Southern Regional Research Center

An empirical method for determining the crystallinity of native cellulose was studied with an x-ray diffractometer using the focusing and transmission techniques. The influence of fluctuations in the primary radiation and in the counting and recording processes have been determined. The intensity of the 002 interference and the amor phous scatter at 2θ = 18° was measured. The percent crystalline material in the total cellulose was expressed by an x-ray "crystallinity index." This was done for cotton cellulose decrystallized with aqueous solutions containing from 70% to nominally 100% ethylamine. The x-ray "crystallinity index" was correlated with acid hydrolysis crys tallinity, moisture regain, density, leveling-off degree of polymerization values, and infrared absorbance values for each sample. The results indicate that the crystallinity index is a time-saving empirical measure of relative crystallinity. The precision of the crystallinity index in terms of the several crystallinity criteria is given. Based on over 40 samples for which acid hydrolysis crystallinity values were available, the standard error was 6.5%.

Mycotoxins are secondary metabolites produced by microfungi that are capable of causing disease and death in humans and other animals. Because of their pharmacological activity, some mycotoxins or mycotoxin derivatives have found use as antibiotics, growth promotants, and other kinds of drugs; still others have been implicated as chemical warfare agents. This review focuses on the most important ones associated with human and veterinary diseases, including aflatoxin, citrinin, ergot akaloids, fumonisins, ochratoxin A, patulin, trichothecenes, and zearalenone.

Abstract Chromatographically homogeneous egg lecithin, as determined by TLC on Silica Gel G, has been isolated from crude egg phosphatides by column chromatography on alumina through modification of existing, lengthy methods. The modified method involved application of crude egg phosphatides to a column of alumina in the proportion of 1 g phosphatide/25 g alumina, and elution of the lecithin fraction with the 2‐component solvent system chloroform:methanol, 9:1 by vol. This method of purification separated lecithin from other choline and non‐choline components of crude phosphatides, avoided overloading of the alumina column, and made unnecessary the need for a second chromatographic fractionation of partially purified lecithin on silicic acid, which is needed in existing methods of purification of lecithin. The use of fresh yolks permitted easier removal of pigment from the final product than was possible with commercially dried yolks. Phosphatides extracted from dried yolks were much more highly colored than were the phosphatides extracted from fresh yolks and the color presisted through chromatography on alumina. The fatty acid/phosphorus molar ratio of the purified lecithin was 2.00, which is the theoretical FA/P molar ratio of phosphatidylcholine; other materials with this ratio were not present.

Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo–assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement. High-quality de novo–assembled genomes of two cultivated allotetraploid cotton species and whole-genome comparative analyses provide insights into the evolution of cotton genomes and improvement of fiber quality and resilience to stress.

Biochar has been heralded as an amendment to revitalize degraded soils, improve soil carbon sequestration, increase agronomic productivity, and enter into future carbon trading markets. However, scientific and economic technicalties may limit the ability of biochar to consistently deliver on these expectations. Past research has demonstrated that biochar is part of the black carbon continuum with variable properties due to the net result of production (e.g., feedstock and pyrolysis conditions) and postproduction factors (storage or activation). Therefore, biochar is not a single entity but rather spans a wide range of black carbon forms. Biochar is black carbon, but not all black carbon is biochar. Agronomic benefits arising from biochar additions to degraded soils have been emphasized, but negligible and negative agronomic effects have also been reported. Fifty percent of the reviewed studies reported yield increases after black carbon or biochar additions, with the remainder of the studies reporting alarming decreases to no significant differences. Hardwood biochar (black carbon) produced by traditional methods (kilns or soil pits) possessed the most consistent yield increases when added to soils. The universality of this conclusion requires further evaluation due to the highly skewed feedstock preferences within existing studies. With global population expanding while the amount of arable land remains limited, restoring soil quality to nonproductive soils could be key to meeting future global food production, food security, and energy supplies; biochar may play a role in this endeavor. Biochar economics are often marginally viable and are tightly tied to the assumed duration of agronomic benefits. Further research is needed to determine the conditions under which biochar can provide economic and agronomic benefits and to elucidate the fundamental mechanisms responsible for these benefits.

A new infrared ratio, α1372 cm. −1/α2900 cm. −1, is proposed for measuring crystallinity in cellulosic materials. The advantage of this ratio over others which have been used is that it can be applied to both celluloses I and II and, therefore, to samples containing a mixed lattice. Two series of samples, encompassing a wide range of crystallinity, were prepared from highly crystalline celluloses I and II. The infrared ratios of these samples were compared with crystallinity values from x-ray diffractograms and density measurements, and with accessibility data from moisture sorption. It was shown that the new infrared ratio ranks samples of both lattice types, as well as partly mercerized cottons, in the same order as do x-ray, density, and moisture sorption data. The correlation of the new infrared ratio with accessibility, derived from moisture regain, is better than with crystallinities from either x-ray or density measurements. Reasons for this are suggested.

