bluuebunny/crossref_metadata_2025 huggingface dataset:
Transport of Oxygen and Carbon Dioxide in Body Fluids
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter discusses the transport of oxygen and carbon dioxide in body fluids. It also introduces the concept of acid-base physiology and shows how this focuses on the regulation of pH and the functions of respiratory pigments in animals. Haemoglobins, haemocyanins, haemerythrins, and chlorocruorins, also known as the four chemical categories of respiratory pigments, resemble the properties of the enzyme proteins. The chapter mentions the oxygen equilibrium curve as a key tool for understanding the function of a respiratory pigment. It also explores the process of carbon dioxide transport by acknowledging the other chemical forms in which carbon dioxide exists in the blood.
Water and Salt Physiology
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter provides an overview of water and salt physiology. It explores the importance and relationships of animal body fluids, citing that body fluids represent 60% of the body weight of adult humans and mature animals. Some animals regulate the composition of their blood plasma through osmotic regulation, ionic regulation, and volume regulation. The chapter then details the living habitat of animals in natural aquatic environments and natural terrestrial environments. The specific composition of food and drinking water often has major implications for the water-salt physiology of animals living in their natural environments. The chapter looks at the case of organs working on blood regulations, and shows that animals living in their natural environments routinely experience circumstances that tend to change their blood composition.
Kidneys and Excretion
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter highlights the importance of kidneys and excretion. The kidneys bear primary responsibility for the maintenance of blood and other body fluids at a normal composition of terrestrial animals. Meanwhile, urine, the product of the kidneys, is typically a complex solution containing multiple inorganic and organic solutes. The chapter considers urine formation in mammals, vertebrates, decapod crustaceans, molluscs, and insects. It then details the process of nitrogen disposition and excretion. Here animals excreting ammonia or ammonium ion are described as ammonotelic and animals with principal nitrogenous end product are known to be ureotelic. However, if uric acid is the principal end product, an animal is uricotelic.
Mammals of Deserts and Dry Savannas
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter covers the interplay of water, salts, and excretion of desert mammals in dry savannas. It details how oryxes and other species of medium-sized and large mammals can live in hot deserts or dry-savanna ecosystems. In dry savanna, water is a dominant controlling factor for biological processes. Thus, the large body size of some animals plays a physiological advantage in terms of water cost. The chapter then considers the dramatic adaptation of particular species, such as wildebeests adapting to walk on long treks to find water to reduce and water expenditure to void metabolic heat and the water-conserving mechanisms of oryxes.
Invertebrates
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

