bluuebunny/crossref_metadata_2025 huggingface dataset:
Sclerenchyma
Authors: Jarvis Michael C
Published: April 2013

Sclerenchyma is a specialised tissue, adapted to withstand both compressive and tensile stresses in plants. Sclerenchyma cell types may be divided into fibres, associated with phloem, xylem and other tissues; and sclereids or varied kinds. Sclereids originate from parenchyma and expand by intrusive growth. Phloem and xylem fibres in trees originate from the vascular cambium through delicately controlled, parallel cell divisions. Sclerenchyma cells have secondary wall layers that are constructed from cellulose microfibrils in a matrix of hemicelluloses and lignin. The cell geometry and the orientation of the cellulose are tailored to provide diverse combinations of strength, flexibility and stiffness in plant organs subjected to different loads by gravity, wind and weather. These properties are utilised in wood textiles and other natural materials of commercial importance.

Key Concepts:

Sclerenchyma is a plant tissue providing mechanical stiffness and strength.

Fibres and sclereids are the main types of sclerenchyma cells.

Most sclerenchyma cells show intrusive growth.

The cell walls of sclerenchyma have thickened secondary layers made from cellulose, hemicelluloses and lignin.

The stiffness of sclerenchyma depends on the orientation of cellulose and varies widely under developmental control.

Formation of sclerenchyma is controlled by a range of transcription factors.
Pericycle
Authors: Dubrovsky Joseph G , Rost Thomas L
Published: April 2013

Pericycle is a primary tissue of plant roots and is the site for the initiation of lateral roots and two secondary meristems, the vascular cambium and cork cambium (phellogen). In this article the characteristics of the pericycle related to each of its functions are reviewed. During lateral root development, three important and coordinated events take place in the pericycle: priming, founder cells specification and patterned cell division leading to primordium formation. The vascular cambium is initiated from the pericycle, just outside the primary xylem, and from residual procambium that originates from vascular parenchyma cells located between the primary xylem and primary phloem resulting in a continuous cylinder of vascular cambium cells which form the secondary xylem and secondary phloem of the root. The pericycle tends to be ‘pushed’ outwards after the vascular cambium forms and it eventually divides again to become the cork cambium. The cork cambium divides to form phellem cells to the outside and phelloderm to the inside. Aspects of the molecular mechanisms involved in the development and function of the pericycle and its derivatives are also discussed.

Key Concepts:

Pericycle is a primary tissue located at the periphery (most outward) of the root vascular cylinder.

In roots, the pericycle is a unique tissue in that its cells continue to cycle for a long period and it has three functions – initiation of lateral roots, contribution to the initiation of the vascular cambium and initiation of the cork cambium.

Lateral root initiation involves the following steps: pericycle cell priming that occurs in a so‐called oscillation zone, founder cell specification that is dependent on local increase in auxin concentration and first divisions of founder cells leading to primordium formation.

Auxin is a key hormone involved in the regulation of pericycle activity related to lateral root formation but it interacts and acts in a complex orchestration with other plant hormones.

Auxin homeostasis‐ and signalling‐related genes are involved in pericycle cell development, lateral root initiation and patterned division of founder cells during lateral root formation; some auxin‐independent genes are also important for pericycle development.

Vascular cambium forms by division of the pericycle cells just outside the primary xylem and also by division of residual procambium cells located between the primary xylem and primary phloem.

Vascular cambium divides toward the inside of the root to form secondary xylem and towards the outside to form the secondary phloem; auxins and cytokinins are essential to initiate the vascular cambium.

The cork cambium, or phellogen, forms from the pericycle outside the secondary phloem. It divides to the outside to form a layer of cells called phellem and to the inside to form the phelloderm. The cell walls of these cell layers are impregnated with a waxy substance called suberin to retard water loss out of the root and to prevent the entry of pathogens.
Phenotypic and Developmental Plasticity in Plants
Authors: Palmer Christine M , Bush Susan M , Maloof Julin N
Published: April 2013

Plants have a remarkable ability to alter their development in response to myriad environmental cues or stress. This phenotypic plasticity allows them to continually adapt to their local environment, a necessity for plants as sessile organisms. A host of environmental cues can be interpreted by plants, including light, temperature and nutrients, and these inputs are integrated and translated into a range of developmental outputs from shoot elongation, regulation of root gravitropism, altered flowering time, growth cessation of leaves, and timing of germination. This plasticity enables growth optimisation for the local environment, allows range expansion into hetergeneous habitats, and may provide an advantage as the changing climate affects growth conditions around the globe. Using model organisms such as
Arabidopsis
, molecular mechanisms for plastic growth responses are becoming more defined. Studies of growth and plasticity in less‐characterized species could expand our knowledge of the range of plasticity present in nature.

Key Concepts:

Multiple environmental signals are integrated to regulate plant development.

Plasticity gives plants the ability to optimise growth in varied environments.

Developmental plasticity comes from the meristem, which continuously produces organs throughout the plant life cycle.

Environmental cues can lead to changes in mRNA and protein abundance or activity, or they can be stored as epigenetic changes.

