A widespread pathway for substitution of adenine by diaminopurine in phage genomes

Science ◽  
2021 ◽  
Vol 372 (6541) ◽  
pp. 512-516
Author(s):  
Yan Zhou ◽  
Xuexia Xu ◽  
Yifeng Wei ◽  
Yu Cheng ◽  
Yu Guo ◽  
...  
Keyword(s):  
Large Scale ◽  
Restriction Enzymes ◽  
Diverse Range ◽  
Host Restriction ◽  
Form And Function ◽  
Multienzyme System ◽  
Dna Modifications ◽  
Dna Production ◽  
And Function

DNA modifications vary in form and function but generally do not alter Watson-Crick base pairing. Diaminopurine (Z) is an exception because it completely replaces adenine and forms three hydrogen bonds with thymine in cyanophage S-2L genomic DNA. However, the biosynthesis, prevalence, and importance of Z genomes remain unexplored. Here, we report a multienzyme system that supports Z-genome synthesis. We identified dozens of globally widespread phages harboring such enzymes, and we further verified the Z genome in one of these phages, Acinetobacter phage SH-Ab 15497, by using liquid chromatography with ultraviolet and mass spectrometry. The Z genome endows phages with evolutionary advantages for evading the attack of host restriction enzymes, and the characterization of its biosynthetic pathway enables Z-DNA production on a large scale for a diverse range of applications.

scholarly journals The cardiac nanoenvironment: form and function at the nanoscale

2021 ◽  
Author(s):  
Jashan P. Singh ◽  
Jennifer L. Young
Keyword(s):  
Large Scale ◽  
New Materials ◽  
Length Scales ◽  
Form And Function ◽  
Molecular Features ◽  
Wide Range ◽  
Physiological Homeostasis ◽  
Organ Level ◽  
And Function

AbstractMechanical forces in the cardiovascular system occur over a wide range of length scales. At the whole organ level, large scale forces drive the beating heart as a synergistic unit. On the microscale, individual cells and their surrounding extracellular matrix (ECM) exhibit dynamic reciprocity, with mechanical feedback moving bidirectionally. Finally, in the nanometer regime, molecular features of cells and the ECM show remarkable sensitivity to mechanical cues. While small, these nanoscale properties are in many cases directly responsible for the mechanosensitive signaling processes that elicit cellular outcomes. Given the inherent challenges in observing, quantifying, and reconstituting this nanoscale environment, it is not surprising that this landscape has been understudied compared to larger length scales. Here, we aim to shine light upon the cardiac nanoenvironment, which plays a crucial role in maintaining physiological homeostasis while also underlying pathological processes. Thus, we will highlight strategies aimed at (1) elucidating the nanoscale components of the cardiac matrix, and (2) designing new materials and biosystems capable of mimicking these features in vitro.

scholarly journals Weighing trees with lasers: advances, challenges and opportunities

2018 ◽  
Vol 8 (2) ◽  
pp. 20170048 ◽  
Author(s):  
M. I. Disney ◽  
M. Boni Vicari ◽  
A. Burt ◽  
K. Calders ◽  
S. L. Lewis ◽  
...  
Keyword(s):  
Laser Scanning ◽  
Large Scale ◽  
Three Dimensional ◽  
Point Clouds ◽  
3D Models ◽  
Tree Form ◽  
Form And Function ◽  
Challenges And Opportunities ◽  
And Function ◽  
Non Destructive

Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements from various tropical and temperate forests and describe how the resulting TLS point clouds can be used to produce quantitative 3D models of branch and trunk size, shape and distribution. These models can drastically improve estimates of AGB, provide new, improved large-scale ASEs, and deliver insights into a range of fundamental tree properties related to structure. Large quantities of detailed measurements of individual 3D tree structure also have the potential to open new and exciting avenues of research in areas where difficulties of measurement have until now prevented statistical approaches to detecting and understanding underlying patterns of scaling, form and function. We discuss these opportunities and some of the challenges that remain to be overcome to enable wider adoption of TLS methods.