Invertebrates starts with an introduction to the topic. It considers systematics, phylogeny, and classification. It also looks at the animal kingdom. Two basal metazoan phyla, porifera and placozoa, are examined. Other topics include phylum cnidaria, phylum ctenophora, bilateria, and phylum xenacoelomorpha. The text also looks at flatworms, four enigmatic protostome phyla, phylum nemertea, phylum mollusca, and phylum annelida. It examines spiralian phyla, the gnathifera, lophophorates, nematoida, scalidophora, and the emergence of the arthropods. It then delves into phylum arthopoda in detail. It looks at deuterostomes and the phylum echinodermata, phylum hemichordata, and phylum chordata.
Systematics, Phylogeny, and Classifications
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter focuses on the elements of systematics, phylogeny, and classifications. It defines systematics as the study of biological diversity and its origins. Systematists aim to describe and organize the many forms of life in evolutionarily meaningful ways either through a phylogenetic tree or a classification. Meanwhile, the most fundamental goals of biological nomenclature are the creation of classifications in which any organism has only one correct name, and no two kinds of organisms bear the same name. The chapter references Charles Darwin's Tree of Life to provide an understanding of phylogenetic inference. It looks into how the field of molecular phylogenetics unveiled a great deal about how species are related to one another.
Phylum Porifera
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter focuses on the phylum Porifera which is one of the earliest-appearing extant animal phyla. The phylum consists of sponges, which are sessile, primarily suspension-feeding, multicellular animals that utilize flagellated cells called choanocytes to circulate water through a unique system of water canals. Despite their seeming simplicity, sponges have experimented with various aspects of higher metazoan body organization. The chapter discusses the taxonomic history and classification of sponges since it was initially recognized as a plant before their international water currents were described and identified as an animal. It features figures of the sponges' different body structures and aquiferous systems.
Phylum Cnidaria
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter examines the phylum Cnidaria which features a highly diverse assemblage of anemones, corals, jellyfish, and their kin. The phylum consists of 13,300 described living species, all of which are predators (or highly modified parasites) that feature forms of cnidae, polypoid, or medusoid. Despite the limitations of a diploblastic, radially symmetrical body plan, cnidarians are a highly successful and extraordinarily diverse group. The chapter details the taxonomic history and classification of phylum Cnidaria that divides into three major lineages: Anthozoa, Medusozoa, and Endocnidozoa. It shows that colonialism and symbiotic relationships with dinoflagellates are common and have evolved independently among the free-living species.
Protostomia, Spiralia, and the Phylum Dicyemida
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter examines the features of the phylum Dicyemida as part of the Spiralia subclade of Protostomia. In spite of the uncertainty in its phylogenetic ties, recent molecular studies all suggest that dicyemidans are probably highly reduced and specialized symbionts in the protostome clade Spiralia. Dicyemidans have a simple, solid body construction, without symmetry, body cavities, or differentiated organs. All dicyemidans are obligate symbionts in the renal sacs of cephalopod molluscs, with over 120 species described. Moreover, future research should address the phylogenetic relationship of Dicyemida among the other spiralians and its full life history outside the body of the host cephalopods.
Phylum Annelida
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter details the features of a large group of primarily segmented spiralian worms, the phylum Annelida. Annelids have successfully occupied virtually all habitats where sufficient water is available. Most annelids are characterized by having a head followed by a segmented body in which most internal and external parts are repeated with each segment, a condition referred to as serial homology. The chapter then tackles the body plan, taxonomic history and classification of segmented worms, peanut worms, spoon worms, siboglinids, and leeches. It explains that three major groups of annelids are viewed as nonpolychaetes, which are Oweniida, Chaetopteridae, and the Amphinomida/Sipuncula clade.
Rouphozoa
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter details the characteristics of the clade Rouphozoa by referencing the lineage of spiralian protostomes which includes two phyla: Platyhelminthes (flatworms) and Gastrotricha (hairy-bellied worms). Platyhelminthes are triploblastic, nonsegmented, bilaterally symmetrical, acoelomate, soft-bodied, dorsoventrally flattened worms. Even though many gastrotrichs bear a superficial resemblance to flatworms and rotifers, they are easily distinguished by their adhesive tubes and cilia restricted to the ventral surface. Moreover, a large amount of species of marine, brackish-water, and freshwater gastrotrichs are microscopic. The chapter also considers the taxonomic history and classification of flatworms and hairy-bellied worms. It also details the body plans of both phyla Platyhelminthes and Gastrotricha.
Panarthropoda and the Emergence of the Arthropods
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter looks into the clade Panarthropoda which comprises three phyla of Arthropoda, Onychophora, and Tardigrada. The clade Panarthropoda is characterized by metamerism, reduced coeloms and a hemocoel, ecdysis, muscles isolated in bands, and paired ventrolateral segmental appendages with terminal claws. The chapter then features illustrations that show the body plan of members of Arthropoda, Onychophora, and Tardigrada. The phylum Arthropoda is unprecedented for its diversity with its four distinguished subphylas of Crustacea, Hexapoda, Myriapoda, and Chelicerata. The chapter also provides a brief overview of arthropod evolution, which includes how arthropods occur in virtually every environment on Earth.
Phylum Arthropoda
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter covers the subphylum Crustacea under the phylum Arthropoda. The subphylum Crustacea is a paraphyletic group because it excludes the Hexapoda (insects and their kin), which evolved from within Crustacea close to 500 million years ago. Moreover, crustaceans are one of the most popular invertebrate groups since they include some of the world's most delectable gourmet fare. Crustaceans are commonly the dominant organisms in aquatic subterranean ecosystems and dominate ephemeral pool habitats, where many undescribed species are known to occur. The chapter discusses the classification of crustaceans and synopses of the crustacean taxa. It also considers the subphylums of Pancrustacea, Oligostraca, Multicrustacea, and Allotriocarida.
Phylum Arthropoda
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter examines the characteristics of the subphylum Hexapopda under phylum Arthropoda. The arthropod subphylum Hexapoda comprises the class Insecta and three other small, wingless, insectlike groups: Collembola, Protura, and Diplura. Hexapods evolved on land, so its groups inhabiting aquatic environments today have secondarily invaded those habitats through physiological adaptations and modifications of their aerial gas exchange systems. The chapter then details the classification, evolution, and synopses of the subphylum Hexapoda. Insects are extremely diverse, and also incredibly abundant in the terrestrial world. The chapter mentions how insects coevolved with flowering plants, citing how many wild plant species rely on them for pollination.
Phylum Arthropoda
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter discusses the subphylum Myriapoda in correlation with phylum Arthropoda. It enumerates the classes of the arthropod subphylum Myriapoda: Chilopoda (centipedes), Diplopoda (millipedes), Pauropoda (pauropods), and Symphyla (symphylans). Myriapods differ from hexapods and most crustaceans in their retention of a largely homonomous trunk with paired segmental appendages. The chapter shows that Millipedes are slow-moving detritus feeders that generally spend their time burrowing through soil and litter. In contrast, most centipedes are fast-running predators, with one pair of legs per segment and poison claws. The chapter mentions how future research should include centipede venoms, millipede defensive secretions and the genomic and physiological adaptations they acquired in adapting to terrestrial environments.
Phylum Arthropoda
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter notes subphylum Chelicereta within phylum Arthropoda, which is the oldest group of extant arthropods that includes some primitive marine groups and a plethora of terrestrial counterparts. The arthropod subphylum Chelicerata is a large and diverse taxon comprising three rather different groups: Xiphosura, Arachnida, and Pycnogonida. In addition to the basic characteristics common to all arthropods, chelicerates are distinguished by several unique features of the body being divided between the prosoma and opisthosoma. The chapter provides illustrations to examine the understanding of members of Chelicereta's body plans. It cites the struggles of understanding the relationship of the other apulmonates and the plethora of extinct arachnid lineages.
Perspectives on Invertebrate Phylogeny
Authors: Brusca Richard C. , Giribet Gonzalo , Moore Wendy
Published: September 2023

