Tool Technology: Acheulean Tool Industry In early African sites associated with Homo erectus, stone tools such as flakes and choppers identified to the Oldowan Industry dominate. Unlike the Oldowan tools, which were cobbles modified by striking off a few flakes, Acheulean toolmakers carefully shaped both sides of the tool. This type of technique, known as bifacial flaking, requires more planning and skill on the part of the toolmaker; he or she would need to be aware of principles of symmetry when crafting the tool. As with the tool illustrated below, handaxes tend to be thicker at the base and then come to a rounded point at the tip. Besides handaxes, forms such as scrapers, cleavers, and flake tools are present at Homo erectus sites. When drawing a stone tool, artists typically show front and back faces, as well as top and side profiles. They are more standardized in form and mode of manufacture than the earlier Oldowan tools. For example, the aforementioned handaxes vary in size, but they are remarkably consistent in regard to their shape and proportions. They were also an incredibly stable tool form over time-lasting well over a million years with little change. It has been suggested that Asian Homo erectus populations used perishable material such as bamboo to make tools. Another possibility is that Homo erectus (or even an earlier hominin) migrated to East Asia before the Acheulean technology developed in Africa. Tool Use and Cognitive Abilities of Homo erectus What (if anything) do the Acheulean tools tell us about the mind of Homo erectus Apart from the actual shaping of the tool, other decisions made by toolmakers can reveal their use of foresight and planning. Did they just pick the most convenient rocks to make their tools, or did they search out a particular raw material that would be ideal for a particular tool Analysis of Acheulean stone tools suggest that at some sites, the toolmakers selected their raw materials carefully-traveling to particular rock outcrops to quarry stones and perhaps even removing large slabs of rock at the quarries to get at the most desirable material. They also likely required cooperation and communication with other individuals, as such actions would be difficult to carry out solo. However, other Homo erectus sites lack evidence of such selectivity; instead of traveling even a short distance for better raw material, the hominins tended to use what was available in their immediate area (Shipton et al. In contrast to Homo erectus tools, the tools of early modern Homo sapiens during the Upper Paleolithic display tremendous diversity across regions and time periods. Additionally, Upper Paleolithic tools and artifacts communicate information such as status and group membership. Such innovation and social signaling seem to have been absent in Homo erectus, suggesting that they had a different relationship with their tools than did Homo sapiens (Coolidge and Wynn 2017). Some scientists assert that these contrasts in tool form and manufacture may signify key cognitive differences between the species, such as the ability to use a complex language. Subsistence and Diet In reconstructing the diet of Homo erectus, researchers can draw from multiple lines of evidence. These include stone tools used by Homo erectus, animal bones and occasionally plant remains from Homo erectus sites, and the bones and teeth of the fossils themselves. These data sources suggest that compared to the australopithecines, Homo erectus consumed more animal protein. Coinciding with the appearance of Homo erectus fossils in Africa are archaeological sites with much more abundant stone tools and larger concentrations of butchered animal bones. Meat Eating and Increased Brain Size It makes sense that a larger body and brain would be correlated with a dietary shift to more calorically dense foods. When biologists consider the evolution of intelligence in any animal species, it is often Early Members of the Genus Homo 393 framed as a cost/benefit analysis: In order for large brains to evolve, there has to be a compelling benefit to having them and a way to generate enough energy to fuel them. One solution that would allow for an increase in human brain size would be a corresponding reduction in the size of the digestive tract (gut). Judging from their skeleton, australopithecines have a wider rib cage and trunk region more similar to apes than humans. More meat in the diet would allow for a smaller gut and could also fuel the larger brain and body size seen in the genus Homo. Some researchers also believe that body fat percentages increased in hominins (particularly females) around this time, which would have allowed them to be better buffered against environmental disruption such as food shortages (Anton and Snodgrass 2012).