Introduction—Minoan Built Environment: Past Studies, Recent Perspectives, and Future Challenges

2017 ◽  
Author(s):  
Quentin Letesson ◽  
Carl Knappett
Keyword(s):  
Twentieth Century ◽  
Built Environment ◽  
Large Scale ◽  
Monumental Architecture ◽  
Form And Function ◽  
Architectural Patterns ◽  
Future Challenges ◽  
Residential Quarters ◽  
And Function ◽  
Intensive Work

Architecture and urbanism have been of constant interest to Minoan archaeologists since the beginning of the twentieth century. While there is some scholarly bias to this, with the field deeply affected by Sir Arthur Evans’s focus on the monumental architecture of Knossos, Minoan Crete continues to yield abundant evidence for a substantial built environment. Focusing on urban and architectural remains creates a strong bias in favour of one block of time, the Neopalatial period, which produced the largest amount of wellpreserved settlements and buildings. Yet, in general, the evidence we now have on the Minoan built environment is an undeniable resource, one that continues to grow thanks to ongoing studies of pre-existing remains as well as new excavation and survey projects. As is clear in Evans’s magnum opus, The Palace of Minos at Knossos, the large-scale excavations typical of the dawn of the last century were heavily directed towards the urban cores of the largest Minoan sites (e.g. Boyd Hawes et al. 1908; Hutchinson 1950). The bulk of what we know about the Minoan built environment comes from the first half of the twentieth century, initially through the intensive work of the foreign schools at Malia, Phaistos, Palaikastro, Gournia, Mochlos, and Pseira, later joined by countless excavations by Greek archaeologists. Yet, synthetic treatments really only began with the work of James Walter Graham, in the form of numerous papers published in the American Journal of Archaeology (see Letesson 2009 for a detailed review), and especially his Palaces of Crete (Graham 1962). Nonetheless, his comparative analyses, which also dealt with non-palatial buildings, were largely focused on polite architecture. With a particular interest in form and function, he built on Evans’s insights to be the first to identify, across a large sample of buildings, recurring architectural patterns in the Minoan built environment (e.g. Piano Nobile, residential quarters, banquet halls). His studies also included an innovative quantitative component, emphasizing the existence of a unit of length that builders would have used to lay out the palaces and some of the so-called ‘villas’.

scholarly journals Identification of osteoclast-specific monoclonal antibodies.

1985 ◽  
Vol 100 (5) ◽  
pp. 1592-1600 ◽  
Author(s):  
M J Oursler ◽  
L V Bell ◽  
B Clevinger ◽  
P Osdoby
Keyword(s):  
Monoclonal Antibodies ◽  
Giant Cells ◽  
Mononuclear Phagocyte ◽  
Antibody Binding ◽  
Enzyme Linked Immunosorbent Assay ◽  
Form And Function ◽  
Titration Curves ◽  
Specific Antigens ◽  
And Function

Studies on the origin, identification, and characterization of osteoclasts have been difficult. This is in part due to a lack of definitive osteoclast markers and the similarity of these cells in form and function to cells of the mononuclear phagocyte system. To solve this problem, we inoculated isolated chick osteoclasts into mice to generate osteoclast-specific monoclonal antibodies. Supernatants from growth-positive hybridomas were screened by indirect immunofluorescent methods against cultured osteoclasts, monocyte-derived multinucleated giant cells, cultured monocytes, fibroblasts, and limb mesenchyme. Select hybridomas were cloned to produce 375 clones, which were analyzed as described above. Antibody from select clones was also reacted with paraffin sections of bone. In addition, two clones have been analyzed by enzyme-linked immunosorbent assay (ELISA) and Western blot analysis. Antibody binding from an osteoclast-specific clone and a clone reactive with osteoclasts, giant cells, and cultured monocytes (as determined by immunohistochemical assay) was confirmed by antibody-binding and titration curves quantitated by ELISA. The above studies demonstrate that osteoclast specific antigens exist, and that osteoclasts, giant cells, and cultured monocytes share common determinants not found on other cells screened.

scholarly journals To form and function: on the role of basement membrane mechanics in tissue development, homeostasis and disease

Open Biology ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 200360
Author(s):  
Nargess Khalilgharibi ◽  
Yanlan Mao
Keyword(s):  
Basement Membrane ◽  
Molecular Mechanisms ◽  
Disease Diagnosis ◽  
Membrane Mechanics ◽  
Form And Function ◽  
And Function ◽  
Tissue Form

The basement membrane (BM) is a special type of extracellular matrix that lines the basal side of epithelial and endothelial tissues. Functionally, the BM is important for providing physical and biochemical cues to the overlying cells, sculpting the tissue into its correct size and shape. In this review, we focus on recent studies that have unveiled the complex mechanical properties of the BM. We discuss how these properties can change during development, homeostasis and disease via different molecular mechanisms, and the subsequent impact on tissue form and function in a variety of organisms. We also explore how better characterization of BM mechanics can contribute to disease diagnosis and treatment, as well as development of better in silico and in vitro models that not only impact the fields of tissue engineering and regenerative medicine, but can also reduce the use of animals in research.

scholarly journals Form and function in hillslope hydrology: in situ imaging and characterization of flow-relevant structures