Roots and shoots respond to different environmental conditions but employ similar cellular processes.

Plants’ ability to optimise growth for a local environment may provide an advantage as habitats are altered by the changing climate.
Pneumocystis
Authors: Kaneshiro Edna S , Limper Andrew H
Published: April 2013

Pneumocystis
is a genus of opportunistic fungal pathogens, which cause a type of pneumonia by proliferating extracellularly in the lung alveoli in immunodeficient mammalian hosts. In immune suppressed patients, such as in those with acquired immune deficiency syndrome and individuals undergoing immunosuppressive treatment for cancer or organ transplantation,
Pneumocystis
pneumonia (PcP) continues to represent an important cause of opportunistic infection, respiratory failure and death. The epidemiology, taxonomy and life cycle features as well as issues related to the transmission of
Pneumocystis
organisms, initiation of infection, organism interactions with the host and the pathogenesis of PcP are areas of research activities. Good culture methods are not available for sustained

in vitro

cultivation of any species of
Pneumocystis
, which is currently viewed as a major challenge to performing experiments on these organisms and precludes genetic manipulations. However, several studies have revealed important insights into the biology of this group of organisms.

Key Concepts:

Pneumocystis
represents a genus of opportunistic fungi that can colonise healthy mammals (transient infections) and cause severe pneumonia in immune compromised mammals.

Genetic studies reveal closest phylogeny of
Pneumocystis
to the ascomycetous fungi and molecular and biochemical studies further indicate that
Pneumocystis
represents a unique and diverse group of organisms.

Each species of
Pneumocystis
infects a specific mammalian host (host species‐specific) and phylogenetic analyses suggest that the association of
Pneumocystis
species with their mammalian host species is among the longest known example of coevolution.

Pneumocystis
undergoes asexual and sexual reproduction; most organisms within the mammalian lung are haploid organisms.

Pneumocystis
organisms attach to type I lung epithelial cells and proliferate extracellularly in the alveolar spaces.

PcP is characterised by intense tissue inflammation that leads to respiratory insufficiency, and can be fatal without treatment.

Colonisation by

P. jirovecii

has been implicated as a comorbidity factor in patients with other pulmonary disorders and those undergoing therapies that affect the host's immune system.
Gastrointestinal Tract: Congenital Abnormalities
Authors: Fotis Lampros , Burns Alan J , Thapar Nikhil
Published: April 2013

The gastrointestinal tract may be subject to a variety of congenital abnormalities (i.e. those present at birth) that arise during embryological development. Specific patterns of malformations of the gastrointestinal tract include abnormal lumenisation (stenoses and atresias), duplications, abnormal rotation and fixation, abdominal defects and a variety of others associated with persistence of embryonic structures (e.g. Meckel's diverticulum), or abnormal formation of specific regions of the gastrointestinal tract (e.g. microgastria) or its cellular components (e.g. nerves in Hirschsprung's disease). These disorders primarily result in symptoms of intestinal obstruction, effects on surrounding structures or of associated anomalies. Early recognition is vital and management consists of timely resuscitation and stabilisation of the patients before institution of definitive surgical therapies.

Key Concepts:

The gastrointestinal tract is composed of anatomically and functionally distinct regions.

The structure of gastrointestinal tract is formed by a complex series of processes that occur to the initial simple gut tube including elongation, herniation out of the abdominal cavity, rotation and fixation.

A variety of genes working in isolation or in concert orchestrate the various facets of gut development.

A failure in any of the various embryological processes that form the gut can lead to congenital abnormalities, which range from extremely rare to relatively common.

Many of these abnormalities are associated with other congenital anomalies.

Clinically, most present soon after birth with symptoms of intestinal obstruction or of associated anomalies.

Early clinical recognition of these disorders is essential to minimise complications and allow the early institution of appropriate therapies.

Although surgery is the commonest intervention early treatment must include adequate resuscitation and stabilisation of the child prior to definitive surgery.
Anaemia: Adaptive Mechanisms and Consequences
Authors: Zarychanski Ryan , Rimmer Emily , Houston Donald S
Published: April 2013

Human life depends on the availability of oxygen and its conversion into energy used by living cells. Reduced oxygen to tissues is referred to as hypoxia, and may result from decreased oxygen delivery or mitochondrial dysfunction. In the setting of tissue hypoxia due to anaemia or other causes, several adaptive and coordinated physiologic processes are initiated to maintain oxygen delivery and limit oxygen consumption. Mechanisms to increase oxygen delivery in the face of anaemia or global hypoxia include the stimulation of erythropoiesis, and increasing cardiac output. Oxygenation availability is further maximised by decreases in the haemoglobin‐oxygen binding affinity, increases in tissue oxygen extraction, and via changes in regional blood flow. Mild to moderate anaemia, especially if chronic, is generally well tolerated given these adaptive processes. In states of inflammation or chronic disease, down regulation of haemoglobin occurs and may represent an important adaptive mechanism.