This chapter examines the perspectives on invertebrate phylogeny. It recalls the evolution of 31 phyla and their internal relationships, referencing how phylogenies can be constructed from a variety of different kinds of data. Early molecular phylogenetic studies relied heavily on the 18S ribosomal RNA gene, but it quickly became apparent that understanding deep-level metazoan phylogeny required analysis of additional genes. In recent times, molecular phylogenetics is now being incorporated into studies of ecology, oceanography, biogeography, conservation biology, medicine, archeology, and anthropology. The chapter argues that morphology remains to have a role in phylogenetics even if molecular phylogenies are resolving the puzzle of the animal tree of life one piece at a time.
What Is a Vertebrate?
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter explains that vertebrates belong to the phylum Chordata, which along with the echinoderms and the hemichordates comprise the Deuterostomia. Deuterostomes and protostomes are the subdivisions of the more complex animals with bilateral symmetry and bodies that develop from three layers of tissue. The chapter looks at non-chordate deuterostomes, which are all small marine animals that are united by the presence of pharyngeal slits at some stage of their lives. The main characteristic of all chordates is the notochord, which is a dorsal stiffening rod to which muscles attach and are seen at some point of development in all chordates. The chapter shows that the notochord is a transient structure in most vertebrates. This is replaced during embryonic development by the vertebral column.
Origin and Radiation of Chondrichthyans
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter looks at chondrichthyans, which are not primitive fishes, but are highly developed. The first definitive chondrichthyan fossils came from the Early Devonian period, although chondrichthyan-like scales are known to have existed from the early Silurian, and possibly the Ordovician periods. The chapter highlights the two main branches of chondrichthyans which reflect a division which had occurred by the start of the Devonian. Elasmobranchii includes the extant neoselachians and extinct relatives, while Holocephali includes the extant chimaeras and related extinct forms. The chapter shows that chimaeras have a single gill opening covered by soft tissue and an immobile upper jaw fused with the skull. It then considers the ecological implications of declining populations of the elasmobranch species, referring to how the life-history characteristics of neoselachians make them vulnerable to overfishing. Policies to protect these specieis revolve around sustainable exploitation of individual species.
Lepidosaurs
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter explains how the crown group Lepidosauria is one of the two largest clades of tetrapods. It looks into the diverse groups of lepidosaurs and their body forms and habitats. Extant lepidosaurs branched into two lineages: a single species of rhynchocephalian (also known as the tuatara), and more than 11,000 species of squamates. Mriad specializations have arisen in different groups in regard to feeding and foraging, social behavior, and reproduction. The chapter elaborates on the evolution of lepidosaurs in terms of skull kinesis, feeding, predator avoidance, and social behavior. It mentions that anthropogenic climate change poses major threats to the lineage of lepidosaurs.
Geography and Ecology of the Cenozoic
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter explores the geography and ecology of the Cenozoic era. It cites how changes in continental positions have affected Earth's climates and the ability of vertebrates to disperse between its regions. By the late Mesozoic era, continental separation and epicontinental seas had isolated populations of terrestrial tetrapods and freshwater vertebrates, which limited possibilities for their migration between continents. While the best-known Cenozoic extinction took place at the end of the Pleistocene era, and this mainly affected only larger land animals. The chapter also considers debates on whether Pleistocene extinctions were mainly caused by climate changes or the spread of humans across the globe.
Defining Conservation Biology
Authors: Sher Anna A.
Published: September 2023

