bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoactivated Localization Microscopy (PALM) of Adhesion Complexes
Authors: Shroff Hari , White Helen , Betzig Eric 
Published: December 2008

AbstractKey to understanding a protein's biological function is the accurate determination of its spatial distribution inside a cell. Although fluorescent protein markers allow the targeting of specific proteins with molecular precision, much of this information is lost when the resultant fusion proteins are imaged with conventional, diffraction‐limited optics. In response, several imaging modalities that are capable of resolution below the diffraction limit (∼200 nm) have emerged. Here, both single‐ and dual‐color superresolution imaging of biological structures using photoactivated localization microscopy (PALM) are described. The examples discussed focus on adhesion complexes: dense, protein‐filled assemblies that form at the interface between cells and their substrata. A particular emphasis is placed on the instrumentation and photoactivatable fluorescent protein (PA‐FP) tags necessary to achieve PALM images at ∼20 nm resolution in 5 to 30 min in fixed cells. Curr. Protoc. Cell Biol. 41:4.21.1‐4.21.27. © 2008 by John Wiley & Sons, Inc.
Embryonic Organ Culture
Authors: Sakai Takayoshi , Onodera Tomohiro 
Published: December 2008

AbstractThis unit provides detailed protocols for dissecting embryonic organs and performing organ culture to study questions in developmental biology. Procedures are described here for dissecting organs such as kidney, lung, and salivary gland. The unit also contains commentary including troubleshooting for embryonic organ culture. Curr. Protoc. Cell Biol. 41:19.8.1‐19.8.8. © 2008 by John Wiley & Sons, Inc.
Searching NCBI Databases Using Entrez
Authors: Baxevanis Andreas D. 
Published: December 2008

AbstractOne of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre‐existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text‐based searches, illustrating the types of information that can be retrieved through the Entrez system. An Alternate Protocol builds upon the first Basic Protocol, using additional, built‐in features of the Entrez system, and providing alternative ways to issue the initial query. The Support Protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed. Curr. Protoc. Bioinform. 24:1.3.1‐1.3.26. © 2008 by John Wiley & Sons, Inc.
Using VMD: An Introductory Tutorial
Authors: Hsin Jen , Arkhipov Anton , Yin Ying , Stone John E. , Schulten Klaus 
Published: December 2008

AbstractVMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. This unit will serve as an introductory VMD tutorial. We will present several step‐by‐step examples of some of VMD's most popular features, including visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication‐quality figures, animating and analyzing the trajectory of a molecular dynamics simulation, scripting in the text‐based Tcl/Tk interface, and analyzing both sequence and structure data for proteins. Curr. Protoc. Bioinform. 24:5.7.1‐5.7.48. © 2008 by John Wiley & Sons, Inc.
Using AutoDock for Ligand‐Receptor Docking
Authors: Morris Garrett M. , Huey Ruth , Olson Arthur J. 
Published: December 2008

AbstractThis unit describes how to set up and analyze ligand‐protein docking calculations using AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring function is a subset of the AMBER force field that treats molecules using the United Atom model. The unit uses an X‐ray crystal structure of Indinavir bound to HIV‐1 protease taken from the Protein Data Bank (UNIT 1.9) and shows how to prepare the ligand and receptor for AutoGrid, which computes grid maps needed by AutoDock. Indinavir is prepared for AutoDock, adding the polar hydrogens, and partial charges, and defining the rotatable bonds that will be explored during the docking. The input files for AutoGrid and AutoDock are created, and then the grid map calculation run, followed by the docking calculation in AutoDock. Finally, this unit describes some of the ways the results can be analyzed using AutoDockTools. Curr. Protoc. Bioinform. 24:8.14.1‐8.14.40. © 2008 by John Wiley & Sons, Inc.
Piezophiles
Authors: Yayanos A Aristides 
Published: December 2008

AbstractPiezophilic bacteria (piezophiles) are adapted to high pressures and are prominent among the inhabitants of the cold deep ocean below depths of approximately 2000 m. Whereas their maximum growth rate is close to the upper limiting growth temperature, it is also at a pressure close to that of their deep‐sea habitat. In contrast, bacteria in the upper 2000 m of the ocean and in terrestrial habitats have their maximum growth rate at atmospheric pressure. ThePTk‐diagram for a bacterium shows clearly how the temperature and pressure of its habitat influences its growth rate and allows for comparing organisms from habitats of disparate temperatures and pressures. Laboratory studies of higher organisms from the very deep ocean are rare. At the present time, research on piezophiles offers the best opportunity for learning about biochemical and molecular biological adaptations essential for all life in the deep sea and possibly in extraterrestrial settings.
Kranz Anatomy and the C
4
Pathway
Authors: Berry James O , Patel Minesh 
Published: December 2008