Key Concepts:

Aerobic metabolism and human life depend on the availability of oxygen.

Anaemia results when the haemoglobin levels are below normal and, if severe, may result in tissue hypoxia.

Adaptive mechanisms exist to compensate for anaemia or other causes of tissue hypoxia so that oxygen delivery is maintained and balanced with oxygen consumption.

A major adaptive mechanism in response to anaemia is to increase production of the growth hormone erythropoietin, leading to the formation of red blood cells.

The anaemia associated with inflammation has features of an adaptive response, is generally well tolerated and rarely requires treatment.
Syphilis: Clinical Aspects
Authors: Wright David J , Norris Steven J , Dhillon Rishi H‐P , Edmondson Diane G
Published: April 2013

Syphilis is a common sexually transmitted disease which, if left untreated, can result in a multiorgan infection. The causative organism is the spirochaete (from the Greek ‘spiral hairs’)

Treponema pallidum

. Other subspecies cause similar diseases such as yaws and pinta but these tend to be less severe and do not cause multisystem morbidity. Syphilis is a classic biphasic illness characterised by an initial skin infection which may be followed years later by involvement of the central nervous system (CNS), skeletal and cardiovascular systems with the great vessel the aorta at particular risk. Congenital transmission can occur and a range of clinical features can afflict the baby. Severe deformities, and even intrauterine death, are associated with transmission late in the pregnancy. Early and appropriate antimicrobial treatment of syphilis in all its guises is therefore of critical importance. Newer imaging techniques have become a useful adjunct in aiding diagnosis, which still relies heavily on serological assays and clinical acumen.

Key Concepts:

Enhancement of infectivity of syphilis and of early syphilitic lesions, in patients with concomitant HIV.

The relapsing nature of syphilis, both in early stages and in the late congenital disease, as in interstitial keratitis and Clutton's joints.

Primary form of syphilis is an early localised primary lesion. The secondary phase is manifested by a systemic disease, whereas the later stages are again localised.

Similarly, early congenital lesions tend to be disseminated, whereas late lesions are localised.

Newer imaging techniques are useful both in diagnosis and for monitoring treatment, especially in those patients with brain and cardiovascular syphilis.
Cell Senescence
In Vitro
Authors: Rattan Suresh IS
Published: April 2013

Cell senescence

in vitro

refers to the multitude of physiological, structural, biochemical and molecular changes that occur progressively during serial subcultivation of normal diploid cells, culminating in the permanent cessation of cell division. The whole duration of serial passaging is considered as the process of cellular ageing, and the end‐stage irreversible growth arrest is termed as replicative senescence. The limited proliferative capacity of normal, diploid and differentiated cells is also known as the Hayflick limit, and the overall phenomenon is called the Hayflick phenomenon. A progressive loss of global
deoxyribonucleic acid (DNA)
methylation and of telomeres is considered to be the critical determinants of the Hayflick limit. However,

in vivo

, it is not the absolute number of senescent cells which is responsible for age‐related impairments, but it is the drift in cell functions occurring during repeated cell division that is relevant to ageing and age‐related diseases. Cell senescence in the body is also considered to be a regulatory mechanism against cancer.

Key Concepts:

Normal, diploid and differentiated cells have a limited division potential, known as the Hayflick limit.

The Hayflick limit can be observed both

in vitro

and

in vivo

, and is both cell type‐specific and species‐specific.

Serial subcultivation of normal cells is accompanied by hundreds of physiological, structural, biochemical and molecular changes, culminating in cellular senescence.

The progressive change in normal cells during serial subcultivation is known as the Hayflick phenomenon, cellular ageing, or replicative senescence.

Cell enlargement, increased cytoskeletal rigidity in terms of polymerisation and cross‐linking, altered cellular responsiveness to stress, accumulation of molecular damage, impaired cellular functions and the reduced activity of maintenance and repair systems are the main changes during cellular ageing.

The senescent phenotype of cells is characterised by the irreversible growth arrest in G0/G1 phase of the cell cycle, which can be bypassed only through cell transformation.

Upregulation of a range of cell cycle check point genes is the hallmark of cellular senescence.

A stochastic and progressive loss of cytosine methylation and of telomeres in genomic DNA appears to be the major factors that limit the cell proliferative ability.

Cellular senescence

in vivo

is considered to be an anticancer mechanism in evolutionary terms.

In the body, it is not the absolute number of senescent cells that is responsible for the age‐related impairments; rather it is the drift in cell functions occurring during repeated cell division that is relevant to ageing and age‐related diseases.
Atomic Force Microscopy
Authors: Galgoczy Roland , Roca‐Cusachs Pere , Alcaraz Jordi
Published: April 2013

Atomic force microscopy (AFM) is a local probe nanotechnique that belongs to the large family of scanning probe microscopies (SPM). It was introduced in 1986, and is the most versatile SPM, because it can be used as an imaging instrument, a force sensor and actuator and as a molecular sensor. AFM enables imaging samples with subnanometer resolution and detecting intermolecular forces as low as a single hydrogen bond. Its high spatial and force resolution, combined with its ability to probe samples in liquid make AFM a very suitable nanotechnique for the life sciences. Accordingly, AFM has been used to examine biological samples embracing all levels of complexity including biomolecules, viruses, prokaryotic and eukaryotic cells and more recently, tissue sections. Moreover, AFM biomedical applications are rising and include their use as a diagnostic tool.