This chapter provides a background of conservation biology. Human activities are causing the extinction of thousands of species both locally and globally, with threats to species and ecosystems accelerating due to human population growth and the associated demands for resources. Conservation biology is a field that combines basic and applied disciplines with three goals: to describe the full range of biodiversity on Earth; to understand human impact on biodiversity; and to develop practical approaches for preventing species extinctions, maintaining genetic diversity, and protecting and restoring ecosystems. It rests on a number of underlying assumptions that are accepted by most professionals in the discipline: biodiversity has value in and of itself; extinction from human causes should be prevented; diversity at multiple levels should be preserved; science plays a critical role, and scientists must collaborate with nonscientists to achieve their goals. Ultimately, the conservation of biodiversity has become an international undertaking.
Extinction Risk
Authors: Sher Anna A.
Published: September 2023

This chapter evaluates the problem of extinction. Many species are currently on the brink of extinction due to increasing human activity; this is well documented in the well-studied groups of birds, mammals, and amphibians. Island species have had a higher rate of extinction than mainland species, due to small population sizes and less previous exposure to humans and mainland species. The island biogeography model is used to predict the numbers of species that will persist in new protected areas and the numbers that will go extinct elsewhere due to habitat destruction and other human activities. Those species that are most vulnerable to extinction have particular features, including a narrow range, one or only a few populations, small population size, declining population size, and economic value to humans that leads to overexploitation. Small populations are vulnerable to further declines in size and eventual extinction due to genetic, demographic, and environmental factors.
The Challenges of Sustainable Development
Authors: Sher Anna A.
Published: September 2023

This chapter examines sustainable development, which is defined as economic development that satisfies the present and future needs of human society while minimizing its impact on biodiversity. Achieving sustainable development is a challenge for conservation biology and society. Legal efforts are made to protect biodiversity at the local, regional, and national levels and to regulate activities affecting both private and public lands. Governments and private land trusts buy land for conservation purposes or acquire conservation easements and development rights for future protection. Moreover, international agreements and conventions that protect biological diversity are needed because species migrate across borders, there is an international trade in biological products, the benefits of biological diversity are of international importance, and the threats to diversity are often international in scope and require international cooperation. The chapter then considers how conservation groups, governments in developed countries, and the World Bank provide funding to protect biodiversity.
Developmental Biology
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

Development Biology presents exciting developments in this field. The first few chapters look at patterns and processes of becoming and provides a framework for understanding animal development. The text then turns to an examination of gametogenesis and fertilization. The next few chapters tackle early development: cleavage, gastrulation, and axis formation. There follow chapters about building with ectoderm and building with mesoderm and endoderm. The next few chapters cover postembryonic development. Finally, the last part looks at development in wider context including an examination of development in health and disease, and the environment, and evolution.
Cell-to-Cell Communication
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter focuses on cell-to-cell communication, which occurs between cells in direct contact with one another or across a distance through cells secreting proteins into the extracellular matrix. It discusses the extracellular matrix, which serves to modify how signals may be secreted across cells to influence differentiation and cell migration. It also describes cell migration that occurs through changes in the actin cytoskeleton, which can be directed by internal or external instructions. The chapter discusses hormone auxin, which is a major morphogen found in plants and plays a major role in the proper morphogenesis of the embryo that is conserved across plant species. It assesses the asymmetric positioning of PIN efflux transporters on select sides of plant cells that functions to control the directional flow of auxin throughout the plant.
Conceptualizing Early Development
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter discusses embryonic cleavages in the earliest stages of animal development and shows how they rapidly produce large numbers of cells. It analyzes the pattern of embryonic cleavage which is determined by the amount and distribution of yolk protein within the cytoplasm. The chapter also looks at factors in the egg cytoplasm which influence the angle of the mitotic spindle and the timing of its formation. It also reviews many and varied patterns of animal gastrulation which are based on invagination, involution, ingression, delamination, epiboly, and convergent extension. The chapter looks at collinear Hox genes which determine cell identities along the anterior-posterior axis. It outlines the use of gastruloids which has helped define the intrinsically conserved patterning systems controlling axis determination.
Snails, Flowers, and Nematodes
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter examines body axes which are established at fertilization in some species through determinants in the egg cytoplasm and axes which are established in other species by cell interactions later in development. It describes snails and nematodes which have holoblastic cleavage, noting how the snail's cleavage is spiral, while the nematode's cleavage is rotational. It also highlights the phyllotactic spiral arrangement of floral organs in Arabidopsis thaliana, which is achieved through a self-regulating mechanism involving the interaction between auxin hormone signaling and mechanical strain in the meristem. The chapter talks about the nematode Caenorhabditis elegans, which has a cuticle through which one can see cell movements. It reviews the blastomere identity in C. elegans which is regulated by both autonomous and conditional specification that begins with an initial symmetry break event involving the segregation of partitioning defective (PAR) proteins.
Sea Urchins and Tunicates
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

