bluuebunny/crossref_metadata_2025_split huggingface dataset:
von
Behring, Emil Adolf
Authors: Parascandola John 
Published: April 2013

Abstract

Emil Adolf von Behring (1854–1917) was a German medical scientist who developed antitoxins against diphtheria and tetanus. For his work on the diphtheria antitoxin, he was elevated to the Prussian nobility (and thereafter known as von Behring) and also awarded the first Nobel Prize in Medicine or Physiology in 1901. In 1895, he assumed the chair of hygiene at the University of Marburg, where he remained until his death, working on tuberculosis and developing an active preventive vaccine against diphtheria.

Key Concepts:

Diphtheria and tetanus bacilli produce toxins which cause the symptoms of these diseases.

Using guinea‐pigs and then sheep, Behring worked to develop serum antitoxin into a useful therapeutic agent for the treatment of diphtheria.

The major success of Behring's later years was the development in 1913 of an active preventive vaccine against diphtheria, based on a toxin–antitoxin mixture rendered stable by formaldehyde.
Safety Considerations in the Tissue Culture Laboratory
Authors: Martin Bernice M 
Published: April 2013

Abstract

The routine work of cell maintenance and some experiments that affect cells in culture can potentially pose a hazard to the researcher. Hazards may be associated with equipment, sterilisation methods, tissue or whole animal sources used to obtain the cells, as well as experiments that are designed to be detrimental to or alter the normal cell function. Essentially, hazards can be of mechanical, chemical, ionising or biological origin. Regardless of the source, the culturist can still work effectively and be safe. To do so, the culturist should be armed with proper training for cell culture studies, adequate personal protection equipment, advanced knowledge of any potential hazard and sources of information for responding in an emergency. With these tools, the risk to the culturist is minimised. The approaches to some of these issues are discussed below.

Key Concepts:

Properly prepared cell culturists can work safely.

Sterilisation used to protect the cells can harm culturists.

Culturists should be fully aware of potential hazards during experiments designed to change or kill cells.
Membrane Targeting: Methods
Authors: Gorfe Alemayehu A , Hocker Harrison J 
Published: April 2013

Abstract

The responsiveness of cells to external signals, or cell signalling, involves highly regulated sequences of biochemical reactions at the plasma membrane. When receptor proteins in the outer surface of the plasma membrane are activated by environmental signals, they undergo shape change or chemical modification to assemble internal proteins into an organised complex on the inner surface. Specific protein domains and lipids (fats) that are physically attached to proteins tether key components of this complex to the lipid bilayer of the membrane. Scientists have developed cell‐based and chemical techniques that allow them to introduce specific membrane‐targeting motifs into proteins to produce and study how this may alter cell behaviour. As a result, a great deal has been learned about the molecular basis of membrane targeting by lipid‐modified proteins. This knowledge holds a promise for the rational design of new compounds to prevent defective membrane targeting that could lead to abnormal signalling and the development of diseases.

Key Concepts:

Lipid bilayers provide the fundamental architecture of biological membranes.

The two‐dimensional surface of membranes provides a structural framework to organise multiple signalling proteins.

Proteins target membranes using globular domains and lipids that are covalently attached to them.

The most common lipid‐based membrane‐targeting motifs in the interior of the cell include modification of cysteine and glycine amino acids by acyl and prenyl groups.

G‐proteins are the quintessential examples of membrane targeting by lipidation.

Modern cell biology and chemical biology techniques can be used to artificially attach lipids to proteins.

Prevention of defective membrane targeting is being pursued as a new therapeutic strategy.
Donné, Alfred
Authors: Hoquet Thierry 
Published: April 2013

Abstract
Alfred François Donné (1801–1878) was a French physician and hygienist. He is mostly celebrated today for his contributions to bacteriology, his use of microscopy and his contribution to the development of photography. Together with his student Léon Foucault, Donné devised a technique to project on screen micro‐daguerreotypes of excellent quality.
Gullstrand, Allvar
Authors: Ljungstrom Olof , Normark Daniel 
Published: April 2013

Abstract
Allvar Gullstrand (1862–1930) was a Swedish ophthalmologist and Nobel Prize laureate (1911), who worked out the mathematical basis of astigmatism, and used mathematical methods to solve a number of other complex problems in geometrical optics. Gullstrand presented his doctoral dissertation at the Karolinska Institutet in Stockholm, but spent the majority of his career at Uppsala University, becoming professor of ophthalmology there in 1894. From 1914 to 1927 he held a personal professorship in physical and physiological optics freed from all teaching duties.
Transmission Electron Microscopy: Preparation of Specimens
Authors: Böttcher Bettina 
Published: April 2013