Key Concepts:

AFM is a nanotechnique that allows visualising the surface of biological samples by directly touching them with a mechanical‐based force sensor or cantilever tip.

The essential components of an AFM are a flexible cantilever provided with a sharp tip at its end and a piezoelectric scanner that controls the tip–sample distance.

AFM can be operated in vacuum, air and liquid. The only sample requirements are immobilisation on a flat substrate and a surface roughness smaller than the height of the tip.

The most common modes of operation of AFM as an imaging device are with the tip in either constant or intermitent contact with the sample.

The topography image obtained with AFM is strongly influenced by both the shape and size of the tip and the elastic properties of the sample.

AFM probes can measure intermolecular forces as low as few piconewtons, and apply user‐defined loading forces on the sample surface, thereby acting as a force sensor or actuator.

Using AFM tips with a suitable functionalisation enables probing the specific intermolecular forces involved in molecular recognition events.

The spatial and force range accessible with AFM enables using it to examine biological samples spanning many length scales of biological complexity, from single biomolecules to tissue sections.

Arrays of cantilevers functionalised with specific recognition sites can potentially be used to detect soluble biomarkers in fluid samples of patients at concentrations lower than current diagnostic devices.
Hydrophobic Interaction Chromatography
Authors: Jennissen Herbert P
Published: April 2013

Hydrophobic interaction chromatography (HIC) involves the separation of protein molecules in their native and biologically active state owing to a differential interaction of these molecules with hydrophobic sites on the surface of a solid support. In the separation process, hydrophobic patches on the protein surface interact with hydrophobic molecules (e.g. alkyl residues) immobilised on the hydrophilic solid phase surface (e.g. agarose). In the paper, a historical overview is followed by a consideration of the biochemical and biophysical mechanisms involved in HIC and a discussion of the critical hydrophobicity method and other approaches to hydrophobic interaction chromatographic methods. A detailed protocol for the individual synthesis of gel libraries for specific needs has been published. The treatise is concluded with a discussion on the predictability of chromatographic results and an outlook into the future.

Key Concepts:

Positive and negative cooperativity manifests itself by binding isotherms of proteins not governed by the Langmuir equation, that is, a single binding constant but depends on site–site interactions leading to multiple binding constants.

Adsorption–desorption hysteresis manifests itself by an adsorption isotherm, which is not retraced by the desorption isotherm, due to conformational changes on the surface, dissipation of entropy and an increase in affinity.

Metastability of adsorption states occurs during adsorption–desorption hysteresis and indicates energetically that a local energy minimum exists (i.e. nonequilibrium state) in distinction to the global energy minimum, that is, true equilibrium.

Critical hydrophobicity is the threshold hydrophobicity under low salt concentrations (e.g. 50 mM Tris, 150 mM NaCl and pH 7.0) at which the adsorption of a protein can first be measured.

A quantised hydrophobicity gradient is a hydrophobicity gradient separated into a library of distinct gels of varying hydrophobicity for determining the critical hydrophobicity.

A homologous gel library consists of gels carrying covalently immobilised hydrocarbons (e.g. alkyl residues) comprising a homologous series.

The lattice‐site binding function is a protein adsorption isotherm (often showing positive cooperativity) as a function of the surface concentration of immobilised hydrocarbons (e.g. alkyl residues).

The bulk ligand binding function is a protein adsorption isotherm on immobilised hydrocarbons (often showing negative cooperativity) as a function of the bulk protein concentration.

Predicting chromatographic behaviour from sorption isotherms is a major aim in understanding HIC.

Predicting chromatographic behaviour from protein structure is the ultimate aim in understanding and utilising HIC.

The critical hydrophobic patch area hypothesis is a method of predicting the chromatographic behaviour of proteins in HIC from protein structure, utilising the area of hydrophobic patches on the surface of proteins.
Chamberland, Charles Edouard
Authors: Harvey Joy
Published: April 2013

Charles Chamberland was an associate of Louis Pasteur whose technical skills and inventive mind added significantly to the experimental investigations ofchicken cholera, anthrax, swine erysipelasandrabiesand the development of vaccines produced by the Pasteur Institute. Trained in physics and mathematics rather than biology or medicine, he is credited with the invention of the first laboratory autoclave and the Chamberland–Pasteur porcelain filter. His laboratory of applied microbiology within the Pasteur Institute had the major responsibility for producing commercialanthrax vaccinesand advising satellite Pasteur institutes.
Theorell, Axel Hugo Theodor
Authors: Ljungstrom Olof , Normark Daniel
Published: April 2013

