bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolating Mechanisms
Authors: Butlin Roger K
Published: April 2013

Isolating mechanisms are intrinsic characteristics of species that reduce or prevent successful reproduction with members of other species. Viewed genetically, they are characters that act as barriers to the exchange of genes between populations. Most of these barriers are incidental consequences of divergence between populations but they can be elaborated by natural selection. They can take many forms, from mismatches between mating signals and preferences to genetic incompatibilities causing sterility of hybrids. A major outstanding challenge is to document the contributions of different forms of isolation to the overall barrier to gene exchange between species and to understand the order in which these barriers evolve.

Key Concepts:

Isolating mechanisms are intrinsic characteristics of species that reduce or prevent successful reproduction with members of other species.

Many, perhaps most, isolating mechanisms are incidental consequences of divergence between populations, not fashioned by selection for the purpose of preventing gene flow.

Individual barriers to gene exchange act sequentially, which means that early acting barriers tend to have the greatest effect even though they may not have been the first to evolve.

Ecological components of isolation evolve through adaptation to local conditions and may reduce the probability of mating or the fitness of hybrids.

Behavioural components of isolation prevent mating even when reproductively active individuals meet and may evolve due to sexual selection on mating signals and responses.

Barriers can occur after mating but before zygote formation. These barriers may be a side‐effect of evolutionary conflicts of interest between males and females.

Divergent populations accumulate genetic differences. Inevitably some of the new genes are incompatible resulting in isolation through reduced viability or fertility of hybrids, especially in the heterogametic sex.

We still need to know more about the range of barriers operating in individual species pairs, the reasons for their evolution and the order in which they evolved.
Ring Species and Speciation
Authors: Blackmon Heath , Demuth Jeffery P
Published: April 2013

A ring species is a monophyletic group whose range has extended around a geographic barrier to produce a ring‐shaped distribution. The populations that make up the ring should be contiguous and without barriers to gene flow anywhere in the ring except where the terminal populations are sympatric but reproductively isolated from one another. Few, if any of the species that have been described as ring species, actually meet all of these requirements. The best documented example of a species that exhibits all of these traits is the greenish warbler complex (Phylloscopus trochiloides). However, even species like the herring gull complex orEnsatinasalamanders that fail to exhibit some of the characteristics of a true ring species offer opportunities to study important evolutionary processes. These species are particularly helpful in understanding how microevolutionary changes can create two unique species, how speciation can occur in spite of gene flow, and how geographic speciation with or without adaptive divergence can occur.

Key Concepts:

Few organisms exhibit all of the requirements to be considered a true ring species.

Ring species are helpful tools that can be used to help elucidate evolutionary processes.

The preponderance of avian and mammal ring species may be an ascertainment bias.
Hybrid Zones
Authors: Kawakami Takeshi , Butlin Roger K
Published: April 2013

A hybrid zone occurs where two distinct genetic forms meet, mate and produce offspring with mixed genomes. Such zones may vary in width, length and patchiness, and are found between species, subspecies, races or forms. Stable hybrid zones may be maintained by selection against hybrids, environmental selection, or a combination of the two. A hybrid zone can arise either by direct environmental selection in contiguous populations or by renewed contact between previously isolated populations. Hybrid zones act as semi‐permeable barriers, which allow gene exchange for neutral or adaptive characters, whereas restricting introgression of alleles that contribute to local adaptation or reduced hybrid fitness. The study of genomic regions that experience barriers to gene flow can provide an important window for identifying specific genes and mutations that underlie reproductive isolation and local adaptation. With the help of recent technological advances in development of thousands of molecular markers, distributed genome‐wide, identification of such genomic regions is becoming possible in natural hybrid zones.

Key Concepts:

A hybrid zone is a narrow geographic region where two genetically distinct populations or species are found in close proximity and hybridise to produce offspring of mixed ancestry.

Hybrid zones are widespread, both geographically and across animal and plant taxa.

A hybrid zone is maintained by a balance between selection and dispersal.

Selective forces can be intrinsic (e.g. selection against less‐fit hybrids) or extrinsic (e.g. environment‐dependent selection).

Spatial analysis of allele‐frequency clines across a hybrid zone provides estimates of important population genetic parameters (e.g. selection, dispersal and linkage disequilibrium).

Surveys of differential gene flow across a hybrid zone have the potential to localise genomic regions that habour genes responsible for barriers to gene exchange.
Hybrid Speciation
Authors: Abbott Richard J , Rieseberg Loren H
Published: April 2013

Hybridisation between genetically divergent populations may lead to the formation of new evolutionary lineages. This may occur via the duplication of a hybrid's chromosome complement (allopolyploid speciation) or by the stabilisation of a fertile hybrid segregant (homoploid hybrid speciation). Although more common in plants, both modes of hybrid speciation also occur in animals, including fish, amphibians and insects. The successful origin and establishment of hybrid species is highly dependant on an ability to occupy novel and/or spatially isolated habitats, in order to escape the effects of competition and gene flow from parental species. This ability is favoured by the generation of genetic novelty resulting from the dramatic effects that hybridisation (and genome duplication in allopolyploids) have on modifying genome structure and gene expression. Examples of new allopolyploid and homoploid hybrid species originating within the last 200–300 years are important models for investigating processes involved in hybrid speciation and establishment.

