bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rhizopoda
Authors: Anderson O Roger 
Published: April 2013

Abstract

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

Abstract

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

Abstract

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

AbstractSeeds 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

Abstract

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

AbstractBark 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.
Sclerenchyma
Authors: Jarvis Michael C 
Published: April 2013

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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.