Axel Hugo Theodor Theorell (1903–1982) was a Swedish biochemist and Nobel Prize laureate (1955), who primarily studied enzymatic oxidation processes. He is best known for his work on cell‐respiration oxidation product at the time known as ‘the yellow ferment’, myoglobin, and alcohol dehydrogenases in the liver. In 1936 he became the first director of the section for biochemisty at the newly established Medical Nobel Institute at the Karolinska Institutet (KI), and a full professor at the KI in 1959.
Tiselius, Arne
Authors: Tunlid Anna
Published: April 2013

Arne Tiselius (1902–1971) was a Swedish biochemist who developed electrophoresis and adsorption methods and applied them to the study of proteins and other substances of biological interest. In 1948 he was awarded the Nobel Prize in Chemistry for his research on electrophoresis and adsorption analysis, especially for his discovery of the complex nature of serum proteins. In the following decades several biochemical separation methods were developed at his laboratory at Uppsala University. Tiselius played an active role in Swedish science policy after World War II. He was a member of the Nobel Committee for Chemistry and served as president of the Nobel Foundation.
Hydrophobic Effect
Authors: Lazaridis Themis
Published: April 2013

The term ‘hydrophobic effect’ refers to the poor solubility of nonpolar substances in water compared to organic solvents or to polar substances. The transfer of small nonpolar molecules from the gas phase or organic solvents to water has a characteristic thermodynamic signature: positive free energy, negative enthalpy, large negative entropy and positive heat capacity. This thermodynamic signature can be explained by considering the structure of water around nonpolar substances, which depends on the size and shape of the nonpolar solute. The poor solubility of nonpolar groups in water leads to aggregation of these groups (hydrophobic interaction) and the formation of self‐assembled structures such as miscelles and lipid bilayers. The hydrophobic interaction is also the major contributor to protein folding. The origin of the hydrophobic effect lies in the fact that water interacts with itself much more strongly than it does with nonpolar groups.

Key Concepts:

The origin of hydrophobicity lies in the strong water–water interactions.

The hydrophobic effect is entropic or enthalpic depending on temperature and the geometry of the associating solutes.

The characteristics of hydrophobic hydration differ depending on the length scale of the solute.

The hydrophobic effect is responsible for the formation of lipid bilayers and the folding of proteins.

Interaction between small hydrophobic solutes is in many ways different from transfer to a bulk phase.

Most studies find anticooperativity in the interaction between three small nonpolar solutes.

Very long‐range attractions between hydrophobic surfaces are probably due to macroscopic phenomena, such as air bubbles.
Electron Cryomicroscopy and Three‐dimensional Computer Reconstruction of Biological Molecules
Authors: Ludtke Steven J , Chiu Wah
Published: April 2013

Electron cryomicroscopy (cryo‐EM) single‐particle analysis is a technique for imaging individual molecules or macromolecules under native‐like conditions. When combined with complex computer algorithms, the resulting images can produce a three‐dimensional (3D) structure at resolutions now beyond 4 Å. At these resolutions, the protein backbone can be traced, and in many cases sufficient side chains identified to build a full atomistic model akin to that produced by X‐ray crystallography. Cryo‐EM can also approach problems, which are difficult or impossible for X‐ray diffraction or NMR. For example, cryo‐EM can be used to characterise the structural flexibility/dynamics of large macromolecules, which is not possible via any other current method. Cryo‐EM is also often the method of choice for studying large membrane proteins, which are generally difficult to crystallise. Additional specialised methods exist for 2D crystals or extended structures with helical symmetry.

Key Concepts:

Owing to the short wavelength of high voltage electrons, it is possible to resolve features at resolutions ∼1000× higher than light microscopes.

Liquid specimens cannot be used under the high vacuum of the microscope and must be either frozen in vitreous ice or chemically fixed before imaging.

Tens of thousands of randomly oriented 2D images are combined to produce a high‐resolution 3D volumetric structure.
Protein Unfolding and Denaturants
Authors: Konermann Lars
Published: April 2013

The biologically active (native) state of most proteins is characterised by a tightly folded and highly ordered conformation. Denaturants are chemical or physical agents that can induce unfolding of the polypeptide chain. Examples include urea, heat, extremes of pH, as well as some detergents. Unfolded proteins adopt a largely disordered structure. Denaturants can interact directly with the protein, or they can alter the properties of the surrounding aqueous environment. Despite the routine use of denaturants in the biochemical laboratory, the mechanisms whereby these agents destabilise the native state remain poorly understood. Folded protein structures are only marginally stable. As a result, relatively subtle alterations in the physical and chemical properties of the solvent can cause major changes in position of the unfolding equilibrium. This review briefly discusses the most commonly used denaturants, their likely mechanisms of action, as well as some thermodynamic aspects.

Key Concepts:

The biologically active (native) state N of proteins represents a highly ordered and tightly folded structure.

N is in equilibrium with an extensively disordered (unfolded) state U.

Denaturing agents (e.g. urea, extremes of pH and temperature) shift the unfolding equilibrium from N to U.

The exact mechanism of action remains unclear for most denaturants.