Key Concepts:

Hybridisation between genetically divergent populations is promoted by habitat disturbance and may lead to the formation of new evolutionary lineages.

Hybrid speciation may occur via the duplication of a hybrid's chromosome complement (allopolyploid speciation) or by the stabilisation of a fertile hybrid segregant (homoploid hybrid speciation).

Allopolyploidy leads to instantaneous reproductive isolation between the allopolyploid neospecies and its parents, and is therefore an example of very rapid speciation.

Allopolyploidy is very common in higher plants, but less common in animals, although examples are known in insects, crustaceans, molluscs, fish, amphibians, reptiles and mammals.

Homoploid hybrid speciation is thought to be relatively rare, although an increasing number of homoploid hybrid species of animals, plants and fungi are being recognised using molecular markers.

Homoploid hybrid speciation can be completed within a few generations, although several hundred generations may be required before the genome of the hybrid neospecies is fully stabilised.

Considerable genetic novelty is generated in the early stages of allopolyploidy and homoploid hybrid speciation due to the marked effects that hybridisation (and genome duplication in the case of allopolyploidy) have on modifying genome structure and gene expression.

Such genetic novelty aids the establishment of hybrid neospecies in ecologically divergent habitats, thus reducing the likelihood of competition and crossing with parents.

Several examples are known of new allopolyploid and homoploid hybrid species originating within the last 200–300 years and these have become important models for investigating processes involved in hybrid speciation and establishment.
Coevolution: Plant–Insect
Authors: Whitney Heather M , Glover Beverley J
Published: April 2013

Coevolution between plants and insects is a relatively frequent phenomenon, in part because of the enormous species diversity of both groups. It is often diffuse, resulting in variability and radiation, and is presumed to result in unstable relationships. Coevolutionary relationships mainly occur between plants and herbivorous insects and between plants and pollinating insects. The mechanisms by which plants and insects interact and perceive each are very diverse, but can be broadly split into two categories: chemical and physical. Insects use a combination of chemical and physical cues to detect and discriminate plants, whereas plants manipulate both of these to either deter or attract insect visitors. These cues can be used either honestly (as warning of potential defences or to advertise offered rewards) or deceptively.

Key Concepts:

Plants and insects have coexisted and interacted for more than 350 million years.

There is a huge diversity of plant–insect interactions; the equally vast diversity of plant and animal species is thought to be due in part to the selective pressures arising from these interactions.

Mechanisms by which plant–insect interactions occur include both physical and chemical.

Multiple physical and chemical mechanisms may be involved in an individual interaction.

Selection has therefore occurred on multiple aspects of both plants and insects, including their morphology, biochemistry, development, sensory systems and life cycles.

Plant–insect relationships are not stable; mutualisms can shift to the detriment of either of the partners.
Functional Constraint and Molecular Evolution
Authors: Forsdyke Donald R
Published: April 2013

While having one or more specific functions, macromolecules have collective functions (e.g. Donnan equilibrium and aggregation pressure), and general functions (e.g. contribution to organism weight). Successful molecular evolution requires an appropriate balance between the constraints on these functions, which arise from selective pressures acting at the levels of conventional phenotypes (natural selection) and genome phenotypes (reprotypic selection). Genome‐wide constraints include fold pressure (nucleic acid stem‐loop extrusion pressure) and GC‐pressure (the pressure for a certain base composition). When these bring about within‐genome reprotypic selection (hybrid sterility), there is the potential for new species to emerge (speciation). Local constraints include protein pressure (the pressure to encode a protein) and purine‐loading pressure (purine‐richmessenger ribonucleic acid(mRNA) synonymous strands). As more pressures are identified, arguments for neutral evolution weaken.

Key Concepts:

Molecules have specific, collective and general functions.

Most macromolecules function by virtue of their higher ordered structure.

Nucleic acids have both structural and templating functions.

Each species achieves its own balance between the competing demands (constraints) of external and internal environments.

The organismal phenotype comprises the classical phenotype and the genome phenotype.

Natural selection operates on the classical phenotype.

Reprotypic selection operates on the genome phenotype.

By balancing natural and reprotypic selection mechanisms, the ‘hand of nature’ resolves conflicts between functions.
Allergy
Authors: Hodge Emily , Sayers Ian
Published: April 2013

Allergy is an exaggerated, hypersensitive immune response to innocuous environmental antigens, characterised by inflammation and mediated by immunoglobulin E (IgE) antibodies. Symptoms of allergy depend on the site of allergen contact and range from being uncomfortable (itching, sneezing and breathlessness) to serious (anaphylaxis). The development of allergy is due to environmental and genetic factors; the heritable component is known as atopy, defined as a predisposition to the overproduction of IgE. The prevalence of allergies such as hay fever (seasonal allergic rhinitis), eczema (atopic dermatitis) and asthma are increasing in Westernised societies. Antihistamines are the first‐line drug treatment for allergy; however, these often fail to alleviate all symptoms satisfactorily and are not clinically effective in asthma, illustrating the heterogeneity of allergic disorders. This has necessitated the development of alternative medication for asthma, which targets airway symptoms, for example, β2‐adrenergic receptor agonists. New, more effective therapeutic approaches are still required to treat allergic disease.