Abstract

C
4
photosynthesis incorporates novel leaf anatomy, metabolic specializations and modified gene expression. Plants that utilize this pathway typically possess a distinctive Kranz (or wreath) leaf anatomy, consisting of two photosynthetic cell types. These are the bundle sheath (bs) cells, which surround the vascular centres, and the mesophyll (mp) cells, which surround the bs cells. This structural framework allows for the compartmentalization and functional separation of two sets of carboxylation and decarboxylation reactions. Within C
4
leaves, selective expression of bs and mp cell‐specific genes leads to the selective accumulation of key photosynthetic enzymes which catalyse the different sets of cell‐type‐specific reactions, thereby enabling these plants to assimilate atmospheric carbon dioxide with very high efficiency. For some plants, C
4
photosynthesis has facilitated their adaptation to arid conditions, high temperatures and marginal environments. Understanding the basis of this pathway has applications for improvements in agricultural productivity and alternative fuel development.
Crassulacean Acid Metabolism
Authors: Lüttge Ulrich 
Published: December 2008

Abstract

Crassulacean acid metabolism (CAM) is a carbon dioxide acquisition, carbon dioxide transient storage and carbon dioxide concentrating mechanism of plants based on organic acid synthesis. In this variant of photosynthesis carbon dioxide can be fixed nocturnally in the dark and is used during the day for assimilation in the light. This has arisen polyphyletically many times during evolution. It is an ecophysiological adaptation that allows carbon dioxide acquisition with exceptionally economic use of water. It is regulated in a natural night/day rhythm but can also oscillate freely under the control of circadian biological clocks.

Key concepts

Metabolic mechanisms concentrating carbon dioxide internally in plants are important for photosynthesis at the low external carbon dioxide concentration in the present atmosphere.

Rearranged internal management of available metabolic housekeeping functions can generate new metabolic options of adaptive value.

Generation of isoforms of housekeeping enzymes can facilitate polyphyletic evolution of new metabolic pathways.

Circadian oscillations can be controlled by different biological clocks, which are feedback related to each other and present in many copies.

Flexibility in the expression of metabolic pathway variants facilitates adaptation under variable stress situations.

Stress adaptation in plants is for survival and mostly not for high productivity.
Plant Respiration
Authors: Sweetlove Lee J , Fernie Alisdair R 
Published: December 2008

Abstract
Respiration is a crucial feature of the metabolism of higher plant cells. Because plants synthesize all their organic molecules from inorganic materials and are sedentary, there are several unique features that distinguish plant respiration from animal respiration. In particular, the respiratory pathways not only oxidize carbohydrate to generate adenosine triphosphate (ATP), but they also provide carbon skeletons that act as precursors for the synthesis of organic molecules such as fatty acids and amino acids. In this article the impact of this dual role for the organization and regulation of the respiratory pathways will be described. Unique features of plant respiration will be detailed and a number of recent discoveries about the organization and regulation of plant respiration will be discussed.
Ion Transport at the Plant Plasma Membrane
Authors: Blatt Michael R 
Published: December 2008

Abstract

Membrane transport plays a fundamental role in virtually every aspect of homeostasis, signalling, growth and development in plants. At the plasma membrane, the boundary with the outside world, ion and solute fluxes underpin inorganic mineral nutrient uptake, they trigger rapid changes in second messengers such as cytosolic‐free Ca
2+
concentrations, and they power the osmotic gradients that drive cell expansion, to name just a few roles. Our understanding of the transporters – the ion pumps that generate an H
+
electrochemical driving force, H
+
ion‐coupled symport and antiport systems, and ion channels – now, more than ever, builds on developments in molecular genetics, protein chemistry and crystallography to gain insights into the fine structure and mechanics of these remarkable enzymes. Even so, it is the interface with the biophysical detail of ion transport that drives scientific enquiry in the field and will continue to be essential in informing both the most fundamental research as well as efforts to apply the knowledge gained in resolving some of the dilemmas that face society today.
Mitochondrial
DNA
and Diseases
Authors: Boesch Pierre , Lightowlers Robert N , Chrzanowska‐Lightowlers Zofia MA 
Published: December 2008

Abstract

The mitochondrial genome (mtDNA, mitochondrial
deoxyribonucleic acid
) is an essential source of extranuclear DNA in mammalian cells, located in the matrix of the organelle. It is much smaller than chromosomal DNA (only 16 569 bp) but thousands of copies per nucleated cell are found in nucleoprotein complexes termed nucleoids, which may constitute the heritable unit. mtDNA is maternally inherited and encodes 13 polypeptides, all fundamental for coupling cellular respiration to ATP (adenosine triphosphate) production. Consequently, mutated mtDNA can cause profound cellular dysfunction and death. Many pathogenic mtDNA mutations are known: single point mutations and rearrangements underlie clinical disorders known as mitochondrial cytopathies or encephalomyopathies; several nuclear gene mutations are known to cause mtDNA rearrangements; there exists an association between mtDNA deletions and the ageing process. Models explain how deletions may occur, but it is unknown how these deleted molecules predominate in individual cells over time, a process termed clonal expansion.
RNA
Virus Genomes
Authors: Domingo Esteban 
Published: December 2008