The position of the unfolding equilibrium is governed by an interplay of enthalpic and entropic contributions that affect the free energy of unfolding according to ΔG0=ΔH0–TΔS0.

The sign and magnitude of ΔG0represents the thermodynamic stability of N; N is stable when ΔG0>0.

Unfolding can be triggered by increasing the temperatureT, because U has a higher entropy than N (ΔS0>0).

Protein stability measurements are commonly carried out by employing urea or guanidinium chloride‐induced unfolding in conjunction with optical detection.

Some proteins adopt semiunfolded structures (intermediates) under mildly denaturing conditions.

Protein (un)folding can be studied under equilibrium conditions and in kinetic experiments.
Protein Disulfide Isomerases
Authors: Gilbert Hiram F
Published: April 2013

Protein disulfide isomerase(PDI) is a multifunctional protein that facilitates the formation of correct disulfide crosslinks between cysteine residues during the early stages of protein folding and secretion in the endoplasmic reticulum. It is a member of a large family of oxidoreductases that catalyse exchange reactions between thiols and disulfides. PDI is a multidomain protein, consisting of four tandem thioredoxin domains. TheN‐ andC‐terminal thioredoxin domains have catalytic disulfide/dithiol centers while the two internal domains are structural and provide additional interactions with the protein substrates. The catalysis of disulfide formation relies almost entirely on the high reactivity of PDI's active site disulfides. However, the ability to catalyse disulfide isomerisation requires multiple domains. In the cell, PDI's essential activity is the formation of disulfide bonds, but it does catalyse isomerisation.

Key Concepts:

PDI structure consists of four tandem thiredoxin domains.

The ability to form disulfides between cysteines in substrate proteins results from highly reactive active site disulfides.

PDI can correct (isomerise) misformed disulfides by reducing incorrect disulfides and reoxidising in a different configuration.

The multidomain structure is needed for catalysis of isomerisation but a single catalytic domain is sufficient to catalyse substrate oxidation.

In the cell, the essential activity of PDI is its ability to form substrate disulfides.
Genome, Proteome and the Quest for a Full Structure–Function Description of an Organism
Authors: Godzik Adam , Wilson Ian A
Published: April 2013

Completion of the Human Genome Project provided thedeoxyribonucleic acid(DNA) sequence of a human genome – a complete blueprint of our organism. Genomic information is processed intoribonucleic acid(RNA) and then into proteins, which carry out most cellular processes that sustain life. All of these molecules – DNA, RNA and proteins – have unique three‐dimensional shapes, and the atomic details of these shapes, and the inherent information they carry, define their function. Every cell, and ultimately the entire organism, may be viewed as a gigantic three‐dimensional jigsaw puzzle where all of the pieces have to fit together for the whole system to function. Elucidating the shapes of the molecular elements of the cell helps decipher the rules that dictate how they hierarchically form larger objects, such as molecular machines, organelles, cells and organs, how the shapes of individual molecules and their assemblies change on regulation, what changes cause disease and eventually, how they can be repaired or how they can be targeted by drugs.

Key Concepts:

Genes are coded in a four‐letter code by linear strings of DNA and define sequences and shapes of all downstream products (RNA and proteins).

DNA has a limited number of three‐dimensional shapes that it can take (three main forms currently known), but even small variations of these shapes are important for gene regulation and interactions between DNA and other molecules.

Products of DNA transcription (RNA) and translation (proteins) have complex but unique three‐dimensional shapes that are defined by their sequence and post‐translational modifications as well as interaction with other molecules.

Experimental determination of DNA, RNA and protein three‐dimensional structures by X‐ray crystallography, NMR spectroscopy and other techniques provide a molecular level understanding of the fundamental processes of life.

The number of basic shapes (or folds) that RNA and proteins can adopt are limited by steric constraints; however, these numbers are very large as compared to the limited number of DNA shapes – it is now known hundreds (RNA) or thousands (protein) of shapes and (probably) thousands of other shapes are still possible.

Regulation of DNA, RNA or protein function often involves changes to their structure and/or dynamics.

DNA, RNA and protein molecules form functional networks where neighbours in the network influence and regulate each other. Analyses and simulations of such networks is a subject of systems biology, which ultimately provides a perspective for predictive modelling of biological systems.

DNA, RNA and protein molecules can form higher order complexes and assemblies – a process driven by a mutual compatibility of their shapes and/or chemical composition. Such complexes define the many nodes in functional cellular networks.

Experimentally determined structures of DNA, RNA and protein complexes and assemblies provide a detailed picture of how regulation of cellular processes is carried out.
History of Scientific Agriculture: Crop Plants
Authors: Hancock JF
Published: April 2013

The first farming communities appeared in the Fertile Crescent above the Tigris River in what is now Iran approximately 13 000 years ago. Agriculture was also invented independently at several other locations in the world including Africa, Asia, China, India, Japan, Mesoamerica, South America and the Eastern US. Most of the early crops were annual types that were self‐pollinating and polyploid. The crops emerging in each region spread gradually across the world. Once humans began to plant and harvest, several profound changes occurred in the crop species due to conscious and unconscious selection. Some of the major changes were nonshattering of seed pods, more determinate growth, more uniform ripening, larger seed size and increased seed production. Levels of genetic diversity were also greatly reduced during the process of crop domestication when humans selected only those types that were most beneficial to them.