Key Concepts:

Allergy describes a variety of symptoms, which cause discomfort but can be life threatening.

Allergic symptoms are a defining feature of diseases such as hay fever, eczema, asthma and food allergy.

Atopy is a heritable trait (defined by elevated IgE or positive skin prick test), which predisposes an individual to allergic disease.

Allergies are becoming increasingly common in Westernised societies and represent a significant economic burden, but the reasons for this are not fully understood.

Recent improvements in technology have facilitated studies, which link genetic variants to atopy susceptibility, with confidence.

New therapeutics are needed to more adequately treat symptoms of allergic diseases such as hay fever, eczema and asthma.

Histamine is a key inflammatory mediator, the action of which might be targeted in new ways to treat the symptoms of allergic disease.
Macular Degeneration, Age Related
Authors: Zayit‐Soudry Shiri , Duncan Jacque L
Published: April 2013

Macular degeneration comprises a group of diseases characterised by progressive deterioration of the retinal photoreceptors, retinal pigment epithelial cells and underlying choriocapillaris, causing progressive central vision loss. The most common form of macular degeneration is age‐related macular degeneration (AMD), the leading cause of irreversible blindness among elderly patients in developed countries. Other types of hereditary early onset macular dystrophies share clinical characteristics with AMD, but a monogenetic basis for many of these conditions has been found. Recent advances in clinical and genetic research have led to a better understanding of the genetics and pathophysiology of AMD, which is currently viewed as a complex disorder in which multiple susceptibility genes combined with environmental factors play a role. The management of neovascular AMD has changed dramatically with the introduction of anti‐VEGF drugs, but treatment options for other types of macular degeneration remain limited because the aetiology and pathogenesis are incompletely defined.

Key Concepts:

Macular degeneration refers to a group of diseases characterised by photoreceptor cell degeneration and death leading to central vision loss.

Recent advances in Optical Coherence Tomography (OCT) technology has led to its major role in diagnosis and management of macular degeneration.

Monthly follow‐up of patients with neovascular AMD is recommended for best visual outcome.

Regular anti‐VEGF therapy with intravitreal injections of ranibizumab or bevacizumab is currently considered to be the standard treatment for neovascular AMD.

Ongoing clinical trials are investigating the efficacy and safety of combination treatments for neovascular AMD and treatments for other forms of macular degeneration.

Research efforts are directed at prevention of AMD and stem cell and gene therapy treatments for Stargardt disease.
Plant Waxes
Authors: von Wettstein‐Knowles Penny
Published: April 2013

Waxes, found primarily in the cuticle of vascular plants, prevent uncontrolled water loss. They comprise a diverse mixture of aliphatics, triterpenoids, flavonoids and/or phenolic lipids, such as, alkylresorcinols. Aliphatic carbon skeletons are fatty acid synthase (FAS) products extended by fatty acid elongase (FAE) enzyme complexes and type III polyketide synthases (PKSs) to 20–34 carbons +/– keto groups that serve as substrates for associated reductive, decarb and enoic pathways plus variants thereof. Study of
eceriferum
(
cer
) mutants, reverse genetic molecular approaches and biochemistry has lead to increasingly detailed biosynthetic pathways in
Arabidopsis
and the
Gramineae
. Nevertheless, many enzymes remain unidentified. How many FAEs and type III PKSs are specific for wax biosynthesis, that is, they do not also participate in other pathways such as sphingolipid biosynthesis, is unknown. Our knowledge is rudimentary, concerning regulation of biosynthesis or translocation of aliphatics during synthesis and thereafter from the endoplasmic reticulum into and onto the cuticle's aerial surface.

Key Concepts:

Epidermal cells synthesise waxes localised in and on the cuticle surface which protect against water loss.

Waxes include a very diverse collection of aliphatic compounds.

Primer substrates for waxes are synthesised by fatty acid synthase (FAS) in plastids.

FAS products are extended by fatty acid elongases (FAEs) and type III polyketide synthases (pkKCSs) to give skeletons with as many as 32 carbons.

Enzymes in associated pathways localised in the endoplasmic reticulum convert the long carbon skeletons into a broad range of compounds.

A handful of genes participating in biosynthesis of the waxes and their translocation within the epidermal cells have been cloned and characterised.

Some of the enzymes may also participate in synthesis of related aliphatics found in cutin, suberin and sphingolipids, for example.