Abstract

Sample preparation of biological specimens for electron microscopy aims at bringing the sample into a suitable size (<500 nm thick, accommodated on a 3 mm diameter, round sample carrier) and to strengthen these samples against the adverse conditions in the electron microscope (beam damage and vacuum). There are two types of samples, one are large cellular structures, which require further sectioning and the other are individual assemblies, which are small enough to be imaged in suspension. Any preparation method of these types of samples has to fulfil four basic requirements: (1) to avoid collapse of the structures in the vacuum of the electron microscope; (2) to provide a sample sufficiently thin to avoid multiple scattering of electrons; (3) to minimise structural alterations as a consequence of the damage by the electron beam; (4) to maximise the contrast in the resolution band of interest. The relative importance of each constraint varies with the type of specimen and with the level of resolution sought.

Key Concepts:

Fragile samples such as tissues, cells and some molecular machines are stabilised by cross‐linking with aldehydes (formaldehyde or glutaraldehyde) or Osmium tetroxide (lipids).

Vitrification by rapid freezing converts liquid water into amorphous solid water.

Vitrification perseveres ultra structures with the least artifacts (cryo fixation).

Vitrification is achieved by plunge freezing of thin objects (<1–2 μm) or by high pressure freezing of thicker objects (<600 μm).

Large samples such as cells and tissues are stabilised by embedding in plastic resins or by vitrification.

Thick objects are cut to appropriate thickness either with conventional ultramicrotomes (diamond knifes or glass knifes) or with a focused ion beam.

Contrast can be enhanced by staining procedures, which use electron dense heavy atom derivates such as Uranyl acetate, Phosphotungstic acid, osmium tetroxide, ammonium molybdate.
Protein Structure: Unusual Covalent Bonds
Authors: Lecomte Juliette TJ , Falzone Christopher J 
Published: April 2013

Abstract

Proteins are linear polypeptides made out of a small set of amino acids. The chemical diversity of the building blocks is limited, but a protein's covalent structure can be amended

in vivo

so that unusual linkages are introduced and new functionalities are conveyed. These covalent modifications may occur during translation or after the protein is fully synthesised; they may be spontaneous or enzymatic and transient or long lived. They are generally consequential to cellular function and integrity of the organism. The broad array of modification includes common and frequent substitutions such as phosphorylation and rarer alterations such as formylglycine formation. A survey of long‐lived modifications is presented from a physicochemical perspective with attention to biological relevance.

Key Concepts:

Covalent bonds other than found in the standard set of amino acids expand the chemical properties of proteins.

Unusual bonds are found in protein‐derived prosthetic groups.

Unusual covalent bonds play functional roles.

Some unusual covalent bonds are irreversibly formed and are markers of aging.

Many unusual bonds are reversibly formed and participate in regulatory mechanisms.

Unusual bonds are often difficult to detect and identify, especially
in vivo
.

Technological advances have improved the ability to detect modifications in entire proteomes.
Chaperonins
Authors: Consalvi Valerio , Chiaraluce Roberta 
Published: April 2013

Abstract

The challenge in protein folding is the production of the native, active conformation from the primary sequence information.

In vivo

, in the cytosolic environment, acquisition of the native conformation is in competition with proteolytic degradation and/or intracellular precipitation. Chaperone proteins assist in finding the native fold in all cellular phases, and these key components of the cellular machinery occur ubiquitously through archaea, bacteria and eukarya. Chaperonins are complex polymeric proteins that form a closed environment, the ‘Anfinsen cage’, to allow correct protein folding triggered by
adenosine triphosphate
hydrolysis, avoiding intermolecular aspecific aggregation. The chaperonins prevent protein unfolding and misfolding, events responsible for several human diseases, such as cancer and amyloid diseases. The chaperonins are considered potential drug targets due to their role in protein misfolding, aggregation and denaturation and in cellular signalling.

Key Concepts:

Proteins must fold properly to acquire their native and functional conformation.

Protein misfolding is characterised by the exposure of buried hydrophobic residues.

Protein misfolding may be followed by protein aggregation.

The folding of many proteins need to be assisted by other proteins to prevent misfolding and/or aggregation.

The chaperonins prevent protein unfolding and misfolding, events responsible for several human diseases, such as cancer and amyloid diseases.