Key Concepts:

Homo sapiensdid not begin agriculture until approximately 13 000 years ago, even though the modern form of humans appeared approximately 50 000 years ago.

The domestication of crops by humans began in what is called the ‘Fertile Crescent’ on the western edge of modern Iran, but at least 13 other locations across the world spawned agriculture.

The act of planting and harvesting plants dramatically altered the genetic and physiological makeup of crop species, effecting traits such as seed retention, growth patterns, uniformity of ripening and levels of seed production.

The earliest crops represented a broad array of plant families, but most were herbaceous annuals and self‐pollinated.

During the domestication process, levels of genetic variation were dramatically reduced as humans selected a narrow range of plant types.
Nucleic Acids: Hybridisation
Authors: Kim Ji Hun , Kalitsis Paul , Pertile Mark D , Magliano Dianna , Wong Lee , Choo Andy , Hudson Damien F
Published: April 2013

Nucleic acid hybridisation is the pairing of complementary
deoxyribonucleic acid
(DNA) strands to produce DNA–DNA hybrids or the pairing of complementary DNA–RNA strands to produce DNA–RNA hybrids. Nucleic acid hybridisation is the basis of many research and diagnostic applications with all relying on simple base pairing specificity of nucleic acids to generate a signal through a labelled probe. This fundamental principle has led to DNA/RNA detection and quantification on solid phase blots, DNA/RNA cytogenetic localisation on cells, detection and purification of specific DNA and comparative gene expression analysis. Most recently, principles of nucleic acid hybridisation have been combined with next generation sequencing technology to create powerful new platforms for analysis which will increase in utility as we enter this new age of genomics and personalised medicine. The concepts and applications of nucleic acid hybridisation will be discussed in this review.

Key Concepts:

Nucleic acid hybridisation using base paring complementary allows detection of genes, mutations and RNA permitting accurate diagnosis of disease in the clinic and providing researchers with many powerful tools to analyse and interpret their work.

Traditional hybridisation technologies have enabled detection of target DNA or RNA sequences on a solid‐base membrane or on chromosomes.

Development of radioactive and nonradioactive probe labelling systems allowed for significantly improved sensitivity and specificity of detection of the target nucleic acids.

Nucleic acid hybridisation in quantitative analysis permits detection of mutations such as deletion, insertion and copy number variation for disease diagnosis.

Incorporation of next‐generation sequencing with nucleic acid hybridisation has opened a new genomic era and has enabled high‐throughput sophisticated analysis for personalised medicine by discovering novel genes and single nucleotide polymorphisms (SNP).
Parasitism: The Variety of Parasites
Authors: Phillips R Stephen
Published: April 2013

Associations between animals of different species can take a variety of forms, ranging from commensalism where the partners live independent lives but benefit each other, to parasitism where one partner of the relationship benefits at the expense of the other, the host. In between, we have mutualism where the partners have an intimate relationship which is obligatory for both partners but is also beneficial to both. The majority of parasites in the animal kingdom are invertebrates. Amongst the protozoa, parasites of medical or veterinary importance are found amongst the amoebae (e.g.Entamoeba histolytica), the flagellates (e.g. trypanosomes) and the sporozoa (such as the malarial parasites), all of which are parasitic. The parasitic worms (helminths) are very important parasites of man and his domestic animals including the flukes (e.g. schistosomes causing bilharzia), round worms or nematodes such asAscaris lumbricoides, the large round worm of humans, and the tapeworms or cestodes (it is the larval stages of tapeworms which are the cause of morbidity). Finally, the arthropods include important parasites such as ticks and mites (arachnids), and insects such as lice and fleas. Many insects such as mosquitoes, of course, act as vectors of parasites. Parasites are also identified as either endoparasites or ectoparasites depending on whether they are located internally or externally with respect to the host. Parasites often have incredibly complicated life cycles and employment of control measures against parasites requires detailed knowledge of these life cycles.

Key Concepts:

Associations between different species of animals can take various forms ranging from commensalism, through mutualism to parasitism.

In commensalism both partners live independently, in mutualism there is an obligatory intimate relationship between the partners which is beneficial to both and, in parasitic relationship one partner benefits at the expense of the other.

Most parasitic species are invertebrates but there are some vertebrate parasites such as the cuckoo.

Parasitic species are found in both single‐celled organisms, the protozoa, and the multi‐celled metazoan organisms.

There are important medical and veterinary parasites in all the major groups of protozoan and metazoan animals.

Parasites can be found inside their host and are known as endoparasites whereas some found outside their hosts and are known as ectoparasites.