Waxes may also include other compounds with long carbon skeletons such as phenolic lipids that function in defence against bacteria and fungi.
Protozoan Pathogens of Humans
Authors: Mehlhorn Heinz
Published: April 2013

Several protozoans are causes of important diseases that kill millions of animals and humans every year. In addition to known parasites, many so‐called opportunistic agents increase the infection risk, especially for immunocompromised people. Owing to the recent process in globalisation leading to a quick transportation of goods and people from one end of the world to the other, the chance for importation of agents of diseases has enormously increased. Thus new rush of epidemics or even pandemics will threaten overcrowded regions. This danger is furthermore supported by the phenomena of global warming, which lead to the further expansion of vectors of diseases. Therefore awareness is highly needed, if diseases should be recognised as early as possible.

Key Concepts:

Teaching in parasitology and epidemics must be strengthened at universities and governmental authorities.

Emergency plans have to be established to fight epidemics.

Research for new and better acting medicaments has to be strengthened.
Trypanosomiases
Authors: Gibson Wendy
Published: April 2013

The human trypanosomiases are vector‐borne tropical diseases that occur in tropical Africa and South America and are caused by parasitic protozoa. Human African trypanosomiasis (or sleeping sickness) is caused by two subspecies of

Trypanosoma brucei

and is transmitted by the bite of the bloodsucking tsetse fly. Chagas disease occurs in Latin America and is caused by

Trypanosoma cruzi

. This parasite is transmitted by triatomine bugs, which acquire infection by feeding on infected blood, but pass the parasites on to the next host

via

their infected faeces. The human trypanosomiases are zoonoses and a range of wild and domestic mammals can act as reservoir hosts for the parasites. There are no vaccines for these diseases and control relies on case treatment and limiting opportunities for transmission.

Key Concepts:

African human trypanosomiasis or sleeping sickness and Chagas disease in Latin America are caused by insect‐borne, parasitic trypanosomes, but the diseases and the parasite life cycles are completely different.

Control of the trypanosomiases relies on treatment of human patients and reduction of transmission, largely achieved through killing the insect vectors.

The human trypanosomiases are zoonotic diseases and a range of wild and domestic mammals act as reservoir hosts for the parasites.

Vector borne diseases with animal reservoirs have complex epidemiology and are difficult to control.

Eradication of human African trypanosomiasis in West Africa seems likely if current treatment, surveillance and tsetse control measures are maintained.

Animal reservoir hosts are more important in maintaining human trypanosomiasis in East Africa than West and Central Africa.

Eradication of Chagas disease is thwarted by the longevity of infection in humans and circulation of the parasite in a wide range of animal reservoir hosts.
Chromista
Authors: Sym Stuart D , Maneveldt Gavin W
Published: April 2013

The concept of chromists, at its most expansive, includes the heterokonts (stramenopiles), alveolates, rhizarians, heliozoans, telonemians, haptophytes and cryptophytes. There is mounting evidence that this grouping is not valid. Even in the narrowest sense (the heterokonts), chromists include very diverse forms, exhibiting a great variety of trophic mechanisms. This great diversity in form and feeding make it difficult to identify any unifying features, but molecular phylogenetic studies have shown that this group of organisms is indeed monophyletic. The distribution of morphological characters over reconstructed trees allows for the identification of potential synapomorphic characters that have been secondarily lost or modified across the group. These include a combination of mitochondria with tubular cristae; the biflagellate heterokont condition; and, if photosynthetic, then with chlorophyll c, girdle lamellae and four membranes around the chloroplast, the outer continuous with the nuclear envelope. Heterotrophy appears to be ancestral but is also occasionally a derived state from autotrophic forms.

Key Concepts:

There is no consistency in the ranking of the various eukaryotic taxa, making reference to particular forms and their relationships awkward.

Molecular studies, particularly over the last decade, indicate an ever‐increasing delimitation of the Chromista to include very diverse forms.

The chromalveolate theory, at the root of the concept of Chromista, has been fiercely debated and most recent evidence points to multiple independent events involving red algal endosymbionts in diverse eukaryotic hosts.

Even the original grouping of Chromista (heterokonts, haptophytes and cryptophytes) is tenuous, making it more sensible to equate chromists with the heterokonts (=stramenopiles).

Heterokonts enjoy robust support from molecular phylogenetic analyses, but there are no universal morphological and physiological characters.

The most universal character is the biflagellate condition of swimming cells, with one tinsel (hairy) and one smooth flagellum. The hairy flagellum is invested with two opposite rows of tri‐partite, tubular hairs that are responsible for reversing thrust.

Plastids of autotrophic heterokonts have consistent features, including two additional surrounding membranes (the periplastidial membrane and the RER), girdle lamellae and thylakoids stacked in groups of three.

The classification within the heterokonts also has a chequered history, but multigene phylogenetic analyses are providing a clearer idea of groupings.

Heterotrophic forms are rooted deeply in phylogenetic trees reconstructed using molecular markers, but some are secondarily derived from autotrophic forms.