Geisbert, Boston University School of Medicine; scale-bar data from Matt Russell) the use of this technology has allowed for the discovery of many viruses of all types of living organisms. They were initially grouped by shared morphology, meaning their size, shape, and distinguishing structures. More recently, molecular analysis of viral replication cycles has further refined their classification. A virion consists of a nucleic-acid core, an outer protein coating, and sometimes an outer envelope made of protein and phospholipid membranes derived from the host cell. The most visible difference between members of viral families is their morphology, which is quite diverse. An interesting feature of viral complexity is that the complexity of the host does not correlate to the complexity of the virion. Some of the most complex virion structures are observed in bacteriophages, viruses that infect the simplest living organisms, bacteria. Viruses come in many shapes and sizes, but these are consistent and distinct for each viral family (Figure 17. All virions have a nucleic-acid genome covered by a protective layer of protein, called a capsid. Some viral capsids are simple polyhedral "spheres," whereas others are quite complex in structure. The outer structure surrounding the capsid of some viruses is called the viral envelope. The virus exploits these cell-surface molecules, which the cell uses for some other purpose, as a way to recognize and infect specific cell types. For example, the measles virus uses a cell-surface glycoprotein in humans that normally functions in immune reactions and possibly in the sperm-egg interaction at fertilization. Attachment is a requirement for viruses to later penetrate the cell membrane, inject the viral genome, and complete their replication inside the cell. Adenovirus, a nonenveloped animal virus that causes respiratory illnesses in humans, uses protein spikes protruding from its capsomeres to attach to the host cell. Nonenveloped viruses also include those that cause polio (poliovirus), plantar warts (papillomavirus), and hepatitis A (hepatitis A virus). Nonenveloped viruses tend to be more robust and more likely to survive under harsh conditions, such as the gut. Chicken pox, influenza, and mumps are examples of diseases caused by viruses with envelopes. Because of the fragility of the envelope, nonenveloped viruses are more resistant to changes in temperature, pH, and some disinfectants than enveloped viruses. Overall, the shape of the virion and the presence or absence of an envelope tells us little about what diseases the viruses may cause or what species they might infect, but is still a useful means to begin viral classification. Viral genomes tend to be small compared to bacteria or eukaryotes, containing only those genes that code for proteins the virus cannot get from the host cell. While most viruses contain a single segment of nucleic acid, others have genomes that consist of several segments. The virus must attach to a living cell, be taken inside, manufacture its proteins and copy its genome, and find a way to escape the cell so the virus can infect other cells and ultimately other individuals. Viruses can infect only certain species of hosts and only certain cells within that host. The molecular basis for this specificity is that a particular surface molecule, known as the viral receptor, must be found on the host cell surface for the virus to attach. The cell must be making the substances the virus needs, such as enzymes the virus genome itself does not have genes for, or the virus will not be able to replicate using that cell. The viral replication cycle can produce dramatic biochemical and structural changes in the host cell, which may cause cell damage. These changes, called cytopathic effects, can change cell functions or even destroy the cell. Some infected cells, such as those infected by the common cold virus (rhinovirus), die through lysis (bursting) or apoptosis (programmed cell death or "cell suicide"), releasing all the progeny virions at once. The symptoms of viral diseases result from the immune response to the virus, which attempts to control and eliminate the virus from the body, and from cell damage caused by the virus. During the budding process, the cell does not undergo lysis and is not immediately killed.
