bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNADamage
Authors: Moore Bryn S , Morris Lydia P , Doetsch Paul W 
Published: September 2009

AbstractVarious biochemical and physical events alter the structure and properties ofdeoxyribonucleic acid(DNA), such as damage to the bases as well as single‐ and double‐strand break (DSB) induction. The sources for cellular DNA damage include exposures to environmental chemicals and radiation as well as endogenous processes resulting from normal cellular metabolism. Conversion of DNA into these forms can have deleterious biological consequences for cells, including development of cancer and other detrimental outcomes. The basis for these biological endpoints is largely dependent on the interactions between the DNA damage and the cell's DNA replication and gene expression machinery. Technologies exist for the detection and measurement of DNA damage in cells. Each of these methods functions in different contexts and with varying degrees of sensitivity.Key conceptsThe rates of induction of variousdeoxyribonucleic acid(DNA) lesions, including spontaneous hydrolysis and oxidative DNA damage, have been estimated.DNA damage has been associated with various physiological conditions including cancer, neurodegenerative diseases, heart disease and the process of ageing.Damage from a variety of exogenous and endogenous sources induces DNA base lesions and strand breaks, which can be detected by various molecular and biochemical methods.Damaged deoxyribonucleotides can be incorporated into DNA during synthesis due to errors by the polymerase and/or disruptions of nucleotide pool balance.Many of the features of DNA in chromatin, including DNA–protein interactions and sequence context, greatly impact the manner in which damage is distributed within the genome.Chemotherapeutic agents, used to treat cancers, often target DNA resulting in tumour cell death.
Polysaccharides
Authors: BeMiller James N 
Published: September 2009

Abstract

Polysaccharides are carbohydrate polymers containing from approximately 35 (usually more than 100) to as many as 60 000 monosaccharide units. Polysaccharides have a range of general structures (from linear to various branched structures) and shapes. They are structural components of cell walls of bacteria, fungi, algae and higher plants and of the exoskeletons of insects and crustaceans, are energy‐ and carbon‐storage substances, and serve various other functions as extracellular materials of plants, animals and microorganisms. They are the most abundant (by mass) of all organic substances in living organisms, comprising about two‐thirds of the dry weight of the total biomass. Some have commercial value as isolated substances.

Key concepts

Polysaccharides are polymers of sugar (carbohydrate) units.

Polysaccharides are ubiquitous in nature. They are present in all plant tissues.

Polysaccharides comprise about three‐fourths of the total biomass on Earth.

Polysaccharides serve as structural materials, as reserve food materials and in other functions.

Polysaccharides occur in a wide range of shapes and sizes.

Polysaccharides are hydrophilic and either dissolve in or absorb water.

Polysaccharides are produced and used commercially in large volumes.
Lipids
Authors: Yeagle Philip L 
Published: September 2009

Abstract

Lipids are molecular building blocks for the most fundamental structures in biology, including the serum lipoproteins, the membranes of cells and cellular organelles and the membranes of enveloped viruses. Lipids provide a form of energy storage, like an electrical battery for an organism. Lipids are the metabolic precursors of hormones and signalling molecules in cells. Lipids regulate, often in specific ways, the functionality of biological membranes. A nearly uncountable catalogue of lipid molecules is found in nature, their individual structures imparting a wide variety of properties essential to the structures and functions of lipids in life.

Key concepts:

The hydrophobic effect, which governs the behaviour of hydrocarbons in water, controls the structures formed by lipids.

Phospholipids, as well as many other lipids, spontaneously form bilayer structures when confronted with water, in accordance with the hydrophobic effect.

Lipid bilayers provide the fundamental architecture of biological membranes.

Lipid bilayers determine many of the properties of biological membranes including their limited permeability.

Thousands of different lipid species are found in biological membranes, but a classification system emphasizes the similarities in specific classes.

Unsaturation in the hydrocarbon chains of lipid bilayers supports the liquid crystal state of bilayers in biology, essential to the proper functioning of membrane enzymes.

Membrane bilayers are highly anisotropic and their dynamics determine further the properties of the membranes.

Although bilayers are inherently stable, defects in bilayer structure are required to initiate critical membrane fusion events.

Membrane lipids play biological roles in membrane biology as well as structural roles.

In biological membranes, lipids are generally asymmetrically distributed across the bilayer.

