Carbon Chapter 105 Carbon IVa

Journal of the Less Common Metals

Volume 100, July 1984, Pages 249-275

Group IVa and Va transition metal interactions with carbon and hydrocarbons I: Thermodynamics of formation of carbon solid solutions and carbides — kinetics and mechanisms of carburization in hydrocarbons, and the influence of oxygen or nitrogen dopants

Abstract

The thermodynamic and kinetic aspects of the interactions of group IVa and Va transition metals with carbon and hydrocarbons are first briefly considered. The kinetics and mechanisms of the carburization of α-Hf, niobium and tantalum in unsaturated and saturated hydrocarbons (C2H2, C2H4, CH4, C2H6, C3H8, n-C4H10 and C6H6) at low pressures (10−4–10 Pa) and high temperatures (1300–2300 K) are treated more comprehensively. Special attention is paid to the influence of oxygen or nitrogen adsorbed on the surface and of surface carbides on the carburization of α-Hf and tantalum. Finally, the oxygen degassing of niobium in C2H2 by the formation of CO at C2H2 pressures of 5 × 10−4 − 2 × 10−3 Pa and temperatures of 1660–2300 K is discussed.

The Group IVa elements carbon, silicon and germanium exhibit a very rich polymorphism that can be accessed under the extreme conditions of pressure and temperature. This rich polymorphism results in useful metastable phases that can be recovered to ambient conditions with diamond being the prime example. Other phases also exist for silicon or germanium, phases that are expected to be superior for solar power generation and other semiconductor applications. Many further phases are predicted but experimental synthesis pathways are not established yet. This is often due to large kinetic barriers toward phase transition in crystalline precursors materials, a challenge which can be overcome through amorphous and disordered precursor materials.

In this presentation here, I will give an overview over recent work on the use of such disordered precursors for high pressure materials synthesis. This work includes in situ X-ray and neutron diffraction on pure amorphous silicon and germanium which indicates the formation of functional metastable phases at the technologically relevant pressures below 10 GPa. It also gives insights into the possible polyamorphism of these elements. I will also describe high pressure synthesis of precursor materials themselves followed by subsequent characterization using neutron total scattering and inelastic neutron scattering. Moreover, I will also present findings on a particular form of disordered carbon, glassy carbon, and the high pressure synthesis of hexagonal diamond based on electron, X-ray and neutron diffraction. Finally, I will give an outlook to future directions in high pressure neutron scattering and corresponding materials studies that could be critically important for the synthesis of novel phases from the Group IVa.

Author Biography

Iva Pichová received her PhD degree in Biochemistry from the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic (IOCB) in Prague in the Czech Republic. She is a head of the group of Microbial proteins at IOCB. The laboratory of Iva Pichová is interested in functional and structural study of proteins involved in the pathogenesis of serious diseases. The research activities currently center on retrovirus assembly and maturation and on enzymes of pathogenic Candida spp. The projects involve protein engineering, molecular biology, enzymology, protein purification, characterization, and structural analysis. The research activity is also concentrated on interactions of pathogen proteins with cellular components. The close cooperation with organic chemists has enabled to carry out a multidisciplinary research focused also on design and testing of potential drugs. She is an author or co-author of 70 papers in international journals.

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Morphology and Structure

Based on homology, T4SSs can be grouped as type IVa, IVb, or "other." Though the secretion apparatus and function are homologous, little sequence similarity is found between Type Iva and IVb systems. The archetypical type IVa system is the A. tumefaciens VirB/D4 cluster, comprising 11 VirB proteins (VirB1–11) and one VirD protein (VirD4).79 The pili formed by IVa T4SSs are short (< 1 μm), rigid rods with a diameter of 8–12 nm, called "IncP-like pili," and are exemplified by TrbC from the IncP plasmid RP4 and by VirB2 from A. tumefaciens. The type IVb systems are assembled from subunits related to the prototypical L. pneumophila Dot/Icm system.80 Compared to IncP-type T4SSs, type IVb systems carry about twice as many genes. Type IVb secretion pili are also called IncF-like pili and form long (2–20 μm), flexible appendages with a diameter of 8–9 nm. They contain pili produced by the IncF, IncH, IncT, and IncJ systems. The "other" systems are often not involved in bacterial conjugation and bear little or no discernible ancestral relatedness to the types IVa or IVb systems. Examples are the A. tumefaciens T-pilus, which has a diameter of 10 nm but is flexible and variable in length, and the 100–200 nm needle-like type IV secretion-related appendages produced by H. pylori.79