The color, flavor, texture, and the nutritional value of fresh-cut fruit and vegetable products are factors critical to consumer acceptance and the success of these products. In this chapter, desirable and undesirable quality attributes of fresh-cut fruit and vegetable products are reviewed. Both instrumental and sensory measurements for determining these critical quality attributes are discussed. The advantages and disadvantages of sensory and instrumental quality measurements are described. A review of typical unit operations involved in the production of fresh-cut products is presented. The effects of fresh-cut processing techniques and treatments on sensory quality, including the appearance, texture, flavor (taste and aroma) of vegetables, and fruits are detailed.

While a large-scale soil amendment of biochars continues to receive interest for enhancing crop yields and to remediate contaminated sites, systematic study is lacking in how biochar properties translate into purported functions such as heavy metal sequestration. In this study, cottonseed hulls were pyrolyzed at five temperatures (200, 350, 500, 650, and 800 °C) and characterized for the yield, moisture, ash, volatile matter, and fixed carbon contents, elemental composition (CHNSO), BET surface area, pH, pHpzc, and by ATR-FTIR. The characterization results were compared with the literature values for additional source materials: grass, wood, pine needle, and broiler litter-derived biochars with and without post-treatments. At respective pyrolysis temperatures, cottonseed hull chars had ash content in between grass and wood chars, and significantly lower BET surface area in comparison to other plant source materials considered. The N:C ratio reached a maximum between 300 and 400 °C for all biomass sources considered, while the following trend in N:C ratio was maintained at each pyrolysis temperature: wood≪cottonseed hull≈grass≈pine needle≪broiler litter. To examine how biochar properties translate into its function as a heavy metal (NiII, CuII, PbII, and CdII) sorbent, a soil amendment study was conducted for acidic sandy loam Norfolk soil previously shown to have low heavy metal retention capacity. The results suggest that the properties attributable to the surface functional groups of biochars (volatile matter and oxygen contents and pHpzc) control the heavy metal sequestration ability in Norfolk soil, and biochar selection for soil amendment must be made case-by-case based on the biochar characteristics, soil property, and the target function.

Carboxymethyl cellulose (CMC) is one of the most promising cellulose derivatives. Due to its characteristic surface properties, mechanical strength, tunable hydrophilicity, viscous properties, availability and abundance of raw materials, low-cost synthesis process, and likewise many contrasting aspects, it is now widely used in various advanced application fields, for example, food, paper, textile, and pharmaceutical industries, biomedical engineering, wastewater treatment, energy production, and storage energy production, and storage and so on. Many research articles have been reported on CMC, depending on their sources and application fields. Thus, a comprehensive and well-organized review is in great demand that can provide an up-to-date and in-depth review on CMC. Herein, this review aims to provide compact information of the synthesis to the advanced applications of this material in various fields. Finally, this article covers the insights of future CMC research that could guide researchers working in this prominent field.

Aflatoxins, a group of polyketide-derived furanocoumarins (Fig. [1][1]), are the most toxic and carcinogenic compounds among the known mycotoxins. Among the at least 16 structurally related aflatoxins characterized, however, there are only four major aflatoxins, B1, B2, G1, and G2 (AFB1, AFG1, AFB2

The infrared spectra of highly crystalline samples of cellulose containing the lattice types I, II, and III were compared with one another and with the spectrum of amorphous cellulose in the 850–1500 cm.−1 region. The spectra of cellulose II and of amorphous cellulose showed interesting similarities at 1420, 893–897, and 1111 cm.−1, three bands which others have used to follow changes in crystallinity and lattice type because the spectrum of cellulose I differs distinctly at these points from that of amorphous cellulose or cellulose II. The similarity between amorphous cellulose and cellulose II prevents the use of these bands for crystallinity determination in samples with mixed lattice types–for instance, partly mercerized cotton. An explanation is offered for the resemblance of the two spectra, based on the hypothesis that a rearrangement of intramolecular hydrogen bonds, tending to stabilize a different conformation of the cellulose chain, occurs upon destruction of the native cellulose I crystal lattice.