2017 ◽  
Vol 21 (7) ◽  
pp. 3749-3775 ◽  
Author(s):  
Conrad Jackisch ◽  
Lisa Angermann ◽  
Niklas Allroggen ◽  
Matthias Sprenger ◽  
Theresa Blume ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Hydraulic Conductivity ◽  
Soil Water ◽  
Time Lapse ◽  
Saturated Hydraulic Conductivity ◽  
Form And Function ◽  
And Function ◽  
Hillslope Scale

Abstract. The study deals with the identification and characterization of rapid subsurface flow structures through pedo- and geo-physical measurements and irrigation experiments at the point, plot and hillslope scale. Our investigation of flow-relevant structures and hydrological responses refers to the general interplay of form and function, respectively. To obtain a holistic picture of the subsurface, a large set of different laboratory, exploratory and experimental methods was used at the different scales. For exploration these methods included drilled soil core profiles, in situ measurements of infiltration capacity and saturated hydraulic conductivity, and laboratory analyses of soil water retention and saturated hydraulic conductivity. The irrigation experiments at the plot scale were monitored through a combination of dye tracer, salt tracer, soil moisture dynamics, and 3-D time-lapse ground penetrating radar (GPR) methods. At the hillslope scale the subsurface was explored by a 3-D GPR survey. A natural storm event and an irrigation experiment were monitored by a dense network of soil moisture observations and a cascade of 2-D time-lapse GPR trenches. We show that the shift between activated and non-activated state of the flow paths is needed to distinguish structures from overall heterogeneity. Pedo-physical analyses of point-scale samples are the basis for sub-scale structure inference. At the plot and hillslope scale 3-D and 2-D time-lapse GPR applications are successfully employed as non-invasive means to image subsurface response patterns and to identify flow-relevant paths. Tracer recovery and soil water responses from irrigation experiments deliver a consistent estimate of response velocities. The combined observation of form and function under active conditions provides the means to localize and characterize the structures (this study) and the hydrological processes (companion study Angermann et al., 2017, this issue).

scholarly journals Global Root Traits (GRooT) Database

2020 ◽  
Author(s):  
Nathaly Guerrero-Ramirez ◽  
Liesje Mommer ◽  
Grégoire T. Freschet ◽  
Colleen M. Iversen ◽  
M. Luke McCormack ◽  
...  
Keyword(s):  
Large Scale ◽  
Experimental Studies ◽  
Root Traits ◽  
Root Trait ◽  
Taxonomic Resolution ◽  
Plant Responses ◽  
Mean Values ◽  
Form And Function ◽  
Plant Form ◽  
And Function

AbstractMotivationTrait data are fundamental to quantitatively describe plant form and function. Although root traits capture key dimensions related to plant responses to changing environmental conditions and effects on ecosystem processes, they have rarely been included in large-scale comparative studies and global models. For instance, root traits remain absent from nearly all studies that define the global spectrum of plant form and function. Thus, to overcome conceptual and methodological roadblocks preventing a widespread integration of root trait data into large-scale analyses we created the Global Root Trait (GRooT) Database. GRooT provides ready-to-use data by combining the expertise of root ecologists with data mobilization and curation. Specifically, we (i) determined a set of core root traits relevant to the description of plant form and function based on an assessment by experts, (ii) maximized species coverage through data standardization within and among traits, and (iii) implemented data quality checks.Main types of variables containedGRooT contains 114,222 trait records on 38 continuous root traits.Spatial location and grainGlobal coverage with data from arid, continental, polar, temperate, and tropical biomes. Data on root traits derived from experimental studies and field studies.Time period and grainData recorded between 1911 and 2019Major taxa and level of measurementGRooT includes root trait data for which taxonomic information is available. Trait records vary in their taxonomic resolution, with sub-species or varieties being the highest and genera the lowest taxonomic resolution available. It contains information for 184 sub-species or varieties, 6,214 species, 1,967 genera and 254 families. Due to variation in data sources, trait records in the database include both individual observations and mean values.Software formatGRooT includes two csv file. A GitHub repository contains the csv files and a script in R to query the database.

scholarly journals Fixing the ecosystem: Conservation, crisis and capital in Rwanda's Gishwati Forest

2019 ◽  
Vol 2 (1) ◽  
pp. 23-46 ◽  
Author(s):  
Nathan Clay
Keyword(s):  
Large Scale ◽  
Ecosystem Approach ◽  
Agrarian Change ◽  
Development Projects ◽  
Landscape Modification ◽  
Form And Function ◽  
The Past ◽  
Hybrid Spaces ◽  
Social Environmental ◽  
And Function

