Louisiana State University Agricultural Center

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

ABSTRACT The use of genotype main effect (G) plus genotype‐by‐environment (GE) interaction (G+GE) biplot analysis by plant breeders and other agricultural researchers has increased dramatically during the past 5 yr for analyzing multi‐environment trial (MET) data. Recently, however, its legitimacy was questioned by a proponent of Additive Main Effect and Multiplicative Interaction (AMMI) analysis. The objectives of this review are: (i) to compare GGE biplot analysis and AMMI analysis on three aspects of genotype‐by‐environment data (GED) analysis, namely mega‐environment analysis, genotype evaluation, and test‐environment evaluation; (ii) to discuss whether G and GE should be combined or separated in these three aspects of GED analysis; and (iii) to discuss the role and importance of model diagnosis in biplot analysis of GED. Our main conclusions are: (i) both GGE biplot analysis and AMMI analysis combine rather than separate G and GE in mega‐environment analysis and genotype evaluation, (ii) the GGE biplot is superior to the AMMI1 graph in mega‐environment analysis and genotype evaluation because it explains more G+GE and has the inner‐product property of the biplot, (iii) the discriminating power vs. representativeness view of the GGE biplot is effective in evaluating test environments, which is not possible in AMMI analysis, and (iv) model diagnosis for each dataset is useful, but accuracy gain from model diagnosis should not be overstated.

This review focuses mainly on eudicot seeds, and on the interactions between abscisic acid (ABA), gibberellins (GA), ethylene, brassinosteroids (BR), auxin and cytokinins in regulating the interconnected molecular processes that control dormancy release and germination. Signal transduction pathways, mediated by environmental and hormonal signals, regulate gene expression in seeds. Seed dormancy release and germination of species with coat dormancy is determined by the balance of forces between the growth potential of the embryo and the constraint exerted by the covering layers, e.g. testa and endosperm. Recent progress in the field of seed biology has been greatly aided by molecular approaches utilizing mutant and transgenic seeds of Arabidopsis thaliana and the Solanaceae model systems, tomato and tobacco, which are altered in hormone biology. ABA is a positive regulator of dormancy induction and most likely also maintenance, while it is a negative regulator of germination. GA releases dormancy, promotes germination and counteracts ABA effects. Ethylene and BR promote seed germination and also counteract ABA effects. We present an integrated view of the molecular genetics, physiology and biochemistry used to unravel how hormones control seed dormancy release and germination.

Hurricanes Katrina and Rita showed the vulnerability of coastal communities and how human activities that caused deterioration of the Mississippi Deltaic Plain (MDP) exacerbated this vulnerability. The MDP formed by dynamic interactions between river and coast at various temporal and spatial scales, and human activity has reduced these interactions at all scales. Restoration efforts aim to re-establish this dynamic interaction, with emphasis on reconnecting the river to the deltaic plain. Science must guide MDP restoration, which will provide insights into delta restoration elsewhere and generally into coasts facing climate change in times of resource scarcity.

Chitosan is a modified, natural biopolymer derived by deacetylation of chitin, a major component of the shells of crustacean. Recently, chitosan has received increased attention for its commercial applications in the biomedical, food, and chemical industries. Use of chitosan in food industry is readily seen due to its several distinctive biological activities and functional properties. The antimicrobial activity and film-forming property of chitosan make it a potential source of food preservative or coating material of natural origin. This review focuses on the applications of chitosan for improvement of quality and shelf life of various foods from agriculture, poultry, and seafood origin.

We evaluated and compared various broken-line regression models and SAS (SAS Inst. Inc., Cary, NC) procedures for estimating nutrient requirements from nutrient dose response data. We used the SAS (Version 9) procedures NLIN and NLMixed and the response data of Parr et al. (2003), who evaluated the isoleucine requirement of growing swine. The SAS NLIN was used to fit 2 different broken-line regression models: a simple 2 straight-line, one-breakpoint model and a quadratic broken-line model in which the response below the single breakpoint was quadratic; there was a plateau above the breakpoint. The latter was fit using 2 different approaches in NLIN. We also used SAS NLMixed to fit 3 different broken-line models: the 2 straight-line, one-breakpoint model that included a random component for the plateau; the quadratic broken-line model that included a random component for the plateau; and the quadratic broken-line model that included random components for both the plateau and the slope of the curve below the requirement. The best fit (greater adjusted R2; least log likelihood) was achieved using SAS NLMixed and the quadratic model with a random component for asymptote included in the model. Model descriptions, SAS code, and output are presented and discussed. Additionally, we provide other examples of possible models and discuss approaches to handling difficult-to-fit data.