Chars, a form of environmental black carbon resulting from incomplete burning of biomass, can immobilize organic contaminants by both surface adsorption and partitioning mechanisms. The predominance of each sorption mechanism depends upon the proportion of organic to carbonized fractions comprising the sorbent. Information is currently lacking in the effectiveness of char amendment for heavy metal immobilization in contaminated (e.g., urban and arms range) soils where several metal contaminants coexist. The present study employed sorbents of a common biomass origin (broiler litter manure) that underwent various degrees of carbonization (chars formed by pyrolysis at 350 and 700 degrees C and steam-activated analogues) for heavy metal (Cd(II), Cu(II), Ni(II), and Pb(II)) immobilization in water and soil. ATR-FTIR, (1)H NMR, and Boehm titration results suggested that higher pyrolysis temperature and activation lead to the disappearance (e.g., aliphatic -CH(2) and -CH(3)) and the formation (e.g., C-O) of certain surface functional groups, portions of which are leachable. Both in water and in soil, pH increase by the addition of basic char enhanced the immobilization of heavy metals. Heavy metal immobilization resulted in nonstoichiometric release of protons, that is, several orders of magnitude greater total metal concentration immobilized than protons released. The results suggest that with higher carbonized fractions and loading of chars, heavy metal immobilization by cation exchange becomes increasingly outweighed by other controlling factors such as the coordination by pi electrons (C=C) of carbon and precipitation.

There are only a few cells in the plant kingdom that are as exaggerated in their size or composition as cotton fibers. It is precisely their highly elongated structure and exceptional chemical make-up that establishes cotton fiber as an ideal model for studies of plant cell elongation and cell wall biogenesis. Cotton fibers are unicellular, therefore cell elongation can be evaluated independently from cell division. Although commonly called fibers, the more botanically appropriate term is trichome, since these cells are not part of the vascular tissue and arise, instead, from the ovule epidermis. The economically important seed trichomes of Gossypium hirsutum, the cotton variety most commonly grown in the United States, typically range in length from 2.2 to 3.0 cm. Fibers from another commercially important species, Gossypium barbadense, may reach lengths of over 6 cm, or one-third the height of an Arabidopsis plant. Fiber cells from G. hirsutumrange in diameter from 11 to 22 μm and are, therefore, 1,000 to 3,000 times longer than they are wide. Cotton fibers are linear cells and are never branched like many leaf trichomes. In addition to being among the longest plant cells ever characterized, a single cell wall biopolymer, cellulose, accounts for more than 95% of the dry weight of mature cotton fiber. Unlike many plant secondary cell walls, the cotton fiber wall contains no lignin. Typical of many plant cells, cotton fibers have a large central vacuole that becomes prominent quite early in development.

UNLABELLED: SUMMARY Aspergillus flavus is an opportunistic pathogen of crops. It is important because it produces aflatoxin as a secondary metabolite in the seeds of a number of crops both before and after harvest. Aflatoxin is a potent carcinogen that is highly regulated in most countries. In the field, aflatoxin is associated with drought-stressed oilseed crops including maize, peanut, cottonseed and tree nuts. Under the right conditions, the fungus will grow and produce aflatoxin in almost any stored crop seed. In storage, aflatoxin can be controlled by maintaining available moisture at levels below that which will support growth of A. flavus. A number of field control measures are being utilized or explored, including: modification of cultural practices; development of resistant crops through molecular and proteomic techniques; competitive exclusion using strains that do not produce aflatoxin; and development of field treatments that would block aflatoxin production. TAXONOMY: Aspergillus flavus Link (teleomorph unknown) kingdom Fungi, phyllum Ascomycota, order Eurotiales, class Eurotiomycetes, family Trichocomaceae, genus Aspergillus, species flavus. HOST RANGE: Aspergillus flavus has a broad host range as an opportunistic pathogen/saprobe. It is an extremely common soil fungus. The major concern with this fungus in agriculture is that it produces highly carcinogenic toxins called aflatoxins which are a health hazard to animals. In the field, A. flavus is predominantly a problem in the oilseed crops maize, peanuts, cottonseed and tree nuts. Under improper storage conditions, A. flavus is capable of growing and forming aflatoxin in almost any crop seed. It also is a pathogen of animals and insects. In humans it is predominantly an opportunistic pathogen of immunosuppressed patients. USEFUL WEBSITES: http://www.aspergillusflavus.org, http://www.aflatoxin.info/health.asp, plantpathology.tamu.edu/aflatoxin, http://www.aspergillus.org.uk.

Seeds of the tung tree (Vernicia fordii) produce large quantities of triacylglycerols (TAGs) containing approximately 80% eleostearic acid, an unusual conjugated fatty acid. We present a comparative analysis of the genetic, functional, and cellular properties of tung type 1 and type 2 diacylglycerol acyltransferases (DGAT1 and DGAT2), two unrelated enzymes that catalyze the committed step in TAG biosynthesis. We show that both enzymes are encoded by single genes and that DGAT1 is expressed at similar levels in various organs, whereas DGAT2 is strongly induced in developing seeds at the onset of oil biosynthesis. Expression of DGAT1 and DGAT2 in yeast produced different types and proportions of TAGs containing eleostearic acid, with DGAT2 possessing an enhanced propensity for the synthesis of trieleostearin, the main component of tung oil. Both DGAT1 and DGAT2 are located in distinct, dynamic regions of the endoplasmic reticulum (ER), and surprisingly, these regions do not overlap. Furthermore, although both DGAT1 and DGAT2 contain a similar C-terminal pentapeptide ER retrieval motif, this motif alone is not sufficient for their localization to specific regions of the ER. These data suggest that DGAT1 and DGAT2 have nonredundant functions in plants and that the production of storage oils, including those containing unusual fatty acids, occurs in distinct ER subdomains.