Heterokonts play an important role both ecologically and economically.
Gymnodinium
and Related Dinoflagellates
Authors: Heimann Kirsten
Published: April 2013

Mounting molecular evidence and ultrastructural differences, in particular the type of apical groove and flagellar apparatus architecture, have provided sufficient evidence over the past decade to demand a revision of the dinoflagellate genus
Gymnodinium
, as it contained a complex assemblage of evolutionarily unrelated species. Consequently, the genus has now been split into four genera:
Gymnodinium
,
Akashiwo
,
Karenia
and
Karlodinium
. The only remaining harmful species within the genus
Gymnodinium
is

Gymnodinium catenatum

, a species that causes paralytic shellfish poisoning, and it was recently introduced into Australian waters via ship ballast water. The genus
Akashiwo
contains no toxic representatives, whilst the genera
Karenia
and
Karlodinium
are close sister lineages with both genera incorporating ichthyotoxic species. Many representatives form blooms and produce toxins thus providing valuable insight into fundamental phylogenetic and biochemical questions. Taxa assigned to these genera are known to be toxin producers of extreme importance to biomedicine.

Key Concepts:

Molecular data have led to substantial changes of classifications within the protists, to which the dinoflagellates belong.

Consequently, names of genera and species have changed many times, resulting in taxonomic confusion, particularly for researchers working in the field of ecology or environmental monitoring.

The former genus
Gymnodinium
has long been recognised to be polyphyletic.

Molecular data and ultrastructural details, such as the type of apical groove and flagellar apparatus architecture, have resulted in a reclassification of the former genus
Gymnodinium
.

Taxonomic revision resulted in splitting the former genus
Gymnodinium
into four genera:
Gymnodinium
,
Akashiwo
,
Karenia
and
Karlodinium
.

Additional revision of the genus
Gymnodinium sensu
Daugbjerg
et al.
(2000) might be necessary, which would transform the very large and species‐rich former genus
Gymnodinium
into one of the smallest.

Irrespective of the reclassification, many of the organisms within these four genera form harmful algal blooms and produce toxins that can affect invertebrates, lead to fish mortality and can severely affect human health.

Some of the toxins produced have been used successfully in biomedical research, which helped to elucidate the mechanisms that control operation of the voltage‐gated sodium channel.

Blooms by these organisms lead to large economic losses for shellfish aquaculture, in particular blooms by
Gymnodinium catenatum
, whose toxins induce paralytic shellfish poisoning, which may result in human death.

The expansion of the aquaculture industry, shellfish and fish trades around the globe, and climate change‐induced range expansions, as well as introduction via ships’ ballast water to nonendemic areas require an efficient monitoring system for dinoflagellate toxins and harmful algal blooms.
Paramecium
Authors: Aufderheide Karl J
Published: April 2013

Members of the genusParamecium(from the classical Greek, παραμηκησ, oblong or oval‐shaped) are ciliated protozoa with an elongated shape (length approximately three to four times the width), a uniform distribution of cilia over the cell surface and a ciliated oral groove leading from the anterior of the cell to a midventral deep oral cavity. The oral apparatus is shaped like a funnel, with 12 rows of oral cilia in a helical array inside. Each cell has two distinct types of nuclei: one large, transcriptionally active, polycopy macronucleus and one or more small, transcriptionally inactive micronuclei. Many features make paramecia favourable organisms for the study of many cellular/developmental/genetic aspects of cells. Their large size allows microscopic observations as well as microinjections and cell surgery. They show Mendelian and non‐Mendelian inheritance, and several different epigenetic inheritance patterns. The genome ofParamecium tetraureliahas been sequenced and is available for analysis.

Key Concepts:

Species ofParameciumare distributed worldwide in freshwater habitats and are easy to cultivate in the laboratory.

Morphological differences are not enough to distinguish some species ofParamecium.

The genomes of the macronucleus and micronucleus are not identical, even though both are derived from the same zygote nucleus.

The genome ofParamecium tetraureliahas been sequenced; 40 000 genes have been identified.

Paramecia do not use two of the three ‘stop codons’ for translation termination.

The trichocysts of paramecia are examples of a regulated exocytotic process.

The cortex of the cell contains the cilia, basal bodies and associated accessory structures.

Paramecia can carry a number of different types of endosymbiotic organisms.
Tetrahymena
Authors: Coyne Robert S
Published: April 2013

Tetrahymena
is a genus of mostly free‐living ciliated protozoa that is intensively employed to investigate and solve fundamental problems in molecular, cellular and developmental biology. Like all ciliates,
Tetrahymena
contains separate germline and somatic nuclei, known as the micronucleus and macronucleus, respectively. The macronucleus is derived from a copy of the micronucleus through a process that involves extensive programmed whole‐genome rearrangement and is under intensive study. The most highly developed experimental model species is

Tetrahymena thermophila

, which can be readily manipulated using the tools of genetics, molecular biology, cell biology and biochemistry. Notable discoveries made using
Tetrahymena
include the structure of telomeres and telomerase, self‐splicing RNA, the first microtubular motor and the link between histone acetylation and gene regulation. The approximately 104 Megabase macronuclear genome of

T. thermophila

has been sequenced and annotated; the micronuclear genome sequence will be completed soon.