Devising strategies to control parasites and avoid infection depends on an understanding of the life cycle of the parasites.
Trophic Cascades
Authors: Gruner Daniel S
Published: April 2013

Trophic cascades in ecological communities are defined as the propagation of indirect effects between nonadjacent trophic levels in a food chain or food web. Typically, cascades are driven by predation from the top‐down, with altered herbivore densities mediating the ultimate effects on the biomass of primary producers. Predator traits and nonconsumptive changes in the behaviour of prey also can propagate cascading indirect effects, and variation in nutrients or energy at the base of food webs may mediate cascades from the bottom‐up. Significant debate has revolved around the relative dynamical strength of top‐down versus bottom‐up forces and over the importance of trophic cascades in different aquatic and terrestrial ecosystems. Polarisation has eased with the increased availability of experimental and comparative case studies, meta‐analytic syntheses of these data and development of theory. The basic conceptual construct of trophic cascades has been applied to classical biological control of agricultural pests, biomanipulation of lakes and streams and the conservation and restoration of apex predators for fisheries and wildlife management.

Key Concepts:

Limited nutrient availability and high C:N and C:P stoichiometry can constrain biomass turnover and the strength of trophic cascades.

Many lake and stream ecosystems support four trophic levels, with piscivorous fish ultimately suppressing phytoplankton in a consumptive interaction chain.

Trophic cascades can occur via direct consumption and density reductions of prey and through behavioural changes in prey foraging from predation risk.

Fisheries intensification has selectively reduced top predators and large‐bodied species and reduced the length of oceanic food chains.

Reintroduction of top predators, such as wolves, to the American west has facilitated recruitment of woody shrubs and trees and reduced stream erosion.

Long‐term studies are critical to testing for and identifying trophic cascades on landscape and regional spatial scales.
Phosphorus Availability in the Environment
Authors: Tiessen Holm
Published: April 2013

Phosphorus is a key element in biological reactions so that small changes in phosphorus availability can have major impacts on ecosystem function and structure. In soils and ecosystems, P is derived from the parent rocks. Although phosphate is relatively insoluble it is eventually weathered and leached out so that many old soils are P deficient and their associated ecosystems are P limited. High productivity agriculture relies on P fertilisation. Phosphorus is highly concentrated in plant seeds (grains), animals and animal (and human) excrements. Consequently environments with intensive animal production or high population density receive a surplus of P that commonly causes environmental pollution. The imbalance between regions of low and of surplus P must be addressed through more efficient P management, both in fertilisation practices and efforts to recycle P from wastes. This is particularly important as the principal source of P, rock phosphates are becoming more expensive, reserves more difficult to find and mine, and are globally strategically unevenly distributed.

Key Concepts:

The only source of P in soils are the parent rocks or added fertilisers.

Weathering slowly removes P from soils, so that many old and tropical environments are P deficient.

P is essential to all life and is concentrated by organisms to levels thousands of times higher than environmental concentrations.

High environmental P concentrations usually result from the excretions or residues of organisms.

Being limiting to life, P stimulates biological growth and when in excess will cause ecosystem disruptions through eutrophication.

The principal source of fertiliser P are rock phosphates which are sedimentary deposits of marine organisms.

Approximately 1000 million t of P have been mined and added to the environment.

Finite P resources have caused concern about ‘peak production’ occurring near the middle of the twenty‐first century, followed by declines and higher prices that may limit food production.
Nitrogen Budgets
Authors: Kätterer Thomas
Published: April 2013

The compilation of inputs and outputs of nitrogen across the boundaries of a system defined in time and space comprises a nitrogen budget. This budget contains information about internal nitrogen fluxes within the system and can be used as an efficiency indicator or policy instrument. Nitrogen cycling at global and ecosystem scale is described as well as transformations of nitrogen between different chemical forms occurring in nature. Chemical and biological processes governing the distribution and transformation of nitrogen within ecosystems are presented including ammonification, nitrification, denitrification and plant uptake. Examples for agricultural systems are shown for illustrating how different nitrogen fluxes can be selected for calculating nitrogen budgets depending on definitions of system boundaries. Environmental consequences due to human interactions with the nitrogen cycle are also presented and discussed.

Key Concepts:

The compilation of inputs and outputs of nitrogen across the boundaries of a system defined in time and space comprises a nitrogen budget.

Nitrogen is an essential element of all living matter and, in addition to carbon, the main building block of many macromolecules, such as proteins and nucleic acids.

Although nitrogen makes up about 78% of the air we breathe it must be transformed into reactive chemical forms for being available for vascular plants.

The amount of nitrogen cycled within ecosystems is about one order of magnitude larger than the amounts crossing ecosystem boundaries.

Generally, more than 90% of the nitrogen needed for primary production is recycled through within ecosystems.

Production of mineral fertilisers is essential for feeding a growing human population.

Human impacts on nitrogen cycling are significant.

Environmental concerns due to human interactions with the nitrogen cycle are mainly related to the presence of nitrate in water and emissions of nitrogen oxides contributing to stratospheric ozone depletion and to the greenhouse effect.

Farmgate nitrogen balances, defined as the difference between nutrient input and output at farm level, are increasingly used as environmental performance indicators or as policy support tools for emission control.