scholarly journals Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection

2010 ◽  
Vol 107 (5) ◽  
pp. 1948-1953 ◽  
Author(s):  
Fei Chen ◽  
Eric A. Gaucher ◽  
Nicole A. Leal ◽  
Daniel Hutter ◽  
Stephanie A. Havemann ◽  
...  
Keyword(s):  
Open Space ◽  
Dna Polymerases ◽  
Structure And Function ◽  
Primer Extension ◽  
Snp Detection ◽  
Parallel Sequencing ◽  
New Class ◽  
Dna Analyses ◽  
History Of ◽  
And Function

Any system, natural or human-made, is better understood if we analyze both its history and its structure. Here we combine structural analyses with a “Reconstructed Evolutionary Adaptive Path” (REAP) analysis that used the evolutionary and functional history of DNA polymerases to replace amino acids to enable polymerases to accept a new class of triphosphate substrates, those having their 3′-OH ends blocked as a 3′-ONH2 group (dNTP-ONH2). Analogous to widely used 2′,3′-dideoxynucleoside triphosphates (ddNTPs), dNTP-ONH2s terminate primer extension. Unlike ddNTPs, however, primer extension can be resumed by cleaving an O-N bond to restore an -OH group to the 3′-end of the primer. REAP combined with crystallographic analyses identified 35 sites where replacements might improve the ability of Taq to accept dNTP-ONH2s. A library of 93 Taq variants, each having replacements at three or four of these sites, held eight variants having improved ability to accept dNTP-ONH2 substrates. Two of these (A597T, L616A, F667Y, E745H, and E520G, K540I, L616A) performed notably well. The second variant incorporated both dNTP-ONH2sand ddNTPs faithfully and efficiently, supporting extension-cleavage-extension cycles applicable in parallel sequencing and in SNP detection through competition between reversible and irreversible terminators. Dissecting these results showed that one replacement (L616A), not previously identified, allows Taq to incorporate both reversible and irreversible terminators. Modeling showed how L616A might open space behind Phe-667, allowing it to move to accommodate the larger 3′-substituent. This work provides polymerases for DNA analyses and shows how evolutionary analyses help explore relationships between structure and function in proteins.

scholarly journals The plant circadian clock influences rhizosphere community structure and function

2017 ◽  
Author(s):  
Charley J. Hubbard ◽  
Marcus T. Brock ◽  
Linda T.A. van Diepen ◽  
Loïs Maignien ◽  
Brent E. Ewers ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Circadian Clock ◽  
Structure And Function ◽  
Plant Performance ◽  
Wild Type ◽  
Night Time ◽  
History Of ◽  
And Function ◽  
Rhizosphere Community

AbstractPlants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function. We performed 16S rRNA gene sequencing to characterize rhizosphere bacterial communities of Arabidopsis thaliana between day and night time points, and tested for differences in community structure between wild-type (Ws) vs. clock mutant (toc1-21, ztl-30) genotypes. We then characterized microbial community function, by growing wild-type plants in soils with an overstory history of Ws, toc1-21 or ztl-30 and measuring plant performance. We observed that rhizosphere community structure varied between day and night time points, and clock misfunction significantly altered rhizosphere communities. Finally, wild-type plants germinated earlier and were larger when inoculated with soils having an overstory history of wild-type in comparison to clock mutant genotypes. Our findings suggest the circadian clock of the plant host influences rhizosphere community structure and function.

Mass Extinctions and the Structure and Function of Ecosystems

2013 ◽  
Vol 19 ◽  
pp. 115-156 ◽  
Author(s):  
Pincelli M. Hull ◽  
Simon A. F. Darroch
Keyword(s):  
Biodiversity Loss ◽  
Structure And Function ◽  
Ecosystem Change ◽  
Mass Extinctions ◽  
General Introduction ◽  
Biodiversity Crisis ◽  
Ecosystem Effects ◽  
History Of ◽  
Research Questions ◽  
And Function

Mass extinctions shape the history of life and can be used to inform understanding of the current biodiversity crisis. In this paper, a general introduction is provided to the methods used to investigate the ecosystem effects of mass extinctions (Part I) and to explore major patterns and outstanding research questions in the field (Part II). The five largest mass extinctions of the Phanerozoic had profoundly different effects on the structure and function of ecosystems, although the causes of these differences are currently unclear. Outstanding questions and knowledge gaps are identified that need to be addressed if the fossil record is to be used as a means of informing the dynamics of future biodiversity loss and ecosystem change.

scholarly journals Structure and function relationships in mammalian DNA polymerases

2019 ◽  
Vol 77 (1) ◽  
pp. 35-59 ◽  
Author(s):  
Nicole M. Hoitsma ◽  
Amy M. Whitaker ◽  
Matthew A. Schaich ◽  
Mallory R. Smith ◽  
Max S. Fairlamb ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
Structure And Function ◽  
And Function

Staging and Embodiment of the Tragic in Pina Bausch's Orpheus and Eurydice (1975)

2016 ◽  
Vol 2016 ◽  
pp. 191-197
Author(s):  
Nicole Haitzinger
Keyword(s):  
Twentieth Century ◽  
Structure And Function ◽  
Dance Studies ◽  
Central European ◽  
Orpheus And Eurydice ◽  
Mise En Scene ◽  
History Of ◽  
Longue Duree ◽  
Longue Durée ◽  
And Function

This paper is concerned with resonances of the tragic in twentieth-century central-European dance theatet, to be discussed with particular reference to Pina Bausch's 1975 Orpheus and Eurydice. In my study Resonances of the Tragic: Between Event and Affect (2015), I have argued that in terms of a history of the “longue durée,” the evocation of the tragic occurs in a field of tension between technique, the mise-en-scène, and conceptions, as well as procedures and moments of interruption, of suspension, of disruption and of the indeterminable resulting from ecstatic corporeality. Its structure and function can generate an event in the emphatic sense of the term; consequently, it provides a paradigm for recognizing structures of form and of an aesthetic of reception, structures emerging from individual constellations of the fictional and choric, absence and presence. From the perspective of dance studies, the tragic emanates from the representation of horrendous monstrosity testing the limits of what can be imagined by means of the moved body in all senses of the word; but how exactly does Bausch produce the qualities of the ambivalent, ambiguous, and paradoxical—and, consequently, the tragic?