The chapter discusses the blastopore of sea urchins, and tunicates, which becomes the anus while the mouth is formed elsewhere, which is a deuterostome mode of gastrulation. It considers differential cell adhesion as important in sea urchin gastrulation, noting how the micromeres detach from the vegetal plate and move into the blastocoel. It also looks at large micromeres that form the skeleton of the larva and the small micromeres that contribute to the coelomic pouches and to the germ cells. The chapter highlights the ingression of the skeletogenic mesenchyme which is accomplished through an epithelial-mesenchymal transition in which cells lose cadherins and gain affinity to adhere to the matrix within the blastocoel. It shows how fibroblast growth factor (FGF) induces expression of Brachyury in neighboring cells to become the notochord.
Early Human Development
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter discusses the conceptus of an embryo on the first eight weeks after fertilization. Subsequently, it is then called a fetus after the eighth week, exploring the stage of growth of humans when cell specification and the beginnings of organ development occur. It details how a woman becomes pregnant when the embryo implants into her uterus at the beginning of the second week of development. It also covers gonadotropic hormones which promote oocyte growth by stimulating reactions in the granulosa cells. The chapter investigates in vitro fertilization, wherein the first successful assisted reproductive technology in humans was made possible when the necessity of sperm capacitation was discovered. It points out how chance plays a role in developmental outcomes as there is a large variation in the levels of gene transcription and translation, noting that cells make more or fewer developmentally important proteins at different stages.
Neural Tube Formation and Patterning
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter looks at the neural tube that forms from the shaping and folding of the neural plate. It analyzes primary neurulation, wherein the surface ectoderm folds into a tube which separates from the surface ectoderm, and secondary neurulation, wherein the ectoderm and mesoderm cells coalesce as a mesenchyme to form first a cord and then a cavity within the cord. It also talks about neural tube closure, which is the result of extrinsic and intrinsic forces. The chapter provides an overview of the bipotential neuromesodermal progenitor (NMP) cells in the caudal end of the developing embryo can become either neural or somitic cells. It highlights the exposure of the pre-neural progenitors to opposing gradients of Fgf/Wnt and retinoic acid that leads to the patterning of the caudal neural tube along its dorsal-ventral axis.
Paraxial Mesoderm
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter provides an overview of the paraxial mesoderm which forms blocks of tissue called somites, which give rise to two major divisions: the sclerotome and the dermomyotome. It highlights the spatiotemporal expression of 3'-to-5' Hox genes along the paraxial mesoderm which correlates with a progressive loosening of chromatin structures via epigenetic regulation and with the timing of ingression into the paraxial mesoderm along the anterior-posterior axis. It also discusses the posterior gradient signals of FGFs and Wnts which maintain neuromesoderm progenitor (NMP) cells in the progenitor state. The chapter assesses the central dermomyotome which forms the dermis of the back, including precursors of muscle and brown fat cells. It investigates how tendons are formed through the conversion of the dorsalmost layer of sclerotome cells into syndetome cells by FGFs secreted by the myotome.
Metamorphosis
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter looks at animals that have a larval stage, covering primary larvae which specify their body axes differently than the adult and secondary larvae that have body axes that are the same as adults of the species. It highlights amphibian metamorphosis that includes both morphological and biochemical changes as the specific timing of metamorphic events can be orchestrated by the different events occurring at different levels of thyroid hormones. It also points out metamorphic change in amphibians brought about by cell death, cell differentiation, or by cell-type switching. The chapter discusses ametabolous insects that undergo direct development and hemimetabolous insects that pass through nymph stages wherein the immature organism is usually a smaller version of the adult. It examines the ecdysone receptor gene which may influence the response of a cell to 20E and bind to DNA to activate or repress transcription.
Population Distribution and Abundance
Authors: Bowman William D. , Hacker Sally D.
Published: September 2023

Key Concepts

CONCEPT 9.1 Populations are groups of individuals of the same species that vary in size over space and time.

CONCEPT 9.2 Species vary in their distribution and abundance across their geographic range.