Abstract
RNA (ribonucleic acid) viruses are the most abundant group of molecular parasites that infect humans, animals and plants. They are associated with important diseases such as human influenza, newly emerging haemorrhagic fevers or several forms of hepatitis. Virus particles are disparate in size, shape and composition, and enclose an RNA genome that can be either single‐stranded, double‐stranded, nonsegmented or segmented. The structural diversity of viral RNA is reflected in differences in their replication cycles that are completed through complex interactions between viral and host proteins. RNA viruses share error‐prone replication that confers on them the capacity to adapt to a wide range or environments. Despite considerable progress in the understanding of virus structure and expression of their genetic programmes, the success of preventive and control strategies has been limited. Application of Darwinian principles to RNA viruses might result in new approaches for viral disease control.
Evolution of Secondary Plant Metabolism
Authors: Wink Michael 
Published: December 2008

Abstract
The biosynthesis of secondary metabolites (SM), which are important for the fitness of the plants as defence and signal compounds, occurs universally in higher plants and shows very high structural diversity. Their evolution in higher plants rests on variation in the enzymatic manipulation of a relatively small number of primary precursors. Evidence is presented that at least some of the genes encoding key enzymes of biosynthesis probably have reached plants by ancient horizontal gene transfer (HGT), for example from protobacteria or cyanobacteria which later became mitochondria and plastids. Another source of SM can be ectomycorrhizal and endophytic fungi; they can directly provide plants with defence compounds or might have transferred their pathway genes into the genome of their host plants times ago.
T
Lymphocytes: Regulatory
Authors: Fehervari Zoltan , Sakaguchi Shimon 
Published: December 2008

Abstract
CD4+ regulatory (Treg) T cells play a central role in the immune system by potently controlling the responses of other immunocytes. Their activity appears to be essential not only for the maintenance of immunological self‐tolerance but potentially also for the control of all physiological immune responses whether against normal self‐proteins, microbes or cancerous cells. A fuller understanding of these cells should allow us to effectively exploit their suppressive functions for clinical benefit.
Microbial Forensics
Authors: Morse Stephen A , Budowle Bruce 
Published: December 2008

Abstract
Microbial forensics is a newly developed discipline with an epidemiological foundation dedicated to the characterization, analysis and interpretation of evidence from the scene of an act of bioterrorism or a biocrime. It is an evolving subdiscipline of forensic sciences, which combines several disciplines including microbiology, molecular biology, genomics, bioinformatics and biochemistry. Microbial forensic investigations are carried out to obtain information regarding the identification or source of the material used in an act of bioterrorism, biocrime, hoax or unintentional release of a microorganism or toxin, with the ultimate goal of identifying those responsible for the crime (i.e. attribution). Attribution could be key to criminal prosecution of the individual or individuals, or for supporting actions that may be taken as a result of national policy decisions.
Glycosyltransferases in Plant Cell Wall Synthesis
Authors: Perrin Robyn M 
Published: December 2008

Abstract

Through their influence on plant cell wall polysaccharide structure, plant cell wall glycosyltransferases influence growth, development, cell division and environmental responses as well as plant‐derived food products, biofuels, textiles, paper and timber. Plant cell wall synthesizing enzymes can be processive (glycan synthases) or nonprocessive, and are integral membrane proteins with single or multiple transmembrane domains. Plant cell wall glycosyltransferases can be challenging to study biochemically, as they tend to be labile, present in multimeric complexes and encoded by large gene families whose members may have overlapping function. Candidate proteins may be identified by homology, but their function must be confirmed with biochemical evidence. Strategies for confirmation include expression in heterologous systems followed by assays of enzymatic activity or detection of carbohydrate products. Loss of function or gain‐of‐function techniques may be useful. Despite challenges, numerous plant cell wall glycosyltransferases have been identified; hundreds more, however, await further characterization.

Key concepts

Plant cell walls are critical for both biological processes and plant‐derived products, and are formed largely of polysaccharides synthesized by glycosyltransferases.

Plant cell wall glycosyltransferases use sugar nucleotides (NDP‐sugars) as donors, and transfer the sugar residue to acceptors to form glycosidic bonds.

These enzymes may transfer a single sugar molecule in nonprocessive fashion, or may transfer molecules iteratively to elongate a polymer. Processive glycosyltransferases are termed synthases whereas nonprocessive enzymes are simply termed glycosyltransferases.