Key Concepts:

Tetrahymena
are large, elaborate eukaryotic cells with many experimental advantages and well‐suited to the study of cellular structure, division and development.

Tetrahymena
have been studied for nearly a century and been the source of a number of groundbreaking discoveries.

A characteristic feature of
Tetrahymena
, and the basis of much biological interest, is the separation of germline and somatic genetic functions into separate nuclei.

Programmed genome rearrangement in
Tetrahymena
shares common mechanistic features with heterochromatic gene silencing in other eukaryotes.

Applying the modern tools of genomics and proteomics has facilitated research with
Tetrahymena
and opened up new areas of investigation.
Trypanosoma
Authors: de Souza Wanderley
Published: April 2013

The trypanosomes comprise a large number of species of pathogenic protozoa of animals and plants. Some present a simple life cycle in the insect; others, however, present a complex life cycle involving vertebrate and invertebrate hosts, with the participation of different developmental stages, some of which are localised within cells of the vertebrate host. These organisms present some characteristic features such as the presence of the kinetoplast, a highly specialised organisation of mitochondrial DNA, compartmentalisation of the glycolytic pathway in glycosomes, the presence of a network of filaments forming the paraflagellar rod connected to the flagelar axonme.

Key Concepts

Ideally the identification and classification of protozoa shall combine the use of classical taxonomic parameters with phylogenetic analysis.

Despite significant advances in biomedical sciences diseases caused by protozoa still constitute important health problem throughout the world.

Cell transformation in response to environmental factors is fundamental for parasitic protozoa survival both in the vertebrate and invertebrate hosts.

Intracellular parasites developed the ability to attach to host cell surface and to trigger various mechanism leading to their internalisation into the cells.

Endocytosis in protozoa of the Trypanosomatidae family is a highly polarised taking place only in the flagellar pocket and the cytostome.

In some protozoa the glycolytic pathway does not take place in the cytosol but is compartmentalised in an organelle known as glycosome, which is part of the family of organelles designated as peroxisome.

Protozoa of the Trypanosomatidae family may contain up to 30% of the total DNA concentrated in a special region of its unique mitochondrion, localised close to the origin of the flagellum, and known as the kinetoplast.
Cryptomonads
Authors: Clay Brec L
Published: April 2013

Cryptomonads are a group of unicellular, biflagellate protists occurring in a variety of aquatic habitats. Several nonpigmented forms exist but the vast majority bear plastids containing chlorophylls
a
and
c
, and accessory pigments known as phycobiliproteins. Plastids of cryptomonads are derived from a secondary endosymbiotic event involving the engulfment of a unicellular red alga, its retention as an endosymbiont, and its conversion into a photosynthetic organelle. Unique features of cryptomonads include the cell covering termed a periplast, the surface architecture consisting of a furrow and/or gullet, extrusive organelles called ejectisomes, and the presence of a reduced eukaryotic genome known as the nucleomorph. Accurate identification of cryptomonad species using light microscopy is problematic owing to the range of morphological plasticity and the presence of two distinct morphotypes in certain species. In addition to traditional morphological characters, proper diagnosis of species cannot exclude molecular data.

Key Concepts:

Accurate identification and estimation of cryptomonads from field samples requires counting cells in the living state.

Proper characterisation of cryptomonad periplast plates requires use of quick‐freezing and freeze‐fracture techniques.

Accumulating karyotypic data continues to provide insight into the genetic variability of nucleomorph genomes, which may prove systematically significant.

Cryptomonad biliproteins all derive from an ancestral phycoerythrin, which has since evolved into at least seven spectral types.

Morphological species concepts are problematic given the increasing awareness of morphological plasticity and dimorphisms among cryptomonads.

Resolution of the large‐scale phylogentic affinities of cryptomonads remains tenuous and additional molecular analyses are required.
Rhizopoda
Authors: Anderson O Roger
Published: April 2013

Rhizopoda are a broad group of protozoan amoeboid organisms placed in the kingdom Protista. They include the naked and testate amoebae, some members of the slime moulds and foraminifera. The latter are almost exclusively marine organisms, either benthic or planktonic. Locomotion is by extension of pseudopodia of varied morphology that are specific to the taxonomic group. Pseudopodial morphology includes broad and fan‐shaped anterior extensions, finger‐like tubular extensions, or a web‐like network, the latter are called rhizopods. The shape of the pseudopodia, and the morphology of the enclosing shell or test, when present, are major defining taxonomic characteristics. The Rhizopoda are important aquatic and terrestrial protozoa at the base of food webs and thus provide a major link in the transfer of energy to higher order consumers. Some are capable of preying on fungi (e.g. large mycophagous amoebae) or other protists and in some cases small invertebrates (e.g. foraminifera).