CONCEPT 9.3 Species are limited in their distribution and abundance...
Competition
Authors: Bowman William D. , Hacker Sally D.
Published: September 2023

Key Concepts

CONCEPT 14.1 Competition can be direct or indirect, vary in its intensity, and occur between similar or dissimilar species.

CONCEPT 14.2 Competing species are more likely to coexist when they use resources in different ways.

CONCEPT 14.3 Competitive interactions can be modeled...
The Nature of Communities
Authors: Bowman William D. , Hacker Sally D.
Published: September 2023

Key Concepts

CONCEPT 16.1 Communities are groups of interacting species that occur together at the same place and time.

CONCEPT 16.2 Species diversity and species composition are important descriptors of community structure.

CONCEPT 16.3 Communities can be characterized by complex networks of direct and...
Conservation Biology
Authors: Bowman William D. , Hacker Sally D.
Published: September 2023

Key Concepts

CONCEPT 23.1 Conservation biology is an integrative discipline that applies the principles of ecology to the protection of biodiversity.

CONCEPT 23.2 Biodiversity is declining globally.

CONCEPT 23.3 Primary threats to diversity include habitat loss, invasive species, overexploitation, pollution, disease, and climate change....

CONCEPT...
Mineral Nutrition
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter focuses on mineral nutrition, which is the study of how plants obtain and use mineral nutrients. It explains that mineral nutrition is an area of research that is central for improving modern agricultural practices and environmental protection, as well as for understanding plant ecological interactions in natural ecosystems. It also considers the key roles nutrients have within plants, including how nutrients serve as components of organic compounds, in energy storage, in plant structures, as enzyme cofactors, and in electron transfer reactions. The chapter discusses how nutrients can be added back to the soil in the form of fertilizers in order to prevent the development of deficiencies, particularly nitrogen, phosphorus, and potassium. It analyzes the development of extensive root systems, formation of symbioses with mycorrhizal fungi, and production and secretion of protons or organic anions into the soil, which are ways for plants to obtain nutrients from the soil.
Photosynthesis: The Light Reactions
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter introduces the basic physical principles that underlie photosynthetic energy storage and the current understanding of the structure and function of the photosynthetic apparatus. It talks about how oxygenic photosynthetic organisms, such as plants, use solar energy to synthesize complex carbon compounds. It also explores the essential concepts that provide a foundation for understanding photosynthesis. The chapter also looks at light energy that drives the synthesis of carbohydrates and the generation of oxygen from carbon dioxide and water. It deals with the role of light in photosynthesis, the structure of the photosynthetic apparatus, and the processes that begin with the excitation of chlorophyll by light and culminate in the synthesis of ATP and NADPH.
Photosynthesis: The Carbon Reactions
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter describes the metabolic cycle and shows how this incorporates atmospheric CO2 into organic compounds called the Calvin–Benson cycle. It considers how the unavoidable reaction of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) with molecular oxygen decreases the efficiency of photosynthetic CO2 assimilation. It also explores how photorespiration releases CO2 while recycling the by-products of the oxygenation reaction that would otherwise be unusable by the cell. The chapter examines C4 photosynthesis and crassulacean acid metabolism (CAM), which are CO2-concentrating mechanisms that land plants have evolved for minimizing the oxygenation of Rubisco and the loss of energy and CO2 during photorespiration. It looks at the formation of the two major products of the photosynthetic CO2 fixation: starch and sucrose.
Assimilation of Inorganic Nutrients
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter outlines the primary reactions through which major nutrients, namely nitrogen, sulfur, and phosphate, are assimilated and discusses the organic products of these reactions. It emphasizes the physiological implications of the required energy expenditures and introduces the topic of symbiotic nitrogen fixation. It also considers nutrient assimilation as the often energy-requiring process by which plants incorporate inorganic nutrients into the carbon constituents necessary for growth and development. The chapter highlights the carbon skeletons for amino acids that derive from intermediates of glycolysis and the tricarboxylic acid cycle. It explains how sulfate is mainly assimilated in leaves and involves subcellular compartments of cytosol, chloroplast, and mitochondria.
Vegetative Growth and Organogenesis: Primary Growth of the Plant Axis
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter discusses the developmental processes by which plants transition from the seedling state, expanding on their primary axis and production of determinate lateral organs. It considers the basic features of cell division and initiation of processes that lead to differentiation in the root and shoot apical meristems. It also examines blade formation in simple leaves, which involves the marginal expansion of leaf tissues, differentiation into adaxial and abaxial domains, and morphogenesis along the proximal–distal axis. The chapter highlights how compound leaves are produced by variations of these developmental pathways. It also looks at the gene networks and hormonal signals that control development of the specialized cells of the epidermis and vascular tissue.
Biotic Interactions
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter discusses biotic interactions through examples of beneficial associations between plants and microorganisms. It considers various types of harmful interactions between plants, herbivores, and pathogens. It also surveys the wide range of inducible defenses, which plants have evolved to fend off insect herbivores, and the signaling molecules and signal transduction pathways that regulate them. The chapter highlights plant responses to microbial pathogens, for which some of the same themes of constitutive and inducible defenses are employed. It reviews the mechanisms of two other types of plant biotic interactions, nematodes, and parasitic plants, and the ecological role that toxic root exudates play during plant–plant competition.
Antagonists of histamine receptors as anti-ulcer remedies
Authors: Saunders John
Published: September 2023

