Optimizing harvest of corn stover fractions based on overall sugar yields following ammonia fiber expansion pretreatment and enzymatic hydrolysis

Background  

Corn stover composition changes considerably throughout the growing season and also varies between the various fractions of the plant. These differences can impact optimal pretreatment conditions, enzymatic digestibility and maximum achievable sugar yields in the process of converting lignocellulosics to ethanol. The goal of this project was to determine which combination of corn stover fractions provides the most benefit to the biorefinery in terms of sugar yields and to determine the preferential order in which fractions should be harvested. Ammonia fiber expansion (AFEX) pretreatment, followed by enzymatic hydrolysis, was performed on early and late harvest corn stover fractions (stem, leaf, husk and cob). Sugar yields were used to optimize scenarios for the selective harvest of corn stover assuming 70% or 30% collection of the total available stover.     

Involvement of the Reck tumor suppressor protein in maternal and embryonic vascular remodeling in mice

Background

The accessibility of the developing zebrafish pharyngeal dentition makes it an advantageous system in which to study many aspects of tooth development from early initiation to late morphogenesis. In mammals, hedgehog signaling is known to be essential for multiple stages of odontogenesis; however, potential roles for the pathway during initiation of tooth development or in later morphogenesis are incompletely understood.

Results

We have identified mRNA expression of the hedgehog ligands shha and the receptors ptc1 and ptc2 during zebrafish pharyngeal tooth development. We looked for, but did not detect, tooth germ expression of the other known zebrafish hedgehog ligands shhb, dhh, ihha, or ihhb, suggesting that as in mammals, only Shh participates in zebrafish tooth development. Supporting this idea, we found that morphological and gene expression evidence of tooth initiation is eliminated in shha mutant embryos, and that morpholino antisense oligonucleotide knockdown of shha, but not shhb, function prevents mature tooth formation. Hedgehog pathway inhibition with the antagonist compound cyclopamine affected tooth formation at each stage in which we applied it: arresting development at early stages and disrupting mature tooth morphology when applied later. These results suggest that hedgehog signaling is required continuously during odontogenesis. In contrast, over-expression of shha had no effect on the developing dentition, possibly because shha is normally extensively expressed in the zebrafish pharyngeal region.

Conclusion

We have identified previously unknown requirements for hedgehog signaling for early tooth initiation and later morphogenesis. The similarity of our results with data from mouse and other vertebrates suggests that despite gene duplication and changes in the location of where teeth form, the roles of hedgehog signaling in tooth development have been largely conserved during evolution.     

Immediate and longer-term effects of managed flooding on floodplain invertebrate assemblages in south-eastern Australia: generation and maintenance of a mosaic landscape

1. We compared assemblages of ground‐active, terrestrial beetles and spiders from different areas of river red gum Eucalyptus camaldulensis floodplain forest in subhumid, south‐eastern Australia before and for 2 years following a managed flood to determine whether the Flood Pulse Concept is an appropriate ecological model for this regulated, lowland river‐floodplain system. 2. Immediately following flooding, the abundance, species richness and biomass of beetles were greatest at sites that had been inundated for the longest period (approximately 4 months). The abundance, species richness and biomass of spiders were not reduced at sites that were flooded for 4 months compared with unflooded or briefly flooded areas. Sites recently flooded for several months had high densities of predatory, hygrophilic beetles (Carabidae) and spiders (Lycosidae). 3. Over the 2 years following the flood, beetles generally were more abundant at sites that had been inundated for longer. At all sampling times, the species richness of beetles at sites increased with the length of time sites were inundated, even before the flood. Neither the abundance nor species richness of spiders was related to duration of flooding. 4. The structure of beetle and spider assemblages at sites that were flooded for different lengths of time did not appear to converge monotonically over the 2 years after the flood. 5. Managed flooding promotes diversity of beetles and spiders both by providing conditions that create a ‘pulse’ in populations of hygrophilic specialists in the short term, and by creating subtle, persistent changes in forest‐floor conditions. Despite its monotypic canopy, river red gum floodplain forest is a habitat mosaic generated by differing inundation histories.     