In a food web, the several trophic connections between each species and the other species that interact with it may cross multiple trophic levels. The matter and energy movements of virtually all ecosystems are more accurately described by food webs (Figure 20. All the producers and consumers eventually become nourishment for the decomposers (fungi, mold, earthworms, and bacteria in the soil). Two general types of food webs are often shown interacting within a single ecosystem. A grazing food web has plants or other photosynthetic organisms at its base, followed by herbivores and various carnivores. A detrital food web consists of a base of organisms that feed on decaying organic matter (dead organisms), including decomposers (which break down dead and decaying organisms) and this content is available for free at cnx. These organisms are usually bacteria, fungi, and invertebrate animals that recycle organic material back into the biotic part of the ecosystem as they themselves are consumed by other organisms. As ecosystems require a method to recycle material from dead organisms, grazing food webs have an associated detrital food web. For example, in a meadow ecosystem, plants may support a grazing food web of different organisms, primary and other levels of consumers, while at the same time supporting a detrital food web of bacteria and fungi feeding off dead plants and animals. Simultaneously, a detrital food web can contribute energy to a grazing food web, as when a robin eats an earthworm. How Organisms Acquire Energy in a Food Web All living things require energy in one form or another. Living organisms would not be able to assemble macromolecules (proteins, lipids, nucleic acids, and complex carbohydrates) from their monomers without a constant energy input. They can also indicate how efficiently organisms acquire energy, use it, and how much remains for use by other organisms of the food web. Energy is acquired by living things in two ways: autotrophs harness light or chemical energy and heterotrophs acquire energy through the consumption and digestion of other living or previously living organisms. Photosynthetic and chemosynthetic organisms are autotrophs, which are organisms capable of synthesizing their own food (more specifically, capable of using inorganic carbon as a carbon source). Photosynthetic autotrophs (photoautotrophs) use sunlight as an energy source, and chemosynthetic autotrophs (chemoautotrophs) use inorganic molecules as an energy source. Without these organisms, energy would not be available to other living organisms, and life itself would not be possible. The rate at which photosynthetic producers incorporate energy from the Sun is called gross primary productivity. However, not all of the energy incorporated by producers is available to the other organisms in the food web because producers must also grow and reproduce, which consumes energy. The net productivity is then available to the primary consumers at the next trophic level. Chemoautotrophs are primarily bacteria and archaea that are found in rare ecosystems where sunlight is not available, such as those associated with dark caves or hydrothermal vents at the bottom of the ocean (Figure 20. Many chemoautotrophs in hydrothermal vents use hydrogen sulfide (H2S), which is released from the vents as a source of chemical energy; this allows them to synthesize complex organic molecules, such as glucose, for their own energy and, in turn, supplies energy to the rest of the ecosystem. Consequences of Food Webs: Biological Magnification One of the most important consequences of ecosystem dynamics in terms of human impact is biomagnification. Biomagnification is the increasing concentration of persistent, toxic substances in organisms at each successive trophic level. These are substances that are fat soluble, not water soluble, and are stored in the fat reserves of each organism. This effect increased egg breakage during nesting and was shown to have devastating effects on these bird populations. These substances are best studied in aquatic ecosystems, where predatory fish species accumulate very high concentrations of toxic substances that are at quite low concentrations in the environment and in producers. The United States Environmental Protection Agency recommends that pregnant women and young children should not consume any swordfish, shark, king mackerel, or tilefish because of their high mercury content. These individuals are advised to eat fish low in mercury: salmon, shrimp, pollock, and catfish.
Biretia is a primitive member of the family that has the primitive trait of an unfused mandibular symphysis. Parapithecids were once thought to be the ancestral stock of platyrrhines; however, their platyrrhine-like features are probably just primitive retentions and the most conservative approach is to consider them stem anthropoids. The postcranial elements known for the group suggest generalized arboreal quadrupedalism. The best known member, Catopithecus, is known from crania that demonstrate a postorbital septum and from mandibles that lack symphyseal fusion (Simons and Rasmussen 1996). The Proteopithecidae had an overall primitive dentition that includes three premolars per quadrant and a generalized skeleton; they are considered stem anthropoids. The best known genus, Proteopithecus, is represented by dentitions, crania, and postcranial elements that suggest a diet of mostly fruit and a generalized style of locomotion, including arboreal quadrupedalism with some leaping (Simons and Seiffert 1999). Other genera of putative anthropoids from the Fayum include the