The degree of crystallinity in cellulose significantly affects the physical, mechanical, and chemical properties of cellulosic materials, their processing, and their final application. Measuring the crystalline structures of cellulose is a challenging task due to inadequate consistency among the variety of analytical techniques available and the lack of absolute crystalline and amorphous standards. Our article reviews the primary methods for estimating the crystallinity of cellulose, namely, X-ray diffraction (XRD), nuclear magnetic resonance (NMR), Raman and Fourier-transform infrared (FTIR) spectroscopy, sum-frequency generation vibrational spectroscopy (SFG), as well as differential scanning calorimetry (DSC), and evolving biochemical methods using cellulose binding molecules (CBMs). The techniques are compared to better interrogate not only the requirements of each method, but also their differences, synergies, and limitations. The article highlights fundamental principles to guide the general community to initiate studies of the crystallinity of cellulosic materials.

Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton (Gossypium spp.) genomes represent a challenging case. To this end, a coalition of cotton genome scientists has developed a strategy for sequencing the cotton genomes, which will vastly expand opportunities for cotton research and improvement worldwide. Cotton bolls at maturity (A) and cotton fibers under electron microscope (B). Photos courtesy of Mike Doughtery from the National Cotton Council (A) and Barbara Triplet (B). Cotton production provides income for approximately 100 million families, and approximately 150 countries are involved in cotton import and export. Its economic impact is estimated to be approximately $500 billion/year worldwide. China is the largest producer and consumer of raw cotton, but more than 80 countries, including Australia, some African countries, India, Pakistan, the United States, Mexico, and Uzbekistan, also produce cotton. The United States is the second largest producer, and grows cotton worth approximately $6 billion/year for fiber and approximately $1 billion/year for cottonseed oil and meal. Cotton is a major economic driver for some developing countries, like Uzbekistan, which annually produces approximately 4 million tons of raw cotton and exports fiber worth approximately $900 million. Cotton fiber is an outstanding model for the study of plant cell elongation and cell wall and cellulose biosynthesis (Kim and Triplett, 2001). Each seed has approximately 25,000 cotton fibers, each of which is a single and greatly elongated cell from the epidermal layer of the ovule (Fig. 1B). The fiber is composed of nearly pure cellulose, the largest component of plant biomass. Compared to lignin, cellulose is easily convertible to biofuels. Translational genomics of cotton fiber and cellulose may lead to the improvement of diverse biomass crops. The genus Gossypium includes approximately 45 diploid (2n = 2x = 26) and five tetraploid (2n = 4x = 52) species, all exhibiting disomic patterns of inheritance. Diploid species (2n = 26) fall into eight genomic groups (A–G, and K). The African clade, comprising the A, B, E, and F genomes (Wendel and Cronn, 2003), occurs naturally in Africa and Asia, while the D genome clade is indigenous to the Americas. A third diploid clade, including C, G, and K, is found in Australia. All 52 chromosome species, including Gossypium hirsutum and Gossypium barbadense, are classic natural allotetraploids that arose in the New World from interspecific hybridization between an A genome-like ancestral African species and a D genome-like American species. The closet extant relatives of the original tetraploid progenitors are the A genome species Gossypium herbaceum (A1) and Gossypium arboreum (A2) and the D genome species Gossypium raimondii (D5) ‘Ulbrich’ (Brubaker et al., 1999). Polyploidization is estimated to have occurred 1 to 2 million years ago (Wendel and Cronn, 2003), giving rise to five extant allotetraploid species. Interestingly, the A genome species produce spinnable fiber and are cultivated on a limited scale, whereas the D genome species do not (Applequist et al., 2001). More than 95% of the annual cotton crop worldwide is G. hirsutum, Upland or American cotton, and the extra-long staple or Pima cotton (G. barbadense) accounts for less than 2% (National Cotton Council, http://www.cotton.org, 2006). Understanding the contribution of the A and D subgenomes to gene expression in the allotetraploids may facilitate improving fiber traits (Jiang et al., 1998; Saha et al., 2006; Yang et al., 2006). Decoding cotton genomes will be a foundation for improving understanding of the functional and agronomic significance of polyploidy and genome size variation within the Gossypium genus. The haploid genome sizes are estimated to be approximately 880 Mb for G. raimondii ‘Ulbrich’, approximately 1.75 Gb for G. arboreum, and approximately 2.5 Gb for G. hirsutum (Hendrix and Stewart, 2005). Variation in DNA content in the diploid species reflects increases and decreases in copy numbers of various repeat families (Zhao et al., 1998), especially retrotransposon-like elements (Hawkins et al., 2006). DNA content of the allopolyploids is approximately the sum of the A and D genome progenitors, and nearly all of the approximately 22,000 amplified fragment length polymorphism fragments surveyed are additive in the allopolyploids (Liu et al., 2001). This suggests a role of genetic and epigenetic mechanisms for gene expression in phenotypic variation and selection of allotetraploid species (Jiang et al., 1998; Wendel, 2000; Adams et al., 2003; Yang et al., 2006; Chen, 2007). Genomic resources such as bacterial artificial chromosomes (BACs), ESTs, linkage maps, and integrated genetic and physical maps provide landmarks for sequence analysis and assembly. Linkage maps in tetraploid cotton have been most densely populated by analysis of interspecific G. hirsutum × G. barbadense F2 families (Reinisch et al., 1994; Rong et al., 2004) and backcross lines (Lacape et al., 2005; Guo et al., 2007) due to low levels of DNA polymorphism within cotton species. Mapping populations have also been developed for G. hirsutum × Gossypium tomentosum F2 (Waghmare et al., 2005) and Gossypium mustelinum × G. hirsutum (P. Chee and A. Paterson, unpublished data). Molecular marker linkage groups were localized and orientated with various interspecific hypoaneuploid F1 hybrids available for most chromosomes, and elsewhere by in situ hybridization (Hanson et al., 1995; Saha et al., 2006; Wang et al., 2006;,Ji et al., 2007). Synteny and locus order were also determined by wide-cross whole-genome radiation hybrid mapping, a method complementary to other forms of cotton genome mapping (Gao et al., 2006). At least a dozen genetic maps of crosses between diverse cotton species and genotypes are available, most made to map specific traits and quantitative trait loci (QTLs). Some of these maps collectively include approximately 5,000 DNA markers (approximately 3,300 restriction fragment length polymorphisms, approximately 700 amplified fragment length polymorphisms, approximately 1,000 simple sequence repeats, and approximately 100 single nucleotide polymorphisms). In addition, sequence-tagged