Key Concepts:

The shape and organisation of pseudopodia are among major characteristics used to classify members of the Rhizopoda.

However, pseudopodial shape is not a conservative feature; and additional evidence, including fine structure and molecular genetic data, is needed to create a natural classification scheme.

The diversity of Rhizopoda is broad, including a wide range in size from small naked amoebae (several microns) to foraminifera (up to several millimetres or larger).

Many of the Rhizopoda are free‐living, forming important links in food chains, but others are parasitic or infectious, including some human pathogens (e.g.
Entamoeba histolytica
).

Some aquatic Rhizopoda, among them at least one amoeba and some foraminifera, form algal symbioses, including associations with green algae and dinoflagellates.

The foraminifera and some testate amoebae, bearing mineralised shells or skeletons, settle into aquatic sediments when they die and contribute to the palaeontological record of life and the environment over vast geological time periods.
Antimicrobials Against Streptococci, Pneumococci and Enterococci
Authors: Donabedian Susan , Shoyinka Adenike
Published: April 2013

Streptococci, pneumococci and enterococci are Gram‐positive bacteria, which cause significant morbidity and mortality in humans, and can also reside in their human host without causing disease. Streptococci are usually classified by their haemolytic reactions (beta‐, alpha‐ and nonhemolytic) or Lancefield antigen groups A, B, C, F, G and L. Enterococci were actually once classified as Group D streptococci, but as a result of chemotaxic and molecular studies are now considered to be a separate genus. Although effective antibiotic treatments exist, threats to public health are posed by antibiotic‐resistant strains of these bacteria. Organisms can be intrinsically resistant to antibiotics or can become resistant through acquisition of mutations or genes, which render a particular antimicrobial agent ineffective in killing or suppressing the organism. This article will describe diseases caused by streptococci, pneumococci and enterococci, and discuss the antimicrobial agents used to combat infections with these organisms.

Key Concepts:

Streptococci, pneumococci and enterococci are extremely common among humans and are capable of causing a wide range of disease.

Group A streptococci cause millions of skin and throat infections per year and are especially common in school‐aged children.

Group A streptococci are usually easily treatable but may become invasive causing serious disease or death.

Group B streptococci are a major cause of morbidity and mortality in newborns, however rigorous screening and prophylactic treatment of pregnant women, and monitoring and treatment of infections in newborns have radically reduced Group B streptococcal disease.

Pneumococci are the leading cause of community‐acquired pneumonia and otitis media.

Enterococci are a frequent cause of nosocomial infections and are usually multiply resistant to antimicrobial agents.

Antimicrobial resistance in streptococci, pneumococci and enterococci is a major healthcare problem worldwide, illustrating the need for development of effective agents against these organisms and prudent use of all antibiotics.
Functional Genomics in Plants
Authors: Helliwell Chris
Published: April 2013

The first complete plant genome sequence to be determined was that of the model plant

Arabidopsis thaliana

, which was published in 2000. This was followed by the first drafts of the rice genome sequence in 2002. Since the publication of these landmark genomes, the development of high throughput sequencing technologies has reduced the time and cost of obtaining genome sequences to a fraction of that required a decade ago. This has enabled the sequencing of many plant genomes and thus a vast amount of genome sequence information is available to the researcher. The goal of functional genomics is to determine how these genome sequences generate plant phenotypes. The focus of most functional genomics research is to determine the function of all the genes involved in a particular process. To achieve this, functional genomics uses techniques and analyses that can survey the entire complement of genes in a genome. This chapter discusses the most commonly used functional genomics methods.

Key Concepts:

Advances in sequencing technologies are making entire genome sequences relatively easy to obtain.

The goal of plant functional genomics is to understand how the genome generates the phenotype of the plant.

Comparison to other gene sequences can often identify a likely function for a gene.

Array and sequencing based methods can be used to show where and when all the genes in an organism are expressed.

Gene function can be determined by knocking out or reducing gene function and can be achieved by insertion, chemical mutagenesis or RNAi.

High throughput methods using recombination‐based cloning enable many tests of gene function to be applied on a genome‐wide scale.
Apomixis
Authors: Koltunow Anna
Published: April 2013

Seeds contribute significantly to world food supply. Flowering plants mainly produce seeds by sexual reproduction, which is a driver of genetic diversity. The combination of meiosis during male and female gamete formation, and subsequent gamete fusion at fertilisation in the ovule of the flower to form the embryo compartment of the seed, leads to segregation of parental alleles in seedling progeny. A second fertilisation event generates the endosperm, a nutritive tissue supporting embryo growth and seedling germination. Remarkably, some flowering plants form seeds asexually by apomixis. Apomixis comprises an ensemble of developmental processes that together alter female reproductive functions in the ovule, converting the sexual programme to an asexual one. The result is that the apomictically derived embryo develops solely from cells in maternal ovule tissues and therefore seedling progeny are genetically identical to the mother. Apomixis is largely absent in important food crops. Harnessing apomixis as a technology in plant breeding would increase food yield and security.