Some lipids are second messengers in intracellular signalling systems.
Glycerophospholipids
Authors: Farooqui Akhlaq A 
Published: September 2009

Abstract

Glycerophospholipids are derivatives of
sn
‐glycero‐3‐phosphoric acid. They contain an
O
‐acyl or
O
‐alkyl or
O
‐alk‐1′‐enyl residue at the
sn
‐1 position and an
O
‐acyl residue at the
sn
‐2 position of the glycerol moiety and are defined on the basis of the substituents on the phosphoric acid at the
sn
‐3 position. Glycerophospholipids are asymmetrically distributed between the two bilayers. They not only constitute the backbone of cellular membranes but also provide the membrane with a suitable environment, fluidity and ion permeability. They are synthesized at the endoplasmic reticulum and are transported to other membranous structures by phospholipid exchange and transfer proteins. Once glycerophospholipids are laid down in a biomembrane, they undergo interconversion reactions (base exchange, methylation and decarboxylation). These reactions and activities of phospholipases may be responsible for the turnover, compositional maintenance and rearrangements of glycerophospholipids in membranes. This process results in the modulation of membrane function. Glycerophospholipids are multifunctional molecules. They are precursors for second messengers. In addition, they may be involved in membrane fusion, apoptosis and regulation of the activities of membrane‐bound enzymes and ion channels.
Arabidopsis
: Flower Development and Patterning
Authors: Krizek Beth A 
Published: September 2009

Abstract

The development of flowers and floral organs is directed by intricate genetic programmes, many aspects of which appear to be shared among all angiosperms. Early acting genes establish floral meristem identity in lateral organ primordia initiated at the periphery of the shoot apical meristem. Later, floral organ primordia arise at precise positions within these floral meristems and take on one of the four distinct identities (sepals, petals, stamens and carpels). A simple model (ABCE model), supported by both molecular and genetic experiments in

Arabidopsis

, explains how a small number of regulatory genes act in different combinations to specify these different organ types. These regulatory genes encode transcription factors that control the expression of many target genes responsible for organogenesis.

Key concepts

Lateral organs produced by the shoot apical meristem during reproductive development acquire their identity as flowers through the action of floral meristem identity genes such as
LEAFY
and
APETALA1
.

The identities of each of the four organ types of a flower (sepal, petal, stamen and carpel) is conferred by a unique combination of floral organ identity gene activities, referred to as class A, B, C and E in the ABCE model.

The activities of the class A, B, C and E genes are restricted to particular regions within a developing flower primarily, but not exclusively, through transcriptional regulation.

The proteins encoded by the class A, B, C and E genes encode transcription factors that form multimeric transcriptional regulatory complexes that control the expression of distinct sets of genes.

Many aspects of the genetic programmes conferring floral meristem identity and floral organ identity are conserved among all angiosperms.
Cleavage and Gastrulation in Mouse Embryos
Authors: Papenbrock Tom , Wild Arthur E , Fleming Tom P 
Published: September 2009

Abstract

After fertilization of the mammalian oocyte, the developmental programme leading to the conceptus begins with the early cleavage divisions. Lineage differentation begins after the early and mammal‐specific event of compaction and continues throughout development of the blastocyst. This structure, unique to mammals, after implantation will give rise to the various embryonic and extraembryonic tissues of the developing conceptus. Soon after implantation, the orientation of the main body axis becomes apparent with the primitive streak, and the node at its anterior end. Gastrulation through the primitive streak results in the formation and segregation of the three germ layers and the establishment of the basic body plan of the developing fetus. Finally, we compare mammalian early development to other vertebrates.

Key concepts:

Being higher animals, the early development of mammals prepares for and culminates in the generation of three tissue layers by gastrulation.

Many aspects of early mammalian development are shared with fellow amniote animals (reptiles and birds) and even with anamniote vertebrates (e.g. amphibians).

Mammals have however evolved specific adaptations to development in the mother's womb, in particular with regard to early stages of development and the role of the extraembyronic tissues.
Immunological Tolerance: Therapeutic Induction
Authors: Anderton Stephen M 
Published: September 2009

AbstractWhen the natural mechanisms of immune tolerance breakdown, autoimmune or allergic disease can result. There is considerable experimental evidence that the ultimate response to antigen, full immunity or tolerance, is dependent on the activation status of the antigen presenting dendritic cells, with those in steady state inducing tolerance. Current therapeutic options either deplete immune cell populations, interfere with immune cell trafficking to the tissues or inhibit inflammatory cytokine function or lymphocyte signalling. Although these treatments can be effective for certain diseases, they carry with them significant adverse effects and it is unlikely that they induce true, long‐lived immune tolerance. Cellular therapies using either tolerogenic dendritic cells, or regulatory T cells may be able to achieve this. Alternatively, administration of antigen in tolerogenic form can provide the most specific therapy, with the least risk of adversely affecting normal immune function against infection or neoplasia.Key conceptsPeripheral tolerance mechanisms consist of lymphocyte apoptosis, anergy and regulation.Current therapeutic options for the clinic can be effective, but in general are nonspecific and may not provide long‐term tolerance.Dendritic cell (DC) activation status determines the type of immune response. Activated DC provokes immunity whereas steady state DC promotes tolerance.‘Tolerogenic’ DC can be administered to give protection from rodent models of autoimmune disease, allergy and graft rejection.Administration of antigen in tolerogenic form (without adjuvant) also provides protection from disease models.Transfer of antigen‐specific regulatory T cells can also protect against disease, and can be curative in some models.Translation of cellular therapies (using DC or regulatory T cells) or tolerogenic antigen will require a fuller understanding of the critical autoantigens/epitopes that drive autoimmune pathology.
Phloem Structure and Function
Authors: Schulz Alexander , Thompson Gary A 
Published: September 2009