site-based maps consisting of 2,584 loci at 1.72-cM (approximately 600 kb) intervals in tetraploids (AD genomes), 1,014 loci at 1.42-cM (approximately 600 kb) intervals in diploids (D genome; Rong et al., 2004, 2005), and an EST-simple sequence repeat-based genetic map of 1,710 loci at 1.92-cM intervals in tetraploids (AD genomes; Guo et al., 2007) are available. There is a high degree of colinearity among the respective genome types (Rong et al., 2005). Of particular long-term value are permanent recombinant inbred lines (RILs) and chromosome substitution lines. RILs have already begun to contribute to QTL definition, e.g. for a G. hirsutum × G. barbadense cross (Frelichowski et al., 2006) and intraspecific crosses within G. hirsutum (Ulloa et al., 2005; Abdurakhmonov et al., 2007; Shen et al., 2007). Near-isogenic disomic substitution lines of G. hirsutum enable the localization of net phenotypic effects. Moreover, chromosome-specific RILs enable high-resolution QTL definition and mapping (Stelly et al., 2005). Reference maps have incorporated diverse types and sources of DNA markers. Jean-Marc Lacape and his colleagues have integrated linkage maps developed by researchers in China (T. Zhang), France (J.M. Lacape), and the United States (A. Paterson and M. Ulloa) into TropGENE-DB (http://tropgenedb.cirad.fr/en/cotton.html) using a CMap comparative map viewer (Nguyen et al., 2004). A similar map viewer has been implemented in the CottonDB (http://cottondb.org) and the Cotton Microsatellite Database (http://www.cottonmarker.org) that contains approximately 8,000 microsatellites (Blenda et al., 2006). The further development of comprehensive linkage maps will be used to anchor and assemble genomic sequences. BAC libraries have been developed for several G. hirsutum cultivars (‘0–613-2R’, ‘Acala Maxxa’, ‘Auburn 623’, ‘Tamcot HQ95’, and ‘TM-1’), G. barbadense (‘Pima S6’), two G. arboreum strains (AKA8401 and Jinglinzhongmian), G. raimondii, Gossypium longicalyx, and an outgroup (Gossypioides kirkii). A total of 10 genome equivalents of G. raimondii BACs has been fingerprinted using standard procedures (Marra et al., 1997). All genetically mapped probes have been incorporated into the fingerprint assembly using the overlapping oligonucleotides hybridization method (Cai et al., 1998). The assembly will be publicly available via a WebFPC site and incorporated into the existing BACMan resource at the Plant Genome Mapping Laboratory (www.plantgenome.uga.edu). A G. hirsutum L. ‘TM-1’ library has been used to develop integrated genetic and physical maps (R. Kohel, J. Yu, and T. Zhang, unpublished data). A G. hirsutum L. ‘0-613-2R’ library has been successfully used to locate the restorer of fertility gene in a 100-kb region (Yin et al., 2006) and to assign linkage groups to identified chromosomes using BAC-fluorescence in situ hybridization (FISH; Wang et al., 2006). As of July 18, 2007, 356,889 Gossypium sequences were in GenBank, including 40,069 ESTs from G. arboreum (A), 67,098 from G. raimondii (D), 232,006 from G. hirsutum (AD tetraploid), and a few from other Gossypium members (Arpat et al., 2004; Udall et al., 2006; Yang et al., 2006; Taliercio and Boykin, 2007). Among these ESTs, many are from developing fiber and are enriched in putative MYB and WRKY transcription factors and phytohormone regulators (Yang et al., 2006). Transcription factors in these families are known to be important in the development of Arabidopsis (Arabidopsis thaliana) leaf trichomes, and phytohormonal effects on fiber cell development in immature cotton ovules cultured in vitro are well documented (Beasley and Ting, 1974). Moreover, A subgenome ESTs of all functional classifications are dramatically enriched in G. hirsutum fiber (Yang et al., 2006), a result consistent with the production of long lint fibers in A genome species. Some ESTs have been used to develop sequence-specific markers in breeding and to construct microarrays, leading to the identification of many candidate genes involved in fiber cell initiation and elongation (Arpat et al., 2004; Lee et al., 2006; Shi et al., 2006; Wu et al., 2006; Udall et al., 2007). The Malvales (including cotton) are the nearest relative to Arabidopsis outside of the Brassicales for which detailed genetic and physical maps have been described (Bowers et al., 2003). Comparative analyses reveal a considerable degree of synteny/colinearity between the ancestral cotton and Arabidopsis genomes. A total of 1,738 (62%) sequenced loci in cotton had matches in Arabidopsis (Rong et al., 2005). Gaining access to the unique features that distinguish cotton from other plants both as an economic crop and a botanical model might benefit from translational genomics, leveraging of structural and functional information from Arabidopsis. A comprehensive strategy needs to consider present needs along with long-term goals in relation to economics, technology, and priorities. A strong case can be made for complete sequencing of one or more representatives of each Gossypium genome group, A, B, C, D, E, F, G, K, and a tetraploid-derived AD (n = 26) genome (Paterson, 2006). Continuing progress in sequencing throughput and cost reduction will render this goal increasingly feasible and desirable. Sequencing representatives from each diploid clade will be important for molecular dissection of evolutionary patterns and biological phenomena, including the genomic and morphological diversity that has permitted species within the genus to adapt to a wide range of ecosystems in warmer and arid regions of the world. Sequences from A and D genome diploid species will aid tetraploid AD genome sequence assembly and could prove to be invaluable for revealing differences in gene content and expression patterns across the ploidy levels and for providing insight into polyploid genome evolution. Although there is an approximately 3-fold variation in genome size among the diploids, the high degree of conservation of gene order at the macro level between diploids and tetraploids (Brubaker et al., 1999; Rong et al., 2004; Desai et al., 2006) suggests that the vast majority of sequence data from diploids will extrapolate directly to tetraploids. Sequencing an elite G. hirsutum genome, AD, will provide the ultimate reference and resource for application-oriented structural, functional, and bioinformatic needs for the species that accounts for >95% of world cotton production. Sequencing an elite G. arboreum or G. herbaceum genome will provide valuable data on fiber genes. Comparisons of four species across two ploidy levels, including A1, A2, D5, and AD tetraploid subgenomes, will provide clues as to how polyploidy and domestication “interact.” Parallel comparisons between domesticated and nondomesticated forms of the A and AD genome species will shed light on the effects of artificial versus natural selection. Based on these considerations, one can envision multiple and parallel approaches to reveal genome diversity and complete genome information of Gossypium genomes. Additional ESTs should be sequenced from other diploid (e.g. C, G, and K genomes) and tetraploid (e.g. G. barbadense, AD) clades and in late fiber development stages such as secondary wall biosynthesis (Haigler et al., 2005). Sequencing using gene enrichment techniques