very poorly known Arsinoea, the contentious Afrotarsius, and the enigmatic Nosmips. The last of these possesses traits of several major primate clades and defies classification (Seiffert et al. However, two very different groups of primates from Asia soon began to change that. One was an entirely new discovery (Eosimiidae), and the other was a poorly known group discovered decades prior (Amphipithecidae). Soon, attention on anthropoid origins began to shift eastward (see Ross and Kay 2004, Simons 2004). If anthropoids arose in Asia instead of Africa, then this implies that the African early anthropoids either emigrated from Asia or evolved their anthropoid traits in parallel with living anthropoids. Eosimiids First described in the 1990s, the eosimiids are best represented by Eosimias (Table 8. This "dawn monkey" is known from relatively complete jaws with teeth, a few small fragments of the face, and some postcranial elements (Beard et al. The lower jaw is distinctive in being very deep relative to its length and breadth, as in some early Fayum anthropoids (Figure 8. The mandibular symphysis is vertically inclined, as in some anthropoids, but is unfused. Eosimias (along with the other less-well-known genera in its family) bears some resemblance to tarsiers as well as anthropoids. The shared features with anthropoids are mainly jaw shape and details of dental morphology. Unfortunately, no good crania are known for this family and the anatomy of, for example, the posterior orbital margin could be very revealing as to higher-level relationships. Amphipithecids Amphipithecids are small- to medium-size primates (up to 10 kg; 22 lbs. They were first discovered in the 1910s, and all of the specimens discovered in the first half of the 20th century were fragmentary jaws with teeth that were mostly worn down. Starting in the 1970s, intensive collecting efforts in Myanmar yielded new material for the best known genera Pondaungia and Amphipithecus (Ciochon and Gunnell 2002; Table 8. It bears some resemblance to the other genera but has longer molar crests, suggesting a higher degree of folivory (Kay et al. Another amphipithecid, Siamopithecus from Thailand, has very rounded molars and was probably a seed-eater (Figure 8. In addition to teeth and jaws, some cranial fragments, ankle material, and ends of postcranial bones have been found for Pondaungia. There are important resemblances between the postcranial bones of Pondaungia and those of adapoids, suggesting adapoid affinities for the amphipithecidae. This would imply that the resemblances with anthropoids in the teeth are convergent, based on similarities in diet (see Primate Evolution 293 Ciochon and Gunnell 2002). Unfortunately, the association between postcranial bones and teeth is not definite. With other primates in these faunas (including eosimiids), one cannot be certain that the postcranial bones belong with the teeth. Perhaps, as suggested by some, some of the bones belong to a sivaladapid (or asiadapid) and others belong to an early anthropoid (Beard et al. Additional well-associated material of amphipithecids would help to clear up this uncertainty.
More complex integration patterns, consisting of a mixture of all the above have also been reported (not shown in figure). For each type of junction, a schematic overview is presented of the structure and the transformants in which they occur. Several possibilities have been put forward, but neither of them has been confirmed and contradictory results have been reported. The high frequency of inverted repeats has been attributed to the use of nopaline-type Vir functions (Jorgensen et al. The frequency of single-copy transformants is much higher after Arabidopsis root transformation than after floral dip transformation (De Buck et al. Transfer could erroneously start at the left border, proceeding through the binary vector, toward the right border, and finish only when the left border is encountered for the second time (Ramanathan and Veluthambi, 1995; van der Graaff et al. Alternatively, backbone Agrobacterium Tumefaciens-Mediated Transformation 467 transfer could be the result of initiation of transfer at the right border and readthrough over the left border (Kononov et al. The frequency of these backbone sequences might rise up to 75% or 80% from the transgenic population (Kononov et al. Recently, the presence of four copies of the left border repeat have been shown to positively prevent readthrough at the left border in rice transformants (Kuraya et al. Most of the target site deletions reported in the literature are smaller than 75 bp (Gheysen et al. Taken together, the process of illegitimate recombination usually introduces only small target site rearrangements. The most dramatic rearrangement was a 158-bp duplication of the plant target in combination with a 27-bp deletion. The final outcome of the chromosomal rearrangement would require two independent recombination events what is also improbable (Nacry et al. Essentially, two different models account for the paracentromeric inversion observed (Laufs et al. Mol Breed 6: 459-468 De Buck S, Jacobs A, Van Montagu M, Depicker A (1998) Agrobacterium tumefaciens transformation and cotransformation frequencies of Arabidopsis thaliana root explants and tobacco protoplasts. Plant Mol Biol 11: 365-377 Dillen W, De Clercq J, Kapila J, Zambre M, Van Montagu M, Angenon G (1997) the effect of temperature on Agrobacterium tumefaciens-mediated gene transfer to plants. Trends Plant Sci 8: 380-386 Fladung M (1999) Gene stability in transgenic aspen (Populus). Microbiol Mol Biol Rev 67: 16-37 Gheysen G, Angenon