AbstractThe phloem collects photoassimilates in green leaves, distributes them in the plant and supplies the heterotrophic plant organs (e.g. fruits, buds and roots). Phloem structure is specialized for loading, long‐distance transport and unloading of assimilates. The conducting cells, called sieve elements, are highly modified to create a low‐resistance pathway composed of contiguous living cells, whose long‐term viability is maintained through an intimate association with companion (or Strasburger) cells. The difference in turgor pressure that is generated by osmotically active assimilates within this living conduit is the physical force that drives long‐distance transport through sieve elements. Plant species have evolved a variety of strategies to generate and maintain turgor pressure between source tissues, where assimilates are synthesized or released, and sink tissues, where assimilates are utilized or stored. Signalling molecules accessing the phloem are swept along with assimilates and trigger important growth processes such as flowering.Key conceptsLong‐distance transport of assimilates occurs from source to sink, that is, from the green leaves, which produce a surplus of assimilates to the plant organs which consume assimilates.The conducting cells are the sieve elements in the phloem which offer a low‐resistance pathway, characterized by a reduced cytoplasm and sieve pores in the connecting cell walls.Reduction of the sieve‐element cytoplasm is accompanied by a dependency of sieve elements on neighbouring cells, called companion cells in angiosperms, and Strasburger cells in gymnosperms, that hold the sieve elements alive.The mechanism of phloem transport is based on a high sugar concentration in the sieve element‐companion cell complexes of source leaves, which osmotically builds up a high turgor pressure.Accumulation of sugars in the source phloem is called phloem loading and depends either on sucrose transporters in the plasma membrane of sieve‐element companion cell complexes, or enzyme activity in the companion cells of the source phloem.Phloem transport is utilized for signal transport, including rapid electropotential waves, mobile noncodingribonucleic acids(RNAs) and mobile transcription factors that are responsible for wound responses and developmental switches in the target tissue.
Ion Motive
ATPases
:
P
‐type
ATPases
Authors: Shin Jai Moo , Sachs George 
Published: September 2009

Abstract

Regulation of ions such as calcium, sodium and potassium ions is very important for cell life. One of ion‐regulating enzymes is classified as ion motive
adenosine triphosphatase
(
ATPase
). Ion motive
ATPases
exchange two different ions across the membrane at the expense of ATP energy. The Ca
2+
‐
ATPase
transports Ca ion in exchange for H ion; the Na
+
/K
+
or H
+
/K
+
ATPase
transports Na ion or hydronium ion from the cytoplasmic region to the exocytoplasmic region with the exchange of K ion from the exoplasmic domain to the cytoplasmic domain. The Ca
2+
‐
ATPase
has single catalytic subunit. The Na
+
/K
+
and H
+
/K
+
ATPases
consist of two subunits α and β. The α subunit is the catalytic subunit, having 10 transmembrane domains. The β subunit is a glycosylated protein.

Key concepts

Ion motive ATPases

P‐type ATPase transport ions across the membrane

Regulating ion concentrations.
Plasmodesmata
Authors: Faulkner Christine R , Oparka Karl J 
Published: September 2009