T4SS pilins, the protein subunits that build up the extracellular appendages associated with T4SSs, are homologous to one another and display a number of common physical properties. Typically, these proteins are synthesized as preproteins with an unusually long signal peptide of 25–50 residues and need extensive processing by dedicated cellular factors to mature (see below). The structure of the F-pilus was examined using X-ray diffraction81 and cryo-EM.82 F-pili are shown to be cylindrical filaments with a central lumen of 2 nm and an external diameter of 8 nm. Two different subunit packing arrangements that seem to coexist in the pilus structure were observed: a stack of pilin rings of C4 symmetry and a one-start helical symmetry with an axial rise of 3.5 Å per subunit and a pitch of 12.2 Å. The 2-nm lumen diameter seems large enough to afford passage of single-stranded DNA but not folded accessory proteins, such as the F-pilus conjugative transfer relaxase TraI.79

The T-pilus of A. tumefaciens consists of a processed form of VirB2, the major structural component, and of an additional minor component, VirB5 (Fig. 2). No structural information for VirB2-like proteins alone is available. However, a crystal structure is available for the VirB5 homolog in pKM101, TraC, which shows that the structure is composed of a three-helix bundle capped and a smaller globular appendage.83 Structure-based mutagenesis studies suggested a role of VirB5 in adhesion and host recognition.83 VirB5 has homologs in other pathogenic bacteria such as Brucella suis or Bartonella henselae (called VirB5 in both species) and in conjugative plasmids such as pKM101 (TraC/), RP4 (TrbF), R388 (TrwJ/), or F factor (TraE).

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Penicillopepsin

Theo Hofmann, in Handbook of Proteolytic Enzymes (Third Edition), 2013

Structural Chemistry

The three-dimensional structure of penicillopepsin-JT1 has been determined, initially at 2.8 Å resolution [6], and subsequently at 1.8 Å resolution [30]. A mode of substrate binding was deduced from the X-ray analysis of complexes with the pepstatin analogs Iva-Val-Val-Sta-OEt and Iva-Val-Val-Lysta-OEt, where Iva is isovaleryl, and Lysta is the lysine analog of statine [31,32]. Deductions about the catalytic pathway for aspartic proteinases are based on structures of penicillopepsin with difluorostatine- and difluorostatone-containing peptides [33] and with peptides, which contain phosphinyl groups as transition state analogs in place of the carbonyl groups of statine in the peptide Iva-Val-Val-StaP-OEt and of leucine in the peptide Iva-Val-Val-LeuP-OPhe-OMe [34]. James and his colleagues have solved structures of penicillopepsin with macrocyclic inhibitors at 1.45 Å and 0.95 Å resolution [35]. This gave them a measure of the entropic contribution to the binding energy in a protein-ligand complex. The pI of penicillopepsin-JT1 is less than 3.0.

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Class Insecta—Insects

John L. Capinera, in Handbook of Vegetable Pests, 2001

Host Plants.

Tuber flea beetle feeds on a variety of solanaceous crops and weeds. The preferred host seems to be potato. Other crops that have been observed to be attacked, when potato was not available, include bean, cabbage, cucumber, lettuce, pepper, radish, spinach, swiss chard, and tomato. Several weeds, such as buffalo bur, Solanum rostratum; ground cherry, Physalis lanceolata; marsh elder, Iva xanthifolia; kochia, Kochia scoparia; dandelion, Taraxacum officinale; wild mustard, Brassica kaber; tansymustard, Descurainia pinnata; and lambsquarters, Chenopodium album; also are consumed by adults.