The ‘Anfinsen cage’ is a closed environment that encapsulates the nonnative protein and allows correct protein folding in the internal chaperonin compartment.
Protein Family Databases
Authors: Mulder Nicola J 
Published: April 2013

AbstractAs new protein sequences continue to flood into public databases with the advancement of sequencing technologies, the importance of protein family databases for automatic protein functional classification increases. These databases are developed independently and each has its own methods and areas of interest, as well as its own strengths and weaknesses. To simplify access to multiple databases by the user, many of these databases have also been amalgamated into integrated protein family resources, which vary in their level of manual curation. These protein family databases or integrated resources have a number of applications in modern biology or bioinformatics, including protein functional annotation, orthologue prediction, protein–protein interaction prediction, gene set enrichment analysis and providing datasets for evaluation of mathematic models of biological systems or networks.Key Concepts:Protein signatures are mathematical descriptions of the sequence characteristics of members of the same protein family or domain.Profiles and hidden Markov models are tools for characterising protein families or domains.Regular expressions or patterns are used for describing short highly conserved motifs.Protein family data has a number of applications, notably for the functional classification of new protein sequences.
RNA
Structural Motifs
Authors: Zhang Ming , Perelson Alan S , Tung Chang‐Shung 
Published: April 2013

Abstract

Chemically,
ribonucleic acid
(RNA) is a close cousin of
deoxyribonucleic acid
(DNA). RNA is, however, involved in a wide range of cellular activities (e.g. translating genetic information, serving as a structural scaffold, catalysing biological reactions) that often require the molecule to fold into a specific structure in order to perform its targeted function. Structurally and functionally it is therefore more closely related to proteins than to DNA. An RNA structural motif is defined as a collection of residues that fold into a stable three‐dimensional (3D) structure and which can be found in naturally occurring RNAs in unexpected abundance. Owing to the fact that stable 3D structures are associated with RNA structural motifs, these motifs often served as nucleation sites for RNA folding.

Key Concepts:

RNA motifs can help stabilise a global RNA structure, as well as guide the RNA folding process.

Hairpins are essential in constituting RNA tertiary architecture and in forming binding sites for other molecules.

Owing to variation of the lengths of loops and stems, as well as the types of interactions between them, pseudoknots represent a structurally diverse group.

Triloops and tetraloops with specific sequences are stable and frequently observed hairpin loops.

Self‐folding RNA structures, including the adenosine platform, ribose zipper, bulge–helix–bulge motif and G‐bulge motif, can provide the nucleation sites for RNA folding.
RNA
Structure: Pseudoknots
Authors: Gultyaev Alexander P , Olsthoorn René CL , Pleij Cornelis WA , Westhof Eric 
Published: April 2013

Abstract

An RNA pseudoknot results from Watson–Crick base pairing of a single‐stranded segment, located between two regions, paired to each other, with a sequence that is not located between these paired regions. This leads to a structure with at least two helical stems and two loops crossing the grooves of the helices. Pseudoknots are further stabilised by coaxial stacking between stems and the formation of triple
ribonucleic acid
(RNA) interactions between stems and loops. RNA pseudoknots adopt different folding topologies and are an essential part of various functional RNA molecules, including ribosomal RNAs, ribozymes and riboswitches. In this review, the thermodynamics and main structural features of pseudoknots, important for their function, are discussed: amongst others, viral tRNA‐like structures, ribosomal frameshifter pseudoknots and pseudoknots formed by S‐adenosylmethionine and pre‐queuosine riboswitches upon binding of their respective ligands.

Key Concepts:

The simplest RNA pseudoknot is formed by base‐pairing of nucleotides within a hairpin loop to a complementary sequence outside the hairpin (H‐pseudoknot).

Classical H‐pseudoknots consist of two coaxially stacked helical stems and two loops that cross one deep groove of one helix and the shallow groove of the other helical stem.

Pseudoknots are usually stabilised by coaxial stacking between stems and triple base pairs formed between the bases of the stems and loops.

Many complex pseudoknots may be interpreted as classical pseudoknots containing additional structural elements inserted in the pseudoknot loops.

Pseudoknots are folded in various types of RNA molecules and have diverse functions.

Limited information is available on thermodynamic stability of pseudoknots.

Computer‐assisted prediction of pseudoknots is partially hampered by a lack of knowledge about the thermodynamics of pseudoknot folding.
Experimental Systems in Aquatic Ecology
Authors: Sommer Ulrich 
Published: April 2013

Abstract

The main experimental approaches in aquatic community and ecosystem ecology will be presented along a gradient of scale: unenclosed field experiments, mesocosms with a natural mix of species, microcosms with an artificial mixture of species from cultures, and single species experiments in batch and continuous culture. Experimental manipulations usually consist of the addition or removal of (supposed) key organisms, addition of chemicals or alterations of the physical environment. Selecting the appropriate scale of experimentation is not only a question of technical and financial feasibility but also it has to consider the inevitable trade‐offs between realism and control. Conclusions will be more widely accepted, if they are supported by experiments at a variety of scales.

Key Concepts:

The choice of the appropriate experimental scale has to face an inevitable trade‐off between realism and control.

Unenclosed field manipulations have the highest degree of realism but the least degree of control.