Key Concepts:

Apomixis is an asexual mode of seed formation that produces clonal progeny with a maternal genotype. It primarily influences reproductive events in the ovule of the flower.

Apomixis is absent in major crops, however, deployment of apomixis as a crop‐breeding tool would economically maintain hybrid vigour that is currently lost in successive seed generations.

Apomixis comprises three developmental components that deviate from the normal sexual pattern: avoidance of meiosis during egg cell development, fertilisation‐independent embryo formation, and generation of viable endosperm with or without fertilisation.

Angiosperms exhibit two mechanistically different types of apomixis termed sporophytic and gametophytic.

Sporophytic apomixis involves direct formation of an embryo from a diploid somatic (nonsexual) ovule cell, and a viable seed forms when the adjacent sexual gametophyte is fertilised and forms endosperm.

Gametophytic apomixis involves formation of a meiotically unreduced (i.e. diploid) female gametophyte, followed by embryo formation from the diploid egg by parthenogenesis (i.e. without fertilisation).

In gametophytic apomixis, endosperm formation may occur autonomously (i.e. without fertilisation) or pseudogamously (i.e. in response to fertilisation of the central cell).

Most apomicts retain the ability to produce some seed via sexual reproduction and studies in some apomicts indicate sexual reproduction is the default reproductive mode on which apomixis is superimposed.

Apomixis is controlled by dominant loci and those controlling the avoidance of meiosis and fertilisation‐independent embryo development are genetically separable in some species and tightly linked in others.

Apomixis loci are proposed to recruit or hijack the sexual machinery in ovule cells undergoing apomixis, modifying the timing of the sexual programme so that meiosis and fertilisation are avoided leading to asexual seed formation.
Roots and Root Systems
Authors: Kerk Nancy M , Sussex Ian M
Published: April 2013

Roots, together with stems and leaves, constitute the major organs of vascular plants. The main functions of the root system are to anchor and support the plant; to seek out, absorb and transport water and ions from the soil; and to transport and store the products of photosynthesis from the shoot system. Each root can be arbitrarily subdivided into several zones each with different functions: the apical zone of cell division, the source of all cells in the root; zone of cell elongation; zone of cell differentiation; zone of cell maturation. A root system is achieved by branchng of the primary root to produce one or more orders of lateral roots. Root hairs are epidermal enations that are functional in water and ion uptake and are an entry site for nitrogen‐fixing bacteria.

Key Concepts:

Roots, stems and leaves are the major organs of vascular plants.

Total extent of the root system usually greatly exceeds that of the shoot system.

The root apical meristem contains self‐perpetuating cells, now called stem cells, whose mitotic products differentiate into the cell types of the root.

Root tissues are arranged in concentric cylinders from the exterior inward are epidermis, cortex, endodermis, pericycle and vascular tissue consisting of alternating of bands of phloem and xylem.

Lateral roots are initiated in acropetal sequence from the pericycle tissue.

Adventitious roots are initiated in response to wounding or other environmental stimuli and disrupt the sequence of lateral root initiation.

Tropistic responses of roots to environmental stimuli such as gravitropism, phototropism, thigmotropism and hydrotropism are regulated by internally produced hormones such as auxin, ethylene and abscisic acid.

Root–microbial interactions result in formation of nitrogen‐fixing root nodules or mycorrhizal associations that are important in phosphorous uptake.
Bark
Authors: Lev‐Yadun Simcha
Published: April 2013

Bark comprises all the tissues outside the vascular cambium of a vascular plant. The majority of the bark of woody plants develops from three meristems: the vascular cambium that gives rise to the secondary phloem, the phellogen that gives rise to the cork and the dilatation meristem that produces parenchyma cells to prevent cracking when the axis increases in diameter. Bark tissues have a critical role in defending plants from pathogens and herbivores through their physical and chemical properties. They also defend from environmental hazards such as sun irradiation, desiccation, wind, flooding, hail, snow and even fire by forming a thick cork layer. The bark has a critical role in storage and transport of organic molecules and in many plants the bark also contributes to photosynthesis. Many of the various defensive and toxic substances found in barks are used by humans as medicines, spices and for various industries. Gene exploring in barks is expected to result in many beneficial molecules for agriculture, medicine, food and industry.

Key Concepts:

Bark comprises all the tissues outside the vascular cambium of a vascular plant.

The majority of the bark of woody plants develops from three meristems: the vascular cambium that gives rise to the secondary phloem, the phellogen that gives rise to the cork and dilatation meristem that produces parenchyma cells to avoid cracking when the axis increases in diameter.

The formation of the bark is regulated by several plant hormones, mainly auxin, ethylene, jasmonates and gibberellin.

After wounding the induced rise in the hormones ethylene and jasmonic acid induces the formation of defensive cork and traumatic resin or gum ducts in many species.

The bark functions in storage, transport and defence from herbivores, pathogens and environmental stresses.

Many bark products (e.g., fibres, food, medicine, resins, rubber, pigments and cork) have been used by humans since antiquity.