This chapter takes a closer look at antagonists of histamine receptors as remedies to ulcers. It includes in the background that while the prototypic H2 antagonist, metiamide, was effective in reducing gastric acid secretion in patients, it had undesirable side effects possibly associated with the thiourea group. Then, it discusses the discovery of the functionality of cimetidine and describes its synthesis which started with ethyl ester. The chapter also tackles the synthesis of ranitidine, which had emerged as a market leader. It highlights that the Mannich reaction on 2-hydroxymethylfuran generated the first intermediate key towards ranitidine. The chapter ends with a discussion on famotidine whose synthesis is characterized by a series of functional modifications.
Nucleoside anaologues which inhibit HIV reverse transcriptase as anti-AIDS drugs
Authors: Saunders John
Published: September 2023

This chapter takes a closer look at nucleoside analogues which are active inhibitors of the HIV replication act. HIV is the causative agent of AIDS-the development of certain opportunistic infections, cancers, and encephalopathy and is associated with catastrophic depletion of CD4+ lymphocytes. The chapter describes the different approaches in producing zidovudine or AZT, the first drug shown to have widespread utility in the management of AIDS. It highlights that this compound had been prepared in 1964 as a potential anti-cancer agent but was shown to be ineffective and was subsequently re-screened as an antiviral when the AIDS epidemic hit Western society in the mid-1980s. The chapter also tackles the synthesis of lamivudine, a compound that has been found to be of immense value in combination with AZT.
Periodicity
Authors: Housecroft Catherine E.
Published: September 2023

This chapter discusses the effects of introducing lanthanoid elements before hafnium, using the ground state electronic configuration of metals in order to illustrate the introduction of the lanthanoid series. It considers properties of the d-block metals that emphasize the distinction between the first and two heavier members of each triad, as well as trends across the second and third periods of the d-block. It also shows the trends in metallic radii, in which the value is equal to half of the internuclear separation in the crystal lattice. The chapter reviews organometallic compounds containing π-acceptor ligands. These have low oxidation states which are stabilized on descending a triad. For non-organometallic compounds, lower oxidation states are less stable for heavier elements.
Aqueous solution species
Authors: Housecroft Catherine E.
Published: September 2023

This chapter focuses on two particular aspects of the chemistry of the second and third row d-block metals in aqueous solution: species present in solution and redox behaviour. It explores the increase in electron withdrawing power of the metal centre which is associated with an increase in oxidation state and is reflected in the fact that the hexaaqua ion of vanadium does not exist in a solution. It also discusses the loss of protons through the polarization of O-H bonds in coordinated water. This leads to the formation of hydroxo ligands and the concomitant generation of dinuclear species. The chapter describes the dramatic effect that the change in ligand has on the relative case of iron(III) reduction. It mentions the use of potential diagrams as a valuable method of displaying the redox behaviour of different species containing a particular element.
Clusters with metal-metal bonds
Authors: Housecroft Catherine E.
Published: September 2023

This chapter discusses clusters that contain higher oxidation state metals from the early to mid d-block metals with π-donor ligands, focusing on metal halide clusters and their derivatives. It considers three cluster cores or metal centres in a closed framework: triangle, square-based pyramid, and octahedron. It cites an example of a semi-interstitial atom that is partially surrounded by metal centres and is rather exposed. The chapter describes the structural features common to niobium and tantalum halide clusters. These generally consist of an octahedral metal core supported by edge-bridging and terminal ligands. It reviews the crucial role of an interstitial atom as it provides valence electrons for the stabilization of an electron-poor compound from within the cage without imposing steric demands among the ligands around the outside of the cage.
Polyoxometallates of molybdenum and tungsten
Authors: Housecroft Catherine E.
Published: September 2023