Hill (1946) conducted plant suitability experiments in Nebraska, assessing adult longevity, egg production, and larval survival on various host plants. Potato foliage was the most suitable food—egg production was highest and mortality lowest. Tomato also was a fairly suitable host, although not as favorable as potato. Buffalo bur was quite suitable for adult survival, but egg production was reduced considerably relative to potato. Plants that were decidedly less suitable included bean, ground cherry, marsh elder, and kochia. However, it is worth noting that even the less suitable hosts considerably extended longevity of adults as compared to the absence of food, and some egg production resulted from beetles fed these plants. No larval development was detected on marsh elder or kochia, but the tests were not exhaustive. Thus, though not optimal hosts, various weeds certainly would assist survival of beetles in the absence of potato and tomato.

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Sunflower Diseases

Samuel G. Markell, ... Thomas J. Gulya, in Sunflower, 2015

Sunflower Rust

Introduction

Sunflower rust occurs in every sunflower-growing region in the world (Gulya et al., 1997). Although the disease tends to be sporadic and often localized, it is capable of causing high levels of yield loss when left unmanaged. In one case, yield in nontreated strips in a naturally infected field in North Dakota, USA, was seven-fold lower than yield in areas of the field treated with fungicides (Markell et al., 2009). Although management tools are often available (resistance, fungicides), the explosive nature of rust epidemics and frequent pathogen race changes make management of the disease a challenge (Friskop et al., 2011, 2012; Markell et al., 2013).

Sunflower Rust Pathogen and Disease History

Sunflower rust is caused by the basidiomycete fungal pathogen Puccinia helianthi. The pathogen is macrocyclic (five spore stages) and autoecious (all spore stages occur on one host) rust (Gulya et al., 1997). The host range of the pathogen includes all perennial and annual Helianthus species, Heliopsis helianthoides, and Iva xanthiifolia. Numerous physiological races have been documented in many geographic locations; prevalence and distribution of the races change frequently (Friskop, 2013; Friskop et al., 2012; Gulya et al., 1997; Klisiewicz and Beard, 1976).

Sunflower Rust Signs and Symptoms

The first stage observed is the pycnia, which appears to the naked eye as a small (often 4–6 mm) yellow-orange bump on the top side of a leaf (Figure 4.15) or cotyledon (Figure 4.16) (Friskop et al., 2011). Aecia may form directly opposite the pycnia on the underside of the leaf, and appear as clusters of small orange cups similar in size to the pycnia (Figure 4.17) (Friskop et al., 2011). If pycnia and aecia are observed, they are usually seen early in the season, and they are difficult to find unless one is specifically looking for them. Rust is most commonly observed as uredinia, which are small (2–4 mm) raised pustules filled with dusty cinnamon-brown urediniospores (Figure 4.18, p. 111) (Friskop et al., 2011). Uredinia can be produced on any green plant part (leaves, bracts, stem, petiole). Early in the season, it is not uncommon to see leaves infected with uredinia and aecia (Figure 4.19, p. 111) and sometimes with evidence of pycnia still on the leaf. Hard and black telia will form at the season's end (Figure 4.20, p. 112) (Friskop et al., 2011).

Figure 4.15. Pycnia of Puccinia helianthi on a leaf.

Figure 4.16. Pycnia of Puccinia helianthi on a cotyledon.

Figure 4.19. Uredinia and aecia of Puccinia helianthi on a heavily infected leaf.

Figure 4.20. Telia of Puccinia helianthi.

Sunflower Rust Disease Cycle and Damage

The sexual cycle begins when telia germinate to produce four haploid basidospores that infect sunflower and produce pycnia (Gulya et al., 1997). Crossing of the strains generates aecia, which generate binucleate aeciospores that infect sunflower tissue and give rise to dikaryotic urediniospores in uredinia pustules. The uredia are a repeating stage that will continue to cycle until production of telia (Gulya et al., 1997).