such as methylation filtration and Cot-based cloning that appear to offer complementary coverage of the low-copy DNA will generate novel genomic sequences that are absent in EST collections. A pilot study in methylation filtration comparing G. raimondii, G. arboreum, G. hirsutum, and G. barbadense is under way (B.E. Scheffler, S. Saha, and Orion Genomics, unpublished data). The whole-genome shotgun sequence of the smallest Gossypium genome, G. raimondii (approximately 880 Mb), will provide fundamental information about gene content and organization. The U.S. Department of Energy Joint Genome Institutes (http://www.jgi.doe.gov/) has selected G. raimondii for a pilot study for shotgun sequencing at 0.5× coverage to better define the genome and establish a workable strategy for its complete sequencing. A partially or fully sequenced G. raimondii genome will establish the critical initial template for characterizing the spectrum of diversity among the eight Gossypium genome types and three polyploid clades (Wendel and Cronn, 2003). A survey of approximately 100 of the most abundant repetitive families in the tetraploid genome showed only four to be abundant in the D genome but rare or absent in the A genome (Zhao et al., 1998), which diverged from the D genome of G. raimondii about 5 to 10 million years ago (Senchina et al., 2003). Thus, most high-copy repetitive DNA families in the D genome are at least 5 to 10 million years old and likely to be amenable to assembly by a whole-genome shotgun approach. A BAC-based AD genome sequence may offer superior opportunities to elucidate the types and frequencies of changes that distinguish polyploid from diploid cottons. The process could be greatly enhanced by using the finished genome sequence of a diploid species as a template and guide. Intergenomic concerted evolution and the presence of recently amplified repetitive DNA families would be problematic for a whole-genome shotgun approach. A reasonable approach is to establish minimum tiling path of fingerprinted contigs of G. hirsutum homoeologous chromosomes. This goal can be achieved by developing integrated homoeologous chromosome maps that include anchored DNA markers in linkage maps and BAC-end sequences in physical maps that can be further validated by radiation hybrid mapping and/or BAC-FISH (Hanson et al., 1995; Wang et al., 2006). FISH of landed BACs indicated that homoeologous segments were readily detectable by BAC-FISH for low-copy probes and that they seemed amenable to differentiation on the basis of FISH signal strength (Wang et al., 2007). Large duplicated segments have been reported within individual corresponding homoeologous chromosomes, suggesting ancient or recent genome expansion in cotton genomes (Rong et al., 2005; Wang et al., 2007). It will be prudent to sequence and assemble representative homoeologous BACs and/or a few pairs of homoeologous chromosomes prior to large-scale sequencing of G. hirsutum tetraploid genomes. The cotton community and industry are cooperatively developing workshops and communication methods for planning, coordinating, and executing sequencing and post-sequencing activities. The key questions under consideration are: (1) which species should we sequence; and (2) which techniques should be used for each genome? In the long term, a singularly important goal will be to establish the complete genome sequence of the most widely cultivated cotton, i.e. G. hirsutum. Given its genomic redundancies, size (approximately 2.5 polyploid and other we a to approaches that range from to on sequence from genomes, e.g. G. raimondii and G. herbaceum or G. this long-term we envision the specific shotgun sequencing of G. raimondii, a of cultivated and among the smallest Gossypium genomes, to provide fundamental information about gene content and organization. Comparative sequencing of corresponding segments of tetraploid G. hirsutum to reveal the likely to be complete sequencing. and a strategy to sequence of G. hirsutum. This may well of a minimum tiling path of contigs of G. hirsutum homoeologous chromosomes. bioinformatic and to and the information to the cotton and of sequence information should functional and structural genomic resources at the molecular and in levels, sequence for genome and expression detailed of the cotton genome sequence to gene and cloning in this species, a large-scale for DNA sequence diversity nucleotide and facilitate high-resolution whole-genome develop genomic tiling to gene expression and analysis of biological and agronomic and sequence and and and To and of comprehensive cotton genomic the most important factors to consider are data and and data analysis and To genomic research in cotton, the Cotton Genome in with a to of the and of the cotton genome for the benefit of the A site will be identified to establish a that will researchers to and about cotton genome sequencing and genomic The of data from various sequencing will be and to for many is to develop a data that can facilitate access and of genomic and sequence In to the CMap and Cotton Microsatellite CottonDB (http://cottondb.org) provides and including genetic and physical maps, trait and The Cotton the community a single of to Cotton the Cotton Database et al., 2006), provides for an to and comparative and is integrated with comparative and genomic sequence expression and the for Cotton consisting of approximately from ESTs can be found at the site There is a to expand bioinformatic for and the cotton genomic sequences that will be in the A model community is The Arabidopsis The cotton sequence of the should be to and cotton information resources in cotton using genome and gene Some existing may be to a of data and community but resources will be to key bioinformatic A for sequencing polyploid genomes is the among and homoeologous sequences in diploid and allotetraploid species. Gossypium species are (Bowers et al., 2003; Rong et al., 2005). Moreover, allopolyploids two or more of homoeologous chromosomes, leading to genetic and epigenetic changes in subgenomes and 2007). bioinformatic and for assembly and of genomes is a for sequencing cotton and other polyploid genomes such as and A sequenced cotton genome will provide a reference for many genomes in Gossypium species using and sequencing (e.g. and 2006). The of will be to establish a reference sequence anchored to physical and genetic This sequence will be used to and genomes and to the gene and basis of phenotypic and evolutionary diversity for cotton cotton genomes will fundamental research on genome and gene cell differentiation and cellulose cell molecular of cell wall and will include improvement of biological key to and production of and and biomass as well as of cotton and will be by improvement in elements key to all of e.g. improvement of and and reduction of and some are more than the and are on both and The community is and of the and value of sequencing cotton genomes. for a cotton genome sequencing and for and from the members of the Cotton Genome members of the cotton genomics and breeding community for and for not many to for cotton research is by from the National U.S. Department of Cotton National of and groups and in Australia, India, Pakistan, the United States, Uzbekistan, and The Cotton Genome Sequencing can be found at