Fibroblasts are a dynamic cell type that achieve selective differentiated states to mediate acute wound healing and long-term tissue remodeling with scarring. With myocardial infarction injury, cardiomyocytes are replaced by secreted extracellular matrix proteins produced by proliferating and differentiating fibroblasts. Here, we employed 3 different mouse lineage-tracing models and stage-specific gene profiling to phenotypically analyze and classify resident cardiac fibroblast dynamics during myocardial infarction injury and stable scar formation. Fibroblasts were activated and highly proliferative, reaching a maximum rate within 2 to 4 days after infarction injury, at which point they expanded 3.5-fold and were maintained long term. By 3 to 7 days, these cells differentiated into myofibroblasts that secreted abundant extracellular matrix proteins and expressed smooth muscle α-actin to structurally support the necrotic area. By 7 to 10 days, myofibroblasts lost proliferative ability and smooth muscle α-actin expression as the collagen-containing extracellular matrix and scar fully matured. However, these same lineage-traced initial fibroblasts persisted within the scar, achieving a new molecular and stable differentiated state referred to as a matrifibrocyte, which was also observed in the scars of human hearts. These cells express common and unique extracellular matrix and tendon genes that are more specialized to support the mature scar.

The sea breeze system (SBS) occurs at coastal locations throughout the world and consists of many spatially and temporally nested phenomena. Cool marine air propagates inland when a cross‐shore mesoscale (2–2000 km) pressure gradient is created by daytime differential heating. The circulation is also characterized by rising currents at the sea breeze front and diffuse sinking currents well out to sea and is usually closed by seaward flow aloft. Coastal impacts include relief from oppressive hot weather, development of thunderstorms, and changes in air quality. This paper provides a review of SBS research extending back 2500 years but focuses primarily on recent discoveries. We address SBS forcing mechanisms, structure and related phenomena, life cycle, forecasting, and impacts on air quality.

Silicon (Si) plays a pivotal role in the nutritional status of a wide variety of monocot and dicot plant species and helps them, whether directly or indirectly, counteract abiotic and/or biotic stresses. In general, plants with a high root or shoot Si concentration are less prone to pest attack and exhibit enhanced tolerance to abiotic stresses such as drought, low temperature, or metal toxicity. However, the most remarkable effect of Si is the reduction in the intensities of a number of seedborne, soilborne, and foliar diseases in many economically important crops that are caused by biotrophic, hemibiotrophic, and necrotrophic plant pathogens. The reduction in disease symptom expression is due to the effect of Si on some components of host resistance, including incubation period, lesion size, and lesion number. The mechanical barrier formed by the polymerization of Si beneath the cuticle and in the cell walls was the first proposed hypothesis to explain how this element reduced the severity of plant diseases. However, new insights have revealed that many plant species supplied with Si have the phenylpropanoid and terpenoid pathways potentiated and have a faster and stronger transcription of defense genes and higher activities of defense enzymes. Photosynthesis and the antioxidant system are also improved for Si-supplied plants. Although the current understanding of how this overlooked element improves plant reaction against pathogen infections, pest attacks, and abiotic stresses has advanced, the exact mechanism(s) by which it modulates plant physiology through the potentiation of host defense mechanisms still needs further investigation at the genomic, metabolomic, and proteomic levels.