Yield loss depends heavily on time of disease onset (Friskop et al., 2011; Markell, 2013; Markell et al., 2009). When the pathogen undergoes sexual reproduction in a commercial field, epidemics begin early and can have devastating potential to reduce yield (Markell et al., 2009). When an epidemic begins as a result of urediniospore dispersal from other fields, onset is often later and yield loss potential may be lower (Friskop et al., 2011). Wild Helianthus species and volunteer H. annuus serve as important reservoirs for the pathogen and can serve as foci for epidemics (Friskop et al., 2011; Gulya et al., 1997).

A minimum of six hours of free moisture is needed for germination and infection by uredniospores (Gulya et al., 1997). The optimal temperatures for uredinospore development are 20–35 °C, but the optimal temperatures for uredinisopore germination are 10–25 °C. However, germination and development can occur at a wider temperature range (Gulya et al., 1997).

Sunflower Rust Management

Rust can occur at any time, and in a favorable environment, can increase in severity very quickly. Additionally, the pathogen has numerous races and a propensity for race changes in response to resistance genes, making utilization of resistance as a sole management tool risky. However, fungicides offer an effective in-season management option if applying at optimal timing. Consequently, scouting for rust is the most critical component of management in season.

▪

The utilization of resistant hybrids reduces the chances of an epidemic by reducing the likely number of races that can infect the crop. However, it is unlikely that a resistant hybrid will be resistant to all pathogen races in the population (Friskop et al., 2012).

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Recent research in the United States suggests a fungicide action threshold occurs when 1% rust severity occurs at or before R5 (early bloom) on the upper four fully emerged leaves (Friskop, 2013; Markell and Khan, 2012), while earlier research in Israel suggested an action threshold of 3% was more appropriate (Shtienberg, 1995).

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Control unwanted hosts (Friskop et al., 2011) such as volunteer sunflowers and wild Helianthus species. These hosts can serve as a source of inoculum early in the season and as a breeding ground for new races.

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Rotate to a non-host, and avoid planting sunflowers adjacent to the previous years residue.

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Volume 2

Daniel J. Funk, in Encyclopedia of Animal Behavior (Second Edition), 2019

An Integrated Example From Uroleucon Aphids

I conclude this article by describing my postdoctoral investigations of ecological specialization in Uroleucon ambrosiae aphids (Funk and Bernays, 2001), research that involved many issues addressed above. Aphids are phloem sapsuckers that feed by penetrating host plant tissues with their beak-like mouthparts. Uroleucon is a genus of aphids whose species tend to be monophagous on hosts in the Asteraceae (the sunflower family). U. ambrosiae was known as a specialist on Ambrosia trifida (the giant ragweed), a common plant in disturbed habitats of the eastern United States. Thus, it was occasional reports of this aphid on other plants in the southwestern United States that first motivated my studies. These confirmed the specialist status of U. ambrosiae in the east where my fieldwork recovered it only on A. trifida, excepting a few collections on another Ambrosia species and a species of the closely related genus Iva. In Arizona, however, I collected U. ambrosiae from 16 host species, representing 11 genera and 4 tribes of Asteraceae, plus a species of Malvaceae, documenting its regionally generalist status.

Individual clones of eastern and southwestern populations were subsequently collected and maintained on host plants in a greenhouse. (Most aphids alternate between periods of clonal and sexual reproduction, but clonality can be maintained using long-day photoperiods.) Four southwestern hosts (including A. trifida) were used for a variety of behavioral assays using wind tunnels, continuous observation of host acceptance behaviors, electrical penetration graph analysis (EPG; in which electrodes record aphid mouthpart activity within plant tissues), and longer-term choice trials of settling behavior.