Cotton fabric was treated with flame-retardant coatings composed of branched polyethylenimine (BPEI) and sodium montmorillonite (MMT) clay, prepared via layer-by-layer (LbL) assembly. Four coating recipes were created by exposing fabric to aqueous solutions of BPEI (pH 7 or 10) and MMT (0.2 or 1 wt %). BPEI pH 10 produces the thickest films, while 1 wt % MMT gives the highest clay loading. Each coating recipe was evaluated at 5 and 20 bilayers. Thermogravimetric analysis showed that coated fabrics left as much as 13% char after heating to 500 degrees C, nearly 2 orders of magnitude more than uncoated fabric, with less than 4 wt % coming from the coating itself. These coatings also reduced afterglow time in vertical flame tests. Postburn residues of coated fabrics were examined with SEM and revealed that the weave structure and fiber shape in all coated fabrics were preserved. The BPEI pH 7/1 wt % MMT recipe was most effective. Microcombustion calorimeter testing showed that all coated fabrics reduced the total heat release and heat release capacity of the fabric. Fiber count and strength of uncoated and coated fabric are similar. These results demonstrate that LbL assembly is a relatively simple method for imparting flame-retardant behavior to cotton fabric. This work lays the foundation for using these types of thin film assemblies to make a variety of complex substrates (foam, fabrics, etc.) flame resistant.