G, Van Montagu M (1998) Agrobacterium-mediated plant transformation: a scientifically intriguing story with significant applications. Bio/Technology 6: 185-189 Grunstein M (1997) Histone acetylation in chromatin structure and transcription. Plant Mol Biol 52: 761-773 Kirik A, Salomon S, Puchta H (2000) Species-specific double-strand break repair and genome evolution in plants. Plant Mol Biol 52: 247-258 Komari T, Ishida Y, Hiei Y (2004) Plant transformation technology: Agrobacterium-mediated transformation. Plant Cell 8: 873-886 Negruk V, Eisner G, Lemieux B (1996) Addition-deletion mutations in transgenic Arabidopsis thaliana generated by the seed co-cultivation method. In H Jones, ed, Plant Gene Transfer and Expression Protocols, Methods in Molecular Biology, Vol 49. Nature 388: 900-903 Tzfira T, Citovsky V (2002) Partners-in-infection: host proteins involved in the transformation of plant cells by Agrobacterium. Theor Appl Genet 105: 878-889 Valentine L (2003) Agrobacterium tumefaciens: the David and Goliath of modern genetics. J Mol Biol 86: 109-127 Zambre M, Terryn N, De Clercq J, De Buck S, Dillen W, Van Montagu M, Van Der Straeten D, Angenon G (2003) Light strongly promotes gene transfer from Agrobacterium tumefaciens to plant cells. Genetic transformation results from a complex interaction between Agrobacterium and host plant cells. However, we understand much less about the plant contribution to the transformation process. Plant species, and even varieties/ecotypes, differ markedly in their susceptibility to Agrobacterium. A genetic component underlies these differences, permitting scientists to identify specific host genes and proteins mediating transformation. In this chapter, I review what is known about the plant contribution to transformation, and the tools which scientists are using to reveal the mechanisms by which host genes and proteins function in various steps of the transformation process. However, our knowledge of the host contribution to the transformation process has lagged.
Cusps: the bumps on the chewing surface of the premolars and molars, which can be quite sharp in some species. Dental formula: the number of each type of tooth in one quadrant of the mouth, written as number of incisors: canines: premolars: molars. Derived trait: A trait that has been recently modified, most helpful when assigning taxonomic classification. Diastema: A space between the teeth, usually for large canines to fit when the mouth is closed. Dry nose: the nose and upper lip are separated and the upper lip can move independently; sometimes referred to as a "hairy" or "mobile" upper lip. Ethnoprimatology: A subarea of anthropology that studies the complexities of human-primate relationships in the modern environment. Evolutionary trade-off: When an organism, which is limited in the time and energy it can put into aspects of its biology and behavior, is shaped by natural selection to invest in one adaptation at the expense of another. Faunivorous: Having a diet consisting of animal matter: insects, eggs, lizards, etc. Fovea: A depressed area in the retina at the back of the eye containing a concentration of cells that allow us to focus on objects very close to our face. Grade: A grouping based on overall similarity in lifestyle, appearance, and behavior. Homology: When two or more taxa share characteristics because they inherited them from a common ancestor. Meet the Living Primates 181 Incisors: the spatula-shaped teeth at the front of the mouth. Ischial callosities: A flattened area of the ischium on the pelvis over which calluses form; functioning as seat pads for sitting and resting atop branches. Knuckle-walking: A form of quadrupedal movement used by Gorilla and Pan when on the ground, where the front limbs are supported on the knuckles of the hands. Male bimaturism: Refers to the alternative reproductive strategies in orangutans in which males can delay maturation, sometimes indefinitely, until a fully mature, "flanged" male disappears. Molars: the largest teeth at the back of the mouth; used for chewing; in primates, these teeth usually have between three and five cusps. Monomorphic: When males and females of a species do not exhibit significant sexual dimorphism. Natal coat: Refers to the contrasting fur color of baby leaf monkeys compared to adults. Opposable thumb or opposable big toe: Having thumbs and toes that go in a different direction from the rest of the fingers, allows for grasping with hands and feet. Polymorphic color vision: A system in which individuals of a species vary in their abilities to see color. In primates, it refers to males being dichromatic and females being either trichromatic or dichromatic. Postorbital closure/plate: A bony plate that provides protection to the side and back of the eye. Prehensile tail: A tail that is able to hold the full body weight of an organism, which often has a tactile pad on the underside of the tip for improved grip. Sagittal crest: A bony ridge along the top/middle of the skull, used for attachment of chewing muscles. Scent marking: the behavior of rubbing scent glands or urine onto objects as a way of communicating with others. Sexually dimorphic: When a species exhibits sex differences in morphology, behavior, hormones, and/or coloration. Animals with a prehensile tail have a tactile pad on the underside of the tail as well. Tetrachromatic: Having the ability to see reds, yellows, blues, greens, and ultraviolet. Tooth comb or dental comb: A trait of the front, lower teeth of strepsirrhines in which, typically, the four incisors and canines are long and thin and protrude outward.