Macroinvertebrate diversity in headwater streams: a review

1. Headwater streams are ubiquitous in the landscape and are important sources of water, sediments and biota for downstream reaches. They are critical sites for organic matter processing and nutrient cycling, and may be vital for maintaining the 'health' of whole river networks.
2. Macroinvertebrates are an important component of biodiversity in stream ecosystems and studies of macroinvertebrate diversity in headwater streams have mostly viewed stream systems as linear reaches rather than as networks, although the latter may be more appropriate to the study of diversity patterns in headwater systems.
3. Studies of macroinvertebrate diversity in headwater streams from around the world illustrated that taxonomic richness is highly variable among continents and regions, and studies addressing longitudinal changes in taxonomic richness of macroinvertebrates generally found highest richness in mid-order streams.
4. When stream systems are viewed as networks at the landscape-scale, α-diversity may be low in individual headwater streams but high β-diversity among headwater streams within catchments and among catchments may generate high γ-diversity.
5. Differing ability and opportunity for dispersal of macroinvertebrates, great physical habitat heterogeneity in headwater streams, and a wide range in local environmental conditions may all contribute to high β-diversity among headwater streams both within and among catchments.
6. Moving beyond linear conceptual models of stream ecosystems to consider the role that spatial structure of river networks might play in determining diversity patterns at the landscape scale is a promising avenue for future research.     

Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

Abstract Two chronosequences of unsaturated, buried loess sediments, ranging in age from <10,000 years to >1 million years, were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession was inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Core samples were collected at two sites 40 km apart in the Palouse region of eastern Washington State, near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the Winona site elevation is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was approximately 250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: approximately 1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Same-age sediments had equal quantities of microorganisms, but different community types. Differences in community makeup between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the microbial community age can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be considerably older than the porewater ages, since microbial transport is severely restricted in unsaturated sediments. This is particularly true at the Winona site, which was never flooded.     

Mitogenic activity of pituitary hormones on cell cultures of normal and carcinogen-induced tumor epithelium from rat mammary glands

Cell suspension containing normal or tumor epithelium were readily obtained by enzymatically digesting rat mammary glands from perphenazine-treated (prolactin-hypersecreting) cycling, female virgin animals or hormone- responsive mammary tumors from animal treated with dimethylbenzanthracene. Cell suspensions were fractioned into predominantly epithelial and predominantly stromal cells by their differential rates of attachment to culture dishes. Both normal mammary and tumor epithelial cells were characterized by the presence of specific cell-junctional complexes, desmosome-like structures, surface microvilli, and their ability to synthesize casein. Serum-dependent protease activity was greater in cultures derived from tumors, and cells from such cultures grew in agarose whereas those from the non-neoplastic gland did not. The addition of prolactin to the culture medium stimulated DNA synthesis in primary or secondary epithelial cultures from tumors, whereas additional insulin and hydrocortisone with prolactin were required for similar levels of DNA synthesis in cultures from non-neoplastic glands. The fraction of cells synthesizing DNA was, however, smaller than that with 10 percent serum measured in the same time period. Both growth hormone and epidermal growth factor stimulated DNA synthesis but to a lesser extent than did prolactin. Prolactin with hydrocortisone and insulin were relatively inactive in promoting DNA synthesis of the nonepithelial cells whereas pituitary fibroblast growth factor was more active. These mitogenic effects were obtained when the hormones were added to the medium at near physiological concentrations, and paralleled the known activities of the hormones in control of mammary gland growth and development in the rat.     

Identification of DNA-binding proteins using support vector machines and evolutionary profiles

Background  

Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation, as these proteins play a crucial role in gene-regulation. In this paper, we developed various SVM modules for predicting DNA-binding domains and proteins. All models were trained and tested on multiple datasets of non-redundant proteins.     

Studies of genotoxicity and mutagenicity of nitroimidazoles: demystifying this critical relationship with the nitro group

Nitroimidazoles exhibit high microbicidal activity, but mutagenic, genotoxic and cytotoxic properties have been attributed to the presence of the nitro group. However, we synthesised nitroimidazoles with activity against the trypomastigotes of Trypanosoma cruzi, but that were not genotoxic. Herein, nitroimidazoles (11-19) bearing different substituent groups were investigated for their potential induction of genotoxicity (comet assay) and mutagenicity (Salmonella/Microsome assay) and the correlations of these effects with their trypanocidal effect and with megazol were investigated. The compounds were designed to analyse the role played by the position of the nitro group in the imidazole nucleus (C-4 or C-5) and the presence of oxidisable groups at N-1 as an anion receptor group and the role of a methyl group at C-2. Nitroimidazoles bearing NO2 at C-4 and CH3 at C-2 were not genotoxic compared to those bearing NO₂ at C-5. However, when there was a CH3 at C-2, the position of the NO2 