This chapter highlights polyoxometallates in which bridging oxo ligands support the metal cluster framework. It discusses the formation of oxoanions of molybdenum and tungsten in a solution and describes how the condensation of [MoO4]2- gives a polyoxoanioin or polyoxometallate. It also analyzes the condensation processes of molybdates and tungstates which are highly pH dependent, including a reaction that takes place at pH=5. The chapter then reviews the process that involves the sharing of oxygen atoms between metal centres and concomitant changes in the coordination environments of the metal centres. It introduces a method of representing the structures of polyoxometallates, which is used to represent silicates.
Ring synthesis
Authors: Grossel Martin
Published: September 2023

This chapter reviews approaches to the synthesis of ring structures which provide a key component in the repertoire of synthetic techniques. It analyses different ring sizes, which impose different constraints and problems requiring a variety of solutions. It also discusses the rate of a reaction, which depends on the activation energy of the process and is made up of enthalpic and other entropic contributions. The chapter describes the loss of rational freedom as the key factor that determines the entropy of activation when the chain precursor is converted into a ring. It clarifies that the longer the chain, the more rational freedom that is lost.
Polycyclic systems
Authors: Grossel Martin
Published: September 2023

This chapter refers to bi- and polycyclic hydrocarbons that are named according to the way in which the component rings are fused to each other. It describes heptane, also known as norbornane, as one of the best studies bicyclic systems. It also discusses the derivatives of the hydrocarbon, which have several interesting properties that partly arise from strain present in the structure and provide a useful framework for testing aspects of reactivity and mechanistic pathways. The chapter highlights features of the reactions of 2-norbornyl derivatives, which includes the occurrence of skeletal rearrangement in which the 2-norbornylcation is an intermediate. It analyses the basis of Bredt's rule, which implies that an elimination process in a bridged structure should always avoid the formation of an alkene at a bridgehead.
Exact symmetries
Authors: Green N. J. B.
Published: September 2023

This chapter describes molecular point group symmetry as an approximate symmetry. The whole idea of a molecular geometry relies on the Born–Oppenheimer approximation. The chapter cites Schrödinger equation of a molecule and states that it is an invariant to a number of other symmetries in the sense of not being dependent on the Born–Oppenheimer approximation. It also emphasizes that the properties of an object do not depend on where it is situated or how it is oriented in the coordinate system. The chapter describes inversion symmetry, which has no classical counterpart, and involves the transformation of the coordinates of all the particles in values inverted through the origin. It describes the inversion of coordinates that alter the configuration of particles.
Perturbations
Authors: Green N. J. B.
Published: September 2023

This chapter describes the rigid rotor approximation that enables the treatment of the rotational and vibrational motions of a molecule separately. It focuses on the perturbation theory, in which the simple theory is used as a starting point for a series of successive refinements. It also highlights the small perturbation of the system that distinguishes the difference between the true Hamiltonian and the approximate Hamiltonian, which stresses that the successive levels of refinement are obtained under the assumption that the effects of the perturbation are small. The chapter cites orbital approximation as one of the many examples of important problems in chemistry that can be treated using perturbation theory. It points out that orbital approximation can be corrected for electron-electron repulsions and for the formation of a chemical bond.
Redox deprotection
Authors: Robertson Jeremy
Published: September 2023

This chapter focuses on redox deprotection. Oxidation-labile protecting groups offer a means of releasing functional groups under essentially neutral conditions which is useful when hydrolytic deprotection is not tolerated and silyl protecting groups are unsuitable. In particular, a CH2 group that links a functional group to an electron-rich aromatic ring is prone to oxidation giving a hemiacetal, which is unstable with respect to aldehyde formation, and release of the functional group. Some oxidising agents activate the CH2 towards nucleophilic attack by water in a process equivalent overall to abstraction of hydride ion. The chapter then looks at internal redox processes, including free-radical deprotection, protecting group interchange, and photochemical deprotection. It also considers reductive methods, including hydrogenolysis.
The acidity of water
Authors: Howard Alan G.
Published: September 2023

This chapter examines the acidity of natural water, which depends on the nature of material dissolved in it and its interaction with other materials such as the rocks, the organisms living in it, and added pollutants. Rivers and lakes in granite areas, for example, are unable to neutralize any added acidity and are therefore highly susceptible to the effects of acid rain. Significant increases in the acidity of these water bodies produces an environment which is not well suited to life for a number of reasons. Firstly, most organisms are not well adapted to acidic conditions or changes in acidity. In addition, acidification leads to the dissolution of a number of toxic elements which can poison flora and fauna. In limestone areas, however, the water can neutralize moderate quantities of added acid. The chapter then considers the chemical nature of water, before studying polyprotic acids and the solubility of gases.