Conservation-development projects are increasingly enacted across large expanses of land where human livelihoods hang in the balance. Recent initiatives–often called ‘landscape approaches’ or ‘ecosystem-based’ conservation–aim to achieve economic development and conservation goals through managing hybrid spaces. I argue that the landscape/ecosystem approach is a socioecological fix: an effort to resolve social-environmental crises through sinking capital (financial, natural, and social) into an imagined ecosystem. Rwanda’s Gishwati Forest has been the locus of diverse crises and fixes over the past 40 years, including an industrial forestry and dairy project, a refugee settlement, a privately managed chimpanzee sanctuary, a carbon sequestration platform, and, most recently, an “integrated silvo-pastoral conservation landscape.” This paper considers how these governance schemes have intersected with broader processes of agrarian change to generate crises that subsequent conservation/development projects then attempt to resolve. I demonstrate how visions for ecosystems privilege certain forms of governance around which imagined socioecological histories are mobilized to frame problems and legitimize certain solutions, technologies, and actors. The Gishwati ecosystem and its fixes are repeatedly defined through an imaginary of crisis and degradation that engenders large-scale landscape modification while foreclosing reflection about root causes of crises or how these might be addressed. Thus, even while conservation/development paradigms have shifted over the past 40 years (from separating people and nature to integrating them in conservation landscapes), this crisis-fix metabolism has consistently generated livelihood insecurity for the tens of thousands of people living in and around Gishwati. Imagining and enacting more just and inclusive social-environmental landscapes will require making space for diverse voices to define ecosystem form and function as well as addressing deeply rooted power imbalances that are at the heart of recurrent crises.

scholarly journals Contemporary Odeon Buildings as a Sustainable Environment for Culture

Buildings ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 308
Author(s):  
Kazimierz Leonard Butelski
Keyword(s):  
Large Scale ◽  
Global Scale ◽  
Cultural Significance ◽  
Open Spaces ◽  
Main Research ◽  
Form And Function ◽  
Sustainable Environment ◽  
Functional Aspects ◽  
Cultural Spaces ◽  
And Function

The subject of this study is contemporary odeons in Poland, where 11 covered amphitheaters (odeons) have been built since 2005. The odeons were selected from a wider collection of 57 functioning amphitheaters. The study collected data on location, form, function, and construction. The data sources included the literature, archival research, design documentation, and competition entries. Descriptive and graphical comparative analyses of the phenomena, based on the statistics for completed structures and on design experiments in the case of unbuilt structures, were the two main research methods used in this study. The emergence and development directions of the typology of open cultural spaces from amphitheaters to odeons are presented in a global and regional context. Their interrelationships, affecting form and function, were also analyzed. The influence of high-end materials that were used to create these complex, large-scale spatial structures, and their impact on the environment, has been presented. The contemporary roofs covering the entertainment and stage complex were analyzed in relation to environmental factors, determining the location of the odeons. The functional aspects of these buildings and their cultural significance on a local, regional and global scale were discussed. The odeon in Biała Podlaska, built in 2019, was chosen as a case study to show, in detail, the complexity of the formation of contemporary odeons. In the discussion on the direction of the further evolution of open spaces for culture, an example of an unrealized competition design proposal of mobile roofing forms for the eighteenth-century amphitheater in the Royal Baths Park in Warsaw, Poland, was presented. The conclusions emphasize the environmental, spatial, functional, social and economic values of the establishment and functioning of contemporary odeons as open spaces of culture that are compliant with the principles of sustainable development.

scholarly journals Microbiomes In Natura : Importance of Invertebrates in Understanding the Natural Variety of Animal-Microbe Interactions

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Jillian M. Petersen ◽  
Jay Osvatic
Keyword(s):  
Human Life ◽  
Diverse Range ◽  
Functional Roles ◽  
Form And Function ◽  
Group Interest ◽  
Invertebrate Animals ◽  
Microbe Interactions ◽  
Almost All ◽  
And Function ◽  
Development And Evolution

ABSTRACT Animals evolved in a world teeming with microbes, which play pivotal roles in their health, development, and evolution. Although the overwhelming majority of living animals are invertebrates, the minority of “microbiome” studies focus on this group. Interest in invertebrate-microbe interactions is 2-fold—a range of immune components are conserved across almost all animal (including human) life, and their functional roles may be conserved. Thus, understanding cross talk between microbes and invertebrate animals can lead to insights of broader relevance. Invertebrates offer unique opportunities to “eavesdrop” on intricate host-microbe conversations because they tend to associate with fewer microbes. On the other hand, considering the vast diversity of form and function that has evolved in the invertebrates, they likely evolved an equally diverse range of ways to interact with beneficial microbes. We have investigated only a few of these interactions in detail; thus, there is still great potential for fundamentally new discoveries.

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