◽

Structural Classification ◽

Sequence Structure ◽

Conceptual Approach ◽

Classification Schemes ◽

Precise Meaning ◽

And Topology ◽

Protein Structural Analysis

OverviewWe suspect that there is a level of granularity of protein structure intermediate between the classical levels of ‘architecture’ and ‘topology’, as reflected in such phenomena as extensive 3D structural similarity above the level of (super)folds. Here, we examine this notion of architectural identity despite topological variability, starting with a concept that we call the ‘Urfold’. We believe that this model could offer a new conceptual approach for protein structural analysis and classification: indeed, the Urfold concept may help reconcile various phenomena that have been frequently recognized or debated for years, such as the precise meaning of ‘significant’ structural overlap and the degree of continuity of fold space. More broadly, the role of structural similarity in sequence/structure/function evolution has been studied via many models over the years; the Urfold may help synthesize these models into a generalized, consistent framework, by addressing a conceptual gap that we believe exists between the architecture and topology levels of structural classification schemes.

Download Full-text

The Role of Protein Structural Analysis in the Next Generation Sequencing Era

Chemical Diagnostics - Topics in Current Chemistry ◽

10.1007/128_2012_326 ◽

2012 ◽

pp. 67-98 ◽

Cited By ~ 9

Author(s):

Wyatt W. Yue ◽

D. Sean Froese ◽

Paul E. Brennan

Keyword(s):

Next Generation Sequencing ◽

Structural Analysis ◽

Next Generation ◽

Protein Structural Analysis ◽

Generation Sequencing

Download Full-text

The role of Constitutional Courts in Transitional Justice: Colombia and South Africa

Criterio Jurídico Garantista ◽

10.26564/21453381.652 ◽

2016 ◽

Vol 9 (15) ◽

Author(s):

Nadiehezka Paola Palencia Tejedor

Keyword(s):

South Africa ◽

Structural Analysis ◽

Transitional Justice ◽

Critical Analysis ◽

Historical Context ◽

Constitutional Courts ◽

Political Background ◽

Similarities And Differences ◽

Peace And Reconciliation

This work focuses on a compared analysis of the South Afri- can decision related to the “peace and reconciliation act” of this country’s Parliament, and the Colombian decision regarding the amendment of the constitution called “The juridical framework for the peace.” Turning to the structure, it is developed in three major topics: 1. It provides a brief of the historical context, political background and an overview of the two decisions.2. It gives a structural analysis of the powers that each Court has and the nature of the constitutional mechanism through which both Courts decided the constitutionality of the said norms 3. It presents a critical analysis on the similarities and differences between the two systems and judgments. It presents some con- clusions.

Download Full-text

Semantic And Structural Properties Of The Banking And Financial Terminology Of The Uzbek Language

The American Journal of Social Science and Education Innovations ◽

10.37547/tajssei/volume02issue08-99 ◽

2020 ◽

Vol 2 (08) ◽

pp. 610-617

Author(s):

Ekaterina Turakulovna Shirinova

Keyword(s):

Structural Analysis ◽

Structural Properties ◽

Human Factor

This article discusses information on the study of terminology in Uzbek and world linguistics. Thematic grouping of banking and financial terms, which play an important role in Uzbek language vocabulary, is considered. The author gives the criteria for the distribution of terms into thematic groups, their peculiar properties examples to substantiate the hypothesis. The paradigmatic relations between the terms of this sphere are indicated. A structural analysis of the banking and financial terms of the Uzbek language is carried out. On the basis of the anthropocentric approach, the role of the human factor in the banking and financial terminology of the Uzbek language is studied. Cognitive metaphors that exist in the terminology are considered.

Download Full-text

Conditioning and Sensitisation in the Longitudinal Course of Affective Illness

The British Journal of Psychiatry ◽

10.1192/bjp.149.2.191 ◽

1986 ◽

Vol 149 (2) ◽

pp. 191-201 ◽

Cited By ~ 247

Author(s):

Robert M. Post ◽

David R. Rubinow ◽

James C. Ballenger

Keyword(s):

Depressive Illness ◽

Manic Depressive Illness ◽

Conceptual Approach ◽

Longitudinal Course ◽

Behavioural Sensitisation ◽

Affective Illness ◽

Biological Variables ◽

Manic Depressive ◽

Progressive Course

Few biological theories of manic-depressive illness have focused on the longitudinal course of affective dysfunction and the mechanisms underlying its often recurrent and progressive course. The authors discuss two models for the development of progressive behavioural dysfunction—behavioural sensitisation and electrophysiological kindling—as they provide clues to important clinical and biological variables relevant to sensitisation in affective illness. The role of environmental context and conditioning in mediating behavioural and biochemical aspects of this sensitisation is emphasised. The sensitisation models provide a conceptual approach to previously inexplicable clinical phenomena in the longitudinal course of affective illness and may provide a bridge between psychoanalytic/psychosocial and neurobiological formulations of manic-depressive illness.