Commentary on “Reflections on culture, structure and function of an intensive support service centred on positive behavioural support”

2016 ◽  
Vol 21 (4) ◽  
pp. 212-219 ◽  
Author(s):  
Sandy Toogood
Keyword(s):  
Support Service ◽  
Structure And Function ◽  
Content Type ◽  
Behavioural Support ◽  
Wide Range ◽  
Service Models ◽  
History Of ◽  
Positive Behaviour Support ◽  
The Uk ◽  
And Function

Purpose The purpose of this paper is to provide a commentary on Patterson and Berry’s paper “Reflections on culture, structure and function of an intensive support service centred on positive behavioural support”. Design/methodology/approach This paper reviews key ideas presented in Patterson and Berry’s article relative to the recent history of service delivery in the UK and the growing interest being shown in positive behaviour support. Findings Patterson and Berry’s article adds to a modest literature on specialist support services and should stimulate further descriptions of service models and the concepts underpinning them. Originality/value The literature on specialist support service models is limited and this addition should be relevant to a wide range of clinicians, consumers and commissioners.

scholarly journals Soul searching: a brief history of the mind/body debate in the neurosciences

2007 ◽  
Vol 23 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Brian Dolan
Keyword(s):  
Early Modern ◽  
Structure And Function ◽  
The Self ◽  
History Of Neuroscience ◽  
History Of ◽  
And Function ◽  
The Mind ◽  
The Brain ◽  
The Way

✓Anatomical and physiological understandings of the structure and function of the brain have worked to establish it as the “seat of the soul.” As an organ of reflection, meditation, and memory, the brain becomes synonymous with what defines the “self” through the existence of consciousness—of mind. Thus, the brain has been associated with a range of transcendent concepts—the soul, spirit, mind, and consciousness—that all relate in fundamental ways to each other both in terms of their perceived location within the brain and because of the way each works ultimately to define the person to whom the brain belongs. In this article, the author provides a brief exploration of how interrelated these categories have been when seen in the context of ancient, Renaissance, early modern, and modern philosophical and medical concerns; how the brain has variously been perceived as home to these intimate states of being; and how practitioners from the neurosciences have reflected on these questions. The author provides novel insights into the interrelationships of philosophy, theology, and medicine by examining these issues through the lens of the history of neuroscience.

The history of the capillary wall: doctors, discoveries, and debates

2007 ◽  
Vol 293 (5) ◽  
pp. H2667-H2679 ◽  
Author(s):  
Charlotte Hwa ◽  
William C. Aird
Keyword(s):  
Basic Structure ◽  
Structure And Function ◽  
The Body ◽  
Capillary Wall ◽  
Central Importance ◽  
Definitive Evidence ◽  
Arterial Blood ◽  
History Of ◽  
And Function

In 1628, William Harvey provided definitive evidence that blood circulates. The notion that blood travels around the body in a circle raised the important question of how nutrients pass between blood and underlying tissue. Perhaps, Harvey posited, arterial blood pours into the flesh as into a sponge, only then to find its way into the veins. Far from solving this problem, Marcello Malpighi's discovery of the capillaries in 1661 only added to the dilemma: surely, some argued, these entities are little more than channels drilled into tissues around them. As we discuss in this review, it would take over 200 years to arrive at a consensus on the basic structure and function of the capillary wall. A consideration of the history of this period provides interesting insights into not only the central importance of the capillary as a focus of investigation, but also the enormous challenges associated with studying these elusive structures.

scholarly journals The Importance of GLWamide Neuropeptides in Cnidarian Development and Physiology

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Toshio Takahashi ◽  
Masayuki Hatta
Keyword(s):  
Basic Structure ◽  
Signaling Molecules ◽  
Structure And Function ◽  
Amino Acid Residues ◽  
Peptide Signaling ◽  
Physiological Processes ◽  
History Of ◽  
Species Specific ◽  
And Function ◽  
Potential Use

The peptide-signaling molecules (<50 amino acid residues) occur in a wide variety of invertebrate and vertebrate organisms, playing pivotal roles in physiological, endocrine, and developmental processes. While some of these peptides display similar structures in mammals and invertebrates, others differ with respect to their structure and function in a species-specific manner. Such a conservation of basic structure and function implies that many peptide-signaling molecules arose very early in the evolutionary history of some taxa, while species-specific characteristics led us to suggest that they also acquire the ability to evolve in response to specific environmental conditions. In this paper, we describe GLWamide-family peptides that function as signaling molecules in the process of muscle contraction, metamorphosis, and settlement in cnidarians. The peptides are produced by neurons and are therefore referred to as neuropeptides. We discuss the importance of the neuropeptides in both developmental and physiological processes in a subset of hydrozoans, as well as the potential use as a seed compound in drug development and aspects related to the protection of corals.

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