The antioxidant activities of vitamin E (alpha-tocopherol, alpha-tocotrienol, gamma-tocopherol, and gamma-tocotrienol) and gamma-oryzanol components (cycloartenyl ferulate, 24-methylenecycloartanyl ferulate, and campesteryl ferulate) purified from rice bran were investigated in a cholesterol oxidation system accelerated by 2,2'-azobis(2-methylpropionamidine) dihydrochloride. All components exhibited significant antioxidant activity in the inhibition of cholesterol oxidation. The highest antioxidant activity was found for 24-methylenecycloartanyl ferulate, and all three gamma-oryzanol components had activities higher than that of any of the four vitamin E components. Because the quantity of gamma-oryzanol is up to 10 times higher than that of vitamin E in rice bran, gamma-oryzanol may be a more important antioxidant of rice bran in the reduction of cholesterol oxidation than vitamin E, which has been considered to be the major antioxidant in rice bran. The antioxidant function of these components against cholesterol oxidation may contribute to the potential hypocholesterolemic property of rice bran.

A challenge facing the biofuel industry is to develop an economically viable and sustainable biorefinery. The existing potential biorefineries in Louisiana, raw sugar mills, operate only 3 months of the year. For year-round operation, they must adopt other feedstocks, besides sugar cane, as supplemental feedstocks. Energy cane and sweet sorghum have different harvest times, but can be processed for bio-ethanol using the same equipment. Juice of energy cane contains 9.8% fermentable sugars and that of sweet sorghum, 11.8%. Chemical composition of sugar cane bagasse was determined to be 42% cellulose, 25% hemicellulose, and 20% lignin, and that of energy cane was 43% cellulose, 24% hemicellulose, and 22% lignin. Sweet sorghum was 45% cellulose, 27% hemicellulose, and 21% lignin. Theoretical ethanol yields would be 3,609 kg per ha from sugar cane, 12,938 kg per ha from energy cane, and 5,804 kg per ha from sweet sorghum.

Plant-mediated interactions between pathogenic microorganisms and arthropod herbivores occur when arthropod infestation or pathogen infection changes the shared host plant in ways that affect a subsequent attacker of the opposite type. Interest in such "tripartite" interactions has increased as the ecological and plant physiological framework for understanding and contextualizing them has developed. The outcomes of plant-mediated interactions are variable, and only a few provisional patterns can be identified at present. However, these interactions can have important consequences not only for individual pathogens and herbivores, but also for the population dynamics of both types of organisms in managed and natural ecosystems. Research has focused on the role of two plant response pathways in mediating tripartite interactions, one involving jasmonic acid and the other salicylic acid. Further studies of plant-mediated interactions will facilitate an understanding of how plants coordinate and integrate their defenses against multiple biotic threats.

The number of all possible linear and branched isomers of a hexasaccharide was calculated and found to be >1.05 × 1012. This large number defines the Isomer Barrier, a persistent technological barrier to the development of a single analytical method for the absolute characterization of carbohydrates, regardless of sample quantity. Because of this isomer barrier, no single method can be employed to determine complete oligosaccharide structure in 100 nmol amounts with the same assurance that can be achieved for 100 pmol amounts with single-procedure Edman peptide or Sanger DNA sequencing methods. Difficulties in the development of facile synthetic schemes for oligosaccharides are also explained by this large number. No current method of chemical or physical analysis has the resolution necessary to distinguish among 1012 structures having the same mass. Therefore the ‘characterization’ of a middle-weight oligosaccharide solely by NMR or mass spectrometry necessarily contains a very large margin of error. Greater uncertainty accompanies results performed solely by sequential enzyme degradation followed by gel-permeation chromatography or electrophoresis, as touted by some commercial advertisements. Much of the literature which uses these single methods to ‘characterize’ complex carbohydrates is, therefore, in question, and journals should beware of publishing structural characterizations unless the authors reveal all alternate possible structures which could result from their analysis. Today, only a combination of quantitative sugar analysis, methylation linkage analysis, partial degradation by enzymes or chemistry, and mass spectrometry can reduce the number of possibilities to one. The present study yields a number of individual formulae and a master set of equations necessary for the determination of all possible reducing-end isomers for di- to octasaccharides, above which branching isomers generate astronomical numbers, larger than Avogadro's number. Because hexasaccharides are generally among the largest biologically active, protein-recognized oligosaccharide sequences, and also among the largest repeating units in polysaccharides, the present calculation was limited to dp6. Despite this simplification, the number of possible structures calculated for reducing hexasaccharides comprised of D hexoses alone is >1012. Available microchemistry for biologically active oligosaccharides requires between 10 and 100 nmol for a minimum necessary combination of wet chemistry/enzymology/mass spectrometry employing partial degradation. The relatively high limiting quantity for analysis of carbohydrates (compared with proteins and DNA) has remained static for 20 years, despite intense research activity. This calculation underscores the reason for the long-standing technology barrier for the development of a microchemistry in carbohydrate analysis comparable in sensitivity with Edman protein and Sanger DNA sequencing methods. It also reveals the barrier to facile synthetic methods for oligosaccharides comparable to those developed for peptide synthesis.