Furthermore, Agrobacterium has been shown to genetically transform, under laboratory conditions, numerous non-plant species, from fungi to human cells, indicating the truly basic nature of the transformation process. It is therefore not surprising that Agrobacterium and its ability to produce genetically modified organisms has also become the focus of numerous ethical and legal debates. These aspects of Agrobacterium research-its history, application, basic biology, and sociology, are reviewed in the present book. The book continues with a description of how Agrobacterium is used as a tool in plant biotechnology. The next two chapters describe our knowledge of the Agrobacterium genome gained with the advent of genomics approaches and place Agrobacterium in the taxonomic context of xxxii Preface related bacterial species. Special attention is paid to a description of the host factors involved in the transformation process, and the biology of the crown gall disease and bacterial oncogenes that cause these neoplastic growths. The next two chapters focus on interactions of Agrobacterium with non-plant species, from communication with its sister agrobacteria to fungi, algae, and mammalian cells, and on horizontal gene transfer from Agrobacterium to plants. The final two chapters of the book discuss ethical and safety issues associated with the use of Agrobacterium for interspecies gene transfer and look at the legal issues surrounding patents that involve Agrobacterium. The result is a comprehensive book which we hope the readers will find useful as a reference source for all major-biological, ethical, and legal-aspects of the Agrobacterium-mediated genetic transformation of plant and non-plant organisms. Tzvi Tzfira July 2007, Ann Arbor Vitaly Citovsky July 2007, New York Color Figures 1. Special thanks are reserved for Vardit Zeevi, who was highly instrumental in preparing the book for print. The common use of Agrobacterium as a gene vector for plants has somewhat obscured the fact that this bacterium remains an important plant pathogen. Pathogenic strains of the genus Agrobacterium cause unorganized tissue growth called crown gall or profuse abnormal root development called hairy root. Agrobacterium tumefaciens induces galls on roots and crowns of several fruit and forest trees and ornamental plants. Plants tissues that become diseased undergo physiological changes resulting in weak growth, low yields or even death of the entire plant. Thus the cambial region becomes unable to differentiate into efficient phloem and xylem elements leading to deficient nutrient transport. Symptoms may appear on roots, crowns and aerial parts of attacked plants (Figure 1-1). Tumors are usually comprised of unorganized tissue, but sometimes they differentiate into roots or shoots. This depends on the host plant, the position on the infected plant or the inducing bacterium (Figure 1-2). As indicated by several reviews, crown gall has been a worldwide problem in agriculture for over hundred years (Moore and Cooksey, 1981; Burr et al. Biotype 3 strains were isolated almost exclusively from grapevine (Vitis vinifera) and allocated to A. Similarly, several isolates from weeping fig (Ficus benjamina) form a distinct group and were classified as A. Samsun with different Agrobacterium vitis strains, showing differences in crown gall morphology. During the infection process agrobacteria suppress plant defense mechanisms via the chromosomally encoded degradation of hydrogen peroxide (Xu and Pan, 2000) and by Ti plasmid-related functions (Veena et al. Transformation of plant cells results in elevated hormone (auxin and cytokinin) production and sensitivity. Both trigger abnormal proliferation leading to tumorous growth or abnormal rooting (Petersen et al. Tumors and hairy roots produce and secrete specific amino acid and sugar derivatives, called opines.
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