This review discusses the basic chemical reactions that affect food flavor quality. Although there are many reactions that can lead to the deterioration of quality in foods, this review focuses on lipid oxidation and how it adversely affects flavor principals. It also presents technological advances for studying the basic mechanism of lipid oxidation, for measuring its intensity, and for retaining food quality. The food commodities that provide the subject matter for this review include vegetable oils, legumes, cereal grains, eggs, beef, lamb, poultry, seafoods, and catfish. The methodologies for assessing food quality form a multidisciplinary approach that includes primarily instrumental analysis by direct gas chromatography, chemical analysis by the TBA test, and sensory analysis by quantitative descriptive determinations. The author hopes that the information presented in this review is applicable to food commodities not discussed.

The genus Aspergillus is one of the most important filamentous fungal genera. Aspergillus species are used in the fermentation industry, but they are also responsible of various plant and food secondary rot, with the consequence of possible accumulation of mycotoxins. The aflatoxin producing A. flavus and A. parasiticus, and ochratoxinogenic A. niger, A. ochraceus and A. carbonarius species are frequently encountered in agricultural products. Studies on the biodiversity of toxigenic Aspergillus species is useful to clarify molecular, ecological and biochemical characteristics of the different species in relation to their different adaptation to environmental and geographical conditions, and to their potential toxigenicity. Here we analyzed the biodiversity of ochratoxin producing species occurring on two important crops: grapes and coffee, and the genetic diversity of A. flavus populations occurring in agricultural fields. Altogether nine different black Aspergillus species can be found on grapes which are often difficult to identify with classical methods. The polyphasic approach used in our studies led to the identification of three new species occurring on grapes: A. brasiliensis, A. ibericus, and A. uvarum. Similar studies on the Aspergillus species occurring on coffee beans have evidenced in the last five years that A. carbonarius is an important source of ochratoxin A in coffee. Four new species within the black aspergilli were also identified in coffee beans: A. sclerotioniger, A. lacticoffeatus, A. sclerotiicarbonarius, and A. aculeatinus. The genetic diversity within A. flavus populations has been widely studied in relation to their potential aflatoxigenicity and morphological variants L- and S-strains. Within A. flavus and other Aspergillus species capable of aflatoxin production, considerable diversity is found. We summarise the main recent achievements in the diversity of the aflatoxin gene cluster in A. flavus populations, A. parasiticus and the non-toxigenic A. oryzae. Studies are needed in order to characterise the aflatoxin biosynthetic genes in the new related taxa A. minisclerotigenes and A. arachidicola.