Annual decreases in soybean (Glycine max L. Merrill) yield caused by diseases were estimated by surveying university-affiliated plant pathologists in 28 soybean-producing states in the United States and in Ontario, Canada, from 2010 through 2014. Estimated yield losses from each disease varied greatly by state or province and year. Over the duration of this survey, soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) was estimated to have caused more than twice as much yield loss than any other disease. Seedling diseases (caused by various pathogens), charcoal rot (caused by Macrophomina phaseolina (Tassi) Goid), and sudden death syndrome (SDS) (caused by Fusarium virguliforme O’Donnell & T. Aoki) caused the next greatest estimated yield losses, in descending order. The estimated mean economic loss due to all soybean diseases, averaged across U.S. states and Ontario from 2010 to 2014, was $60.66 USD per acre. Results from this survey will provide scientists, breeders, governments, and educators with soybean yield-loss estimates to help inform and prioritize research, policy, and educational efforts in soybean pathology and disease management.

The history of the last 100 years of the science and technology of yogurt, sour cream, cultured butter, cultured buttermilk, kefir, and acidophilus milk has been one of continuous development and improvement. Yogurt leads the cultured dairy product category in terms of volume of production in the United States and recent research activity. Legal definitions of yogurt, sour cream and acidified sour cream, and cultured milk, including cultured buttermilk, are presented in the United States Code of Federal Regulations and summarized here. A tremendous amount of research has been done on traditional and novel ingredients, starter cultures and probiotics, mix processing, packaging, chemical aspects, physical and sensory properties, microstructure, specialized products, composition, quality and safety of yogurt and various manufacturing methods, addition of flavorings, viscosity measurements, and probiotic use for sour cream. Over time, there have arisen alternative manufacturing methods, flavor problems, addition of flavorings, and use of probiotics for cultured buttermilk. Many health benefits are provided by yogurt and other cultured dairy products. One hundred years of testing and development have led to wider uses of cultured dairy products and new processing methods for enhanced shelf life and safety. Future research directions will likely include investigating the effects of probiotic dairy products on gut microbiota and overall health.

In Part One of this dissertation* the propertied of a simple arc which possesses the osculating circle at every point are studied* If the equation of the arc in vector notation is P-0 <?(t) end if the osculating circle exist at a ingle point P0 of this are* it is shown in Theorem I that Pd is interior to a sub-are qp which is rectifiable. This is accomplished by proving that for every partition of the arc cpt* the length L of the Inscribed broken line is such that Z * * r. QR (l*^*)# where r is the radius of the osculating circle* eQa is the plane angle determined by the normal to the osculating plane at the center of the osculating circle and by the points Q , and R, and where <^1 a number which vanishes as % and R approach P0* Having the result of Theorem I* Theorem II applies the Keine-Borel-Lebesgu theorem to prove that an are i rectifiable which possesses the osculating circle at every point. Thus in arc possessing the osculating circle everywhere, s, the length of arc can b used as the parameter replacing the general parameter t* Theorem II gives the result that z * 1 everywhere on such arcs* In Part Two, nth ordered total variation of a function f(x) over an interval (ab) is denoted b y the symbol ^\/nt CL and i defined by the equation where f (x*...x^n} is the Ampere~Gauchy function of order n derived from f(x) end where the bound i over all partition of (ab) given by a x Q<x,<.. <x^ b. Theorems I-IV give the proof that if is finite, f1 (x)*. * tfC ^(x) exist almost everywhere on the interval (ab). These theorems are next shown to hold when vector functions are used, end in the the or m s that follow, it is proved that if exists, C L the parameter can be taken as length of are and *l almost everywhere over the given interval. The simplified formula for curvature , p is'shown to be valid almost everywhere*