Download Full-text

What is the role of fear and escape/avoidance in chronic pain? Models, structural analysis and future directions

Pain Management ◽

10.2217/pmt.12.15 ◽

2012 ◽

Vol 2 (3) ◽

pp. 295-303 ◽

Cited By ~ 19

Author(s):

Gordon JG Asmundson ◽

Holly A Parkerson ◽

Mark Petter ◽

Melanie Noel

Keyword(s):

Chronic Pain ◽

Structural Analysis ◽

Future Directions ◽

Pain Models

Download Full-text

The idea of community and its practice: Tensions, disruptions and hope in Glasgow’s urban growing projects

The Sociological Review ◽

10.1177/0038026120982272 ◽

2021 ◽

Vol 69 (2) ◽

pp. 484-499

Author(s):

Helen Traill

Keyword(s):

Social Life ◽

Participant Observation ◽

Community Gardening ◽

Conceptual Approach ◽

The Everyday ◽

Community Theory ◽

Communal Space ◽

Work Done ◽

Do So

The question of what community comes to mean has taken on increasing significance in sociological debates and beyond, as an increasingly politicised term and the focus of new theorisations. In this context, it is increasingly necessary to ask what is meant when community is invoked. Building on recent work that positions community as a practice and an ever-present facet of human sociality, this article argues that it is necessary to consider the powerful work that community as an idea does in shaping everyday communal practices, through designating collective space and creating behavioural expectations. To do so, the article draws on participant observation and interviews from a community gardening site in Glasgow that was part of a broader research project investigating the everyday life of communality within growing spaces. This demonstrates the successes but also the difficulties of carving out communal space, and the work done by community organisations to enact it. The article draws on contemporary community theory, but also on ideas from Davina Cooper about the role of ideation in social life. It argues for a conceptual approach to communality that does not situate it as a social form or seek it in everyday practice, but instead considers the vacillation between the ideation and practices of community: illustrated here in a designated community place. In so doing, this approach calls into focus the frictions and boundaries produced in that process, and questions the limits of organisational inclusivity.

Download Full-text

Amino Acid Transporter LAT1 (SLC7A5) Mediates MeHg-Induced Oxidative Stress Defense in the Human Placental Cell Line HTR-8/SVneo

International Journal of Molecular Sciences ◽

10.3390/ijms22041707 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1707

Author(s):

Sebastian Granitzer ◽

Raimund Widhalm ◽

Martin Forsthuber ◽

Isabella Ellinger ◽

Gernot Desoye ◽

...

Keyword(s):

Oxidative Stress ◽

Amino Acid ◽

De Novo ◽

Structural Similarity ◽

Amino Acid Transporter ◽

Cell Number ◽

Mehg Exposure ◽

Acid Transporter ◽

And Oxidative Stress

The placental barrier can protect the fetus from contact with harmful substances. The potent neurotoxin methylmercury (MeHg), however, is very efficiently transported across the placenta. Our previous data suggested that L-type amino acid transporter (LAT)1 is involved in placental MeHg uptake, accepting MeHg-L-cysteine conjugates as substrate due to structural similarity to methionine. The aim of the present study was to investigate the antioxidant defense of placental cells to MeHg exposure and the role of LAT1 in this response. When trophoblast-derived HTR-8/SVneo cells were LAT1 depleted by siRNA-mediated knockdown, they accumulated less MeHg. However, they were more susceptible to MeHg-induced toxicity. This was evidenced in decreased cell viability at a usually noncytotoxic concentration of 0.03 µM MeHg (~6 µg/L). Treatment with ≥0.3 µM MeHg increased cytotoxicity, apoptosis rate, and oxidative stress of HTR-8/SVneo cells. These effects were enhanced under LAT1 knockdown. Reduced cell number was seen when MeHg-exposed cells were cultured in medium low in cysteine, a constituent of the tripeptide glutathione (GSH). Because LAT1-deficient HTR-8/SVneo cells have lower GSH levels than control cells (independent of MeHg treatment), we conclude that LAT1 is essential for de novo synthesis of GSH, required to counteract oxidative stress. Genetic predisposition to decreased LAT1 function combined with MeHg exposure could increase the risk of placental damage.

Download Full-text

Unipolarity

World Politics ◽

10.1017/s0043887109000070 ◽

2008 ◽

Vol 61 (1) ◽

pp. 188-213 ◽

Cited By ~ 44

Author(s):

Robert Jervis

Keyword(s):

United States ◽

Structural Analysis ◽

Current System ◽

Nuclear Proliferation ◽

Balance Of Power ◽

The United States

In analyzing the current unipolar system, it is useful to begin with structure. No other state or plausible coalition can challenge the unipole's core security, but this does not mean that all its values are safe or that it can get everything that it wants. Contrary to what is often claimed, standard balance of power arguments do not imply that a coalition will form to challenge the unipole. Realism also indicates that rather than seeking to maintain the system, the unipole may seek further expansion. To understand the current system requires combining structural analysis with an appreciation of the particular characteristics of the current era, the United States, and its leaders. Doing so shows further incentives to change the system and highlights the role of nuclear proliferation in modifying existing arrangements.

Download Full-text