These experiments showed eastern aphids to be significantly more specialized and efficient than southwestern aphids. The use of replicate clonal genotypes established a genetic basis for this differentiation. These findings showed that southwestern aphids have evolved increased generalism and supported the cognitive constraints hypothesis on advantages of the specialization, while likewise raising the question of what advantages to generalism might outweigh the reduced efficiency of the southwestern aphids. A potential mechanism for this generalism was provided by the significantly and consistently reduced numbers of antennal sensilla across southwestern versus eastern populations. We hypothesized that the loss of sensory structures used in host plant selection could diminish the capacity to distinguish among alternative plants (cf. Bernays, 2001), resulting in the broader host range of the southwestern aphids. The capacity of these aphids to develop on this wide range of hosts was also demonstrated, by host performance studies showing that eastern and southwestern aphids each performed best on the ancestral A. trifida host, but exhibited no differences in their relative capacity to perform on the four test plants. Thus, eastern aphids appeared physiologically preadapted to use plants they did not locally encounter. Intriguingly, however, no further physiological adaptation to these new hosts had occurred in the southwest. Likewise, no host-associated molecular genetic differentiation was observed.

Further findings contributed more pieces to the puzzle. Cross-continental DNA sequence variation proved astonishingly low, with no evidence of geographic structure. Population genetic analyses indicated that the former result could reflect the loss of variation under bottleneck-induced genetic drift. The latter result suggested that U. ambrosia may represent an approximately panmictic population across the entire United States. Indeed, the small size and limited flying ability of aphids make them 'insect aeroplankton' that may be transported great distances by air currents, thus potentially homogenizing populations via long-distance gene flow.

A final suite of environmental observations potentially completes this puzzle. The riparian areas suitable for host plant growth proved to be rare and patchy in Arizona. Further, I experienced the unpredictability of desert environments in the form of dramatically varying levels of annual rainfall. Correspondingly, I observed great annual variation in the density of host plants, and associated aphid densities that varied by at least two orders of magnitude.

Cumulatively, the above findings support the following scenario for the evolution of host generalism in southwestern U. ambrosiae aphids: Eastern specialists blown to the southwest initially failed to become established due to the patchiness and unpredictable presence of their host plant. Eventually, mutations occurred that yielded the reduction of antennal sensilla and a correspondingly reduced capacity to discriminate against plants they were actually capable of developing on. This 'behavioral release' freed southwestern aphids to adopt multiple hosts, and from the precarious existence formerly imposed by the difficult challenge of consistently locating one specific host plant. Selective forces favoring this generalism are apparently strong enough to maintain the low-sensilla mutation(s) at high frequency in the face of considerable gene flow. Thus, in the unpredictable southwest, the advantages of U. ambrosiae generalism apparently far outweigh the efficiency advantages offered by specialization.

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Thermoregulation during Aging

B.A. Horwitz, ... R.B. McDonald, in Functional Neurobiology of Aging, 2001

2. Cold Tolerance in Rats

The larger size of the rat compared to the mouse makes it relatively more resistant to passive heat loss because of its lower ratio of body surface area to mass. However, the ability of rats to effectively cope with acute and chronic cold still deteriorates with advanced age. An early investigation by Hügin and Verzár (1957) involving 1 hr exposure to −0.5 to −14°C showed that with increasing age (from 3 to 31 months), groups of male rats exhibited significantly greater drops in rectal temperature. With exposure to colder temperatures, the age difference became even more pronounced (Verzár, 1958). As summarized in Table 59.1, subsequent studies have reported age-related alterations of cold-induced thermoregulation in male Long–Evans male rats, male and female Sprague–Dawley rats, female EMD:Wi-AF/Han rats, female Iva:WIWU rats, and male F344 rats. In contrast, the aging male Osborne–Mendel rat remains cold tolerant up to at least 24 months of age (McDonald et al., 1989b), and aging F344 females are more cold-resistant than are males at a comparable age (McDonald et al., 1989a).