Mesocosms operate with natural species assemblages, permit replication and control of experimental manipulations but are limited in temporal scale (weeks).

Microcosm experiments operate with artificial communities assembled from cultures, offer a high degree of control, but lack the pre‐history a mutual adaptation of the participating species.

Experiments with single or few species rely on the ‘model organism’ concept.

Small‐scale experiments are biased against the detection of slow and space requiring processes.
Primary Succession
Authors: Walker Lawrence R , del Moral Roger 
Published: April 2013

Abstract

Primary succession is the assembly of ecosystems on barren landscapes following severe disturbances that leave little or no biological legacy (lava flows, landslides and mine wastes). The assembly process involves colonisation of newly exposed substrates and subsequent interactions among the colonising plants, animals and soil microbes. Successional trajectories of sequential community replacement then develop, but some may diverge from nearby trajectories, making succession a challenging process to predict. Understanding how plant, animal and microbial communities develop under such extreme conditions is essential for restoration of damaged lands, as restoration is fundamentally the manipulation of successional trajectories by humans. Successional studies also provide insights into loss of biodiversity, climate change and the influences of invasive species on community dynamics.

Key Concepts:

Primary succession is the process of assembly of ecosystems on barren landscapes following severe disturbances that leave little biological legacy.

Primary succession is difficult to predict because it is the net result of many interacting processes including dispersal, colonisation, species interactions and biotic responses to on‐going disturbances.

Restoration is the attempt to manipulate succession and what is known about primary succession can be applied to the amelioration of severely disturbed habitats.

Primary succession provides insights into biodiversity loss, climate change and the influences of invasive species.
Secondary Succession
Authors: Shugart Herman H 
Published: April 2013

Abstract

Secondary succession refers to the sequential changes in vegetation that occur after a disturbance such as wildfires, hurricanes or human alterations. The rate of change in secondary succession is faster than in primary successions. The studies at different scales on the phenomena studied to understand succession has produced contrasting theories on the succession process. Arguments as to whether succession features competition among plants or some sort of positive process where the presence of one species reinforces the subsequent occurrence of another species at the site have produced considerable argument among ecologists. Ecological models that reproduce successional patterns provide insight into this issue as well as in the nature of successional outcomes. Restoration ecology represents a significant application of succession theory.

Key Concepts:

Secondary successions are the changes in vegetation that occur after agricultural abandonment or the disturbance of an existing ecosystem. They can be contrasted with primary successions that occur on new substrates.

The concept of succession has a long history in ecology and is a central concept in understanding the dynamics of ecosystems.

There have been and continue to be considerable debate about the nature of succession. The time and space scales considered in ecological succession studies have a pronounced effect on the processes and resultant patterns identified in the studies.

The concept of secondary succession and how it functions is essential a systems theory application in ecology.

Models of ecological succession have developed to investigate the roles of individual species and even of individual plants on determining the patterns of successional change.

Complex nonlinear responses in ecosystems components and the environment can produce complex successions with multiple stable states and multiple paths.

Secondary succession has significant application in the restoration of altered ecosystems.
Soils and Decomposition
Authors: McClaugherty Charles , Berg Björn 
Published: April 2013

AbstractSoils are dynamic, complex systems of inorganic, organic and biotic components that have the capacity to support plant life. Soils are classified on the basis of their chemical and physical properties. These properties include texture, structure, colour and the nature and properties of soil horizons. Soils are an important component of natural capital, providing for food and fibre production and physical support of cultural infrastructure, but soils are degrading. Soils are the major site for plant nutrient regeneration through the process of decomposition. Decomposition processes also generate long‐term soil organic matter and play an important role in the global carbon cycle. Decomposition of organic matter in soils is accomplished largely by microorganisms, often in association with animals. The rate and course of decomposition is influenced by climate, organic matter composition and nutrient availability from the environment.Key Concepts:Soils are dynamic systems composed of organic, inorganic and living components.Soils are classified according to measurable and observable properties, but there are many different classification schemes around the world.Key physical characteristics of soils are texture, bulk density and porosity all of which influence nutrient and water dynamics in the soil.Key chemical properties of soils include acidity (pH), cation exchange capacity (CEC), base saturation, organic matter content and nutrient availability.Soils are a slowly renewable natural resource that is being degraded worldwide due to erosion, desertification, salinisation and overuse.Decomposition of organic matter is regulated by climate and the nature and chemical composition of the organic matter.Soil organisms, particularly microorganisms (fungi and bacteria) and animals, play a major role in the decomposition process.Decomposition is important in regulating soil nutrient availability to plants.Soils are an important reservoir for carbon in the global carbon cycle and sequester significant amounts of atmospheric carbon dioxide.