AbstractPlasmodesmata are plasma membrane‐lined pores that span the adjoining walls of plant cells. They permit the intercellular passage of molecules and signals and play a central role in plant physiology and development. Plasmodesmata are also conduits through which viral genomes spread during infection, and many viruses encode movement proteins that modify plasmodesmata, facilitating the intercellular trafficking of macromolecules. Recent evidence suggests that many endogenous plant proteins and systemicribonucleic acid(RNA)‐based signals also utilize plasmodesmata for cell‐to‐cell and long‐distance movement. It appears that the substructural morphology of plasmodesmata is central to their role in cell‐to‐cell communication, allowing them to function as controllable ‘valves’ that regulate the intercellular passage of molecules.Key ConceptsPlant cells are connected to each other by cytoplasmic bridges called plasmodesmata. The continuous interconnected cytoplasm in plants is referred to as the symplasm.A tube of endoplasmic reticulum passes though plasmodesmata and connects the endoplasmic reticulum of neighbouring cells, thus providing endomembrane continuity between cells.Primary plasmodesmata are formed at cytokinesis when strands of endoplasmic reticulum are trapped between fusing vesicles in the developing cell wall.Secondary plasmodesmata are formed across existing cell walls, including those at graft unions, and usually arise immediately adjacent to existing plasmodesmata.Molecules smaller than the size exclusion limit (SEL) of plasmodesmata are able to move freely through the cytolplasmic channel of plasmodesmata by simple diffusion.The SEL of plasmodesmata may increase or decrease to allow changes in plasmodesmatal conductance. This may occur under different conditions, for example, in response to intracellular factors such as cytoplasmic calcium levels or in response to changes in turgor pressure between cells.Some endogenous proteins and some movement proteins encoded by plant viruses are able to increase the SEL of plasmodesmata to facilitate their own passage into neighbouring cells. This enables these proteins to function in cells in which they are not normally expressed.Regions of cells may be connected by plasmodesmata that share an SEL different to the SEL of neighbouring cells. These regions of cells are called symplasmic domains.Some proteins and RNA molecules pass into the plant's translocation stream and move over long distances. These macromolecules traffic through the plasmodesmata that join sieve elements (SE) and companion cells within the phloem. These macromolecules may have a site of action distant to their site of expression and synthesis.
Plant Microtubules: Their Role in Growth and Development
Authors: Lloyd Clive W 
Published: September 2009

Abstract

The close association of cortical microtubules with cell walls is a characteristic of immobile plant cells. In interphase, the cortical array helps organize the cell wall and before division is replaced by a narrower preprophase band that forecasts where the new cross‐wall will be attached after mitosis. The mitotic spindle is essentially similar to the general eukaryotic model but the lack of centrosomes at the poles means that the plant spindle looks different, having broader poles and reduced astral microtubules. During cytokinesis, the rigid cellulose‐rich wall does not contract inwards to separate the divided chromosomes; instead, a new cross‐wall is laid down by a ring of phragmoplast microtubules that expands outwards until it fuses with the parent wall at the site predicted by the preprophase band. In plants, microtubules therefore have a particularly direct connection with morphogenesis.

Key concepts:

Plant cells are immobile – their shape held by a cellulose‐rich cell wall.

The passive entry of water into the vacuole generates the turgor pressure that drives cell expansion.

The direction of cell expansion is regulated according to the way that inelastic cellulose microfibrils are oriented in the cell wall.

Cortical microtubules attached to the cytoplasmic face of the plasma membrane channel the movement of the enzyme complexes as they extrude cellulose microfibrils into the wall.

Plant microtubules are highly dynamic, moving by a modified form of treadmilling in which new tubulin subunits are added at one end, as other subunits are lost from the opposite end.

The cortical array of microtubules arises out of the self‐organization of microtubules that emerge from multiple, scattered nucleation sites.

The plane of cell division is forecast by the preprophase band. This transient, cortical structure contains microtubules, actin, endoplasmic reticulum and Golgi vesicles.

In higher plants, which have no centrioles, the mitotic spindle has broad poles and few astral microtubules.

The cytokinetic apparatus, the phragmoplast, is comprised of two interdigitating circlets of microtubules and actin filaments. Golgi vesicles are directed to the line of overlap to deposit the cell plate.

The new cross‐wall grows out centrifugally, like a ripple in a pond, until it contacts the parental wall previously marked by the preprophase band.
Bone Homeostasis: Extracellular Calcium Levels and Their Control
Authors: McDonald Fraser 
Published: September 2009

AbstractCalcium (Ca2+) is an essential ion within the human body. It is an extraordinary ion whose homeostasis is controlled and managed by many organs (bone, intestine, kidney, skin and thyroid). For a student, Ca2+is a clear example of the complexities of biological control and understanding these basic principles is a very sound foundation for understanding other biological control mechanisms. The ion is responsible for the correct coordination of many functions and constitutes a large part of the inorganic component of the skeleton in the form of hydroxyapatite crystals. Calcium levels are kept within a specific range, regulated principally by three hormones – parathyroid hormone, calcitonin and cholecalciferol (vitamin D3) – although other paracrine substances can have a major effect. Excessive variations can lead to abnormalities of nerve function and porous bones (hypocalcaemia) or pathological calcification (hypercalcaemia).Key conceptsCa2+is a unique ion maintaining both the independent functional capacity of the organism being part of the rigid endoskeleton and having unique qualities controlling, very precisely, cell function.Its characteristic role at cellular level can not only control ‘immediate’ cellular events such as exocytosis and contraction but it can also influence genetic effects in the longer term.As an ion whose serum levels are controlled closely it demonstrates clearly basic principles of homeostasis that can serve as a foundation for understanding control of other ions/metabolites.The control of serum Ca2+demonstrates very clearly the interaction of several systems that are required to function correctly.