The fact that different strains of mice and rats often exhibit different degrees of age-related decline in cold-induced thermoregulatory abilities (Kiang-Ulrich and Horvath, 1984a, 1985b; Martin et al., 1985; Talan and Ingram, 1986a; McDonald et al., 1989b) may be correlated with strain-specific life span, as suggested by Talan and Ingram (1986a), who observed greater age-related loss of cold tolerance in relatively shortlived A/J (mean life span of 22 months) vs longer-lived B6/AF1/J (mean life span of 29 months) males of an inbred strain of M. musculus. Cold-induced thermoregulation may also be influenced by the level of domestication, as indicated by the far better cold tolerance of old mice of a pen-bred strain of M. musculus captured from the wild than that seen in old mice of the domesticated strains A/J, C57BL/6J, and B6/AF1/J (Talan and Ingram, 1986a). In some cases, there are also strain differences in cold-induced thermoregulatory abilities of younger animals. For example, Kiang-Ulrich and Horvath (1984a) reported that 3- to 4-month-old male F344 rats better maintained core temperature during exposure to −10°C for 3 hr than did male Sprague–Dawley rats of the same age; in fact, even non-cold-acclimated older (24-month-old) male F344 rats exhibited greater tolerance to cold than did cold-acclimated young Sprague–Dawley rats (Kiang-Ulrich and Horvath, 1985b). The strain effect in younger rats reflected a blunted cold-induced increase in oxygen consumption in Sprague–Dawley vs F344, indicating that differences in heat production were partly responsible (Kiang-Ulrich and Horvath, 1984a). In other cases, strain differences in cold tolerance do not appear until later age. For example, at 12 months of age, both Osborne-Mendel and F344 male rats maintained colonic temperature during exposure to cold (6 hr at 6°C); at 24 months of age, however, only the Osborne-Mendel rats remained cold-tolerant, whereas the F344 rats developed a hypothermia of ∼5°C (McDonald et al., 1989b). This hypothermia occurred in spite of thermogenesis equivalent to that of older Osborne-Mendel rats, indicating that the older F344 rats had experienced greater heat loss and had a poorer ability to compensate for it metabolically. The primary cause of heat loss was unclear, but did not appear to be due simply to differences in body size and composition. The F344 rat is much smaller in size than the Osborne-Mendel rat (carcass mass of 311.8 gas in grams vs 460.7 g at 24 months), which suggests a greater body surface area-to-mass ratio and thus an increased potential for passive heat loss. However, the higher percentage carcass fat of F344 vs Osborne-Mendel rats (20.6% vs 15.1% at 24 months) implies a greater relative tissue insulation capacity to offset some of the body size effect. It thus seems that the peripheral vasoconstrictor response to cold, which leads to augmented thermal resistance of the body shell (Kenney and Buskirk, 1995), is attenuated in older F344 vs Osborne-Mendel rats. However, the involvement of other heat conservation mechanisms cannot be excluded. The percentage lean body mass and brown adipose tissue thermogenic capacity also differed with strain—both were significantly higher in Osborne-Mendel vs F344 rats (young and old) (McDonald et al., 1989b). These data suggest that Osborne-Mendel rats have a greater capacity for shivering and nonshivering thermogenesis than do F344 rats. The finding that cold-induced oxygen consumption did not differ between the two strains could reflect a greater reliance on shivering in the F344 than in the Osborne-Mendel rats (thermogenesis from brown fat is more effective than is shivering in warming the core of the animal because a greater proportion of the heat generated by shivering is lost to the environment due in part to increased blood flow to peripheral muscles and in part to the generation of heat closer to the animal's surface). It could also indicate that the two strains used their thermogenic capacities to different degrees—sub-maximally in the Osborne-Mendel rats and maximally (or closer to maximal) in the F344

Independent vector analysis for common subspace analysis: Application to multi-subject fMRI data yields meaningful subgroups of schizophrenia

Chapter 105 - Carbon IVa

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