Cellulose synthesis and callose synthesis occurs at the plasma membrane. All other plant cell wall polymers are synthesized within the Golgi and secreted to the cell wall in vesicles.

Nonprocessive glycosyltransferases tend to have a single transmembrane domain, whereas processive glycan synthases tend to have multiple transmembrane domains. There are exceptions to this rule, however.

Glycosyltransferases and glycan synthases tend to be highly specific for each donor and acceptor, and are specialized for formation of one type of carbohydrate linkage.

Numerous strategies exist for biochemical characterization of glycosyltransferases and glycan synthases, including heterologous expression and use of loss of function and gain‐of‐function genetic methods.

Plant cell wall glycosyltransferases and glycan synthases tend to be encoded by genes that are members of large multigene families.

Plant cell wall glycosyltransferases and glycan synthases often function in multimeric complexes.

Numerous enzymes involved in synthesis of plant cell wall biosynthesis have been identified. These include cellulose synthase, callose synthase, xyloglucan biosynthetic enzymes, pectin biosynthetic enzymes, mixed‐linkage glycan synthase and enzymes synthesizing mannans. However, many hundreds of enzymes remain to be identified at the biochemical level.
Ecological Genetics
Authors: Urban Mark C 
Published: December 2008

Abstract

Ecological genetics is the study of how ecologically relevant traits evolve in natural populations. Early research in ecological genetics demonstrated that natural selection often is strong enough to generate rapid adaptive changes in nature. Modern ecological geneticists combine field observations, laboratory experiments and rapidly improving laboratory techniques to further our understanding about how traits evolve in nature and also to identify which genes are evolving. Ecological geneticists increasingly explore how evolutionary dynamics shape ecological properties. As a consequence, ecological genetics is highly relevant to practical questions that lie at the interface of ecology and evolution.

Key concepts

Definition of ecological genetics.

How ecological genetics differs from similar fields?

Why ecologists need to know evolutionary biology and evolutionary biologists need to know ecology?

Major explanations of phenotypic variation in natural populations.

How experiments can discern among these explanations?

The importance of identifying the genes underlying adaptive trait variation.

Constraints to adaptive evolution.

How gene flow affects the evolution of interconnected populations?

How a consideration of multiple adapting species can alter evolutionary predictions?
Nonconsumptive Effects of Predators and Trait‐Mediated Indirect Effects
Authors: Peacor Scott D , Werner Earl E 
Published: December 2008

Abstract

Phenotypic plasticity in species’ traits is ubiquitous across taxa and habitats. This plasticity can affect the qualitative and quantitative nature of species interactions and thereby affect food webs. Empirical work has focused on predator–prey interactions, in part because most prey respond to predator presence through a suite of traits that reduce risk. These responses can incur costs in fitness correlates (e.g. growth and survival) of the prey, i.e. are nonconsumptive effects (NCEs) of predators. Further, these responses can lead to indirect effects transmitted through the prey to other species in the food web, termed trait‐mediated indirect effects (TMIEs). NCEs and TMIEs have been demonstrated in a wide range of communities and across diverse taxa. These effects can contribute substantially to the influence of predators (including through competition, trophic cascades and keystone predation), and therefore can play a critical role in the dynamics and structure of ecological communities.

Key concepts

Phenotypic plasticity in species traits is widespread and represented across diverse taxa and ecosystems.

To reduce predation risk, organisms respond to predator (including herbivore) presence by modifying traits, including developmental, morphological, physiological, life historical and behavioural characteristics.

Phenotypic responses to predators often incur a cost to prey fitness correlates such as growth rate and survival. These costs to fitness are termed nonconsumptive effects (NCEs) of the predator on its prey, to distinguish them from the consumptive effects (CEs) due to predation.

Phenotypic responses by prey to predators alter the nature of the interactions between prey and
other
(third) species. The predator is said to have a trait‐mediated indirect effect (TMIE) on the third species through induced changes in the intermediate species’ (prey's) traits.

Predator‐induced changes in prey traits can lead to TMIEs of the predator on prey resources (resulting in trait‐mediated trophic cascades), prey competitors and other predators of the prey.

NCEs and TMIEs can qualitatively change the nature of species interactions. For example, predator‐induced changes in prey traits can reverse competitive interactions, and lead to increases in prey growth rates due to strong TMIEs on prey resources.

NCEs and TMIEs can contribute strongly, and even dominate, the net effect of predators on prey and net indirect effect of the predator on species the prey interacts with. Thus, they can strongly affect prey population growth rates, community structure and ecosystem processes.

Factors, such as temperature, resource growth rates, prey density and prey–competitor density, can strongly influence the magnitude of NCEs and TMIEs.

It will be necessary to formally incorporate phenotypic responses of prey to predators into the conceptual foundations of ecology and strategies for the management of ecological systems.