Multiple comparisons tests (MCTs) include the statistical tests used to compare groups (treatments) often following a significant effect reported in one of many types of linear models. Due to a variety of data and statistical considerations, several dozen MCTs have been developed over the decades, with tests ranging from very similar to each other to very different from each other. Many scientific disciplines use MCTs, including &gt;40,000 reports of their use in ecological journals in the last 60 years. Despite the ubiquity and utility of MCTs, several issues remain in terms of their correct use and reporting. In this study, we evaluated 17 different MCTs. We first reviewed the published literature for recommendations on their correct use. Second, we created a simulation that evaluated the performance of nine common MCTs. The tests examined in the simulation were those that often overlapped in usage, meaning the selection of the test based on fit to the data is not unique and that the simulations could inform the selection of one or more tests when a researcher has choices. Based on the literature review and recommendations: planned comparisons are overwhelmingly recommended over unplanned comparisons, for planned non-parametric comparisons the Mann-Whitney-Wilcoxon U test is recommended, Scheffé’s S test is recommended for any linear combination of (unplanned) means, Tukey’s HSD and the Bonferroni or the Dunn-Sidak tests are recommended for pairwise comparisons of groups, and that many other tests exist for particular types of data. All code and data used to generate this paper are available at: https://github.com/stevemidway/MultipleComparisons .

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.

In this article a preliminary analysis of the loss of life caused by Hurricane Katrina in the New Orleans metropolitan area is presented. The hurricane caused more than 1,100 fatalities in the state of Louisiana. A preliminary data set that gives information on the recovery locations and individual characteristics for 771 fatalities has been analyzed. One-third of the analyzed fatalities occurred outside the flooded areas or in hospitals and shelters in the flooded area. These fatalities were due to the adverse public health situation that developed after the floods. Two-thirds of the analyzed fatalities were most likely associated with the direct physical impacts of the flood and mostly caused by drowning. The majority of victims were elderly: nearly 60% of fatalities were over 65 years old. Similar to historical flood events, mortality rates were highest in areas near severe breaches and in areas with large water depths. An empirical relationship has been derived between the water depth and mortality and this has been compared with similar mortality functions proposed based on data for other flood events. The overall mortality among the exposed population for this event was approximately 1%, which is similar to findings for historical flood events. Despite the fact that the presented results are preliminary they give important insights into the determinants of loss of life and the relationship between mortality and flood characteristics.

Silicon (Si) is the second most abundant element in the earth’s crust and plays a number of important roles in the mineral nutrition of plants. In the past 20 years, the scientific documentation on the benefits of Si to crops has helped establish Si fertilization as an agronomic practice in many agricultural lands worldwide. However, very little information has been consolidated on the use of Si specifically for US agriculture. Consequently, the objectives of this review are to provide (1) information on the dynamics of Si in soil, use, and sources; (2) a history and up-to-date documentation on Si-related research in many areas of US production agriculture; and (3) perspectives on Si as a plant beneficial nutrient and the potential of Si fertilization as an agronomic practice in US crop production systems. The Si-driven mechanisms enhancing the productivity of a wide array of crops under stressed conditions are discussed in this review. Based on the recent 10-year average production level and published shoot Si content, the principal crops grown in the United States can collectively take up 9.55 million tons of Si annually, whereas the annual Si removal rate for the entire US cropland area is estimated at 21.1 million tons. On the basis of this projected annual Si removal rate, adoption of continuous intensive farming systems in the country, low solubility of soil Si, and complex chemical dynamics of Si in soil, increasing plant-available Si levels through fertilization is therefore foreseen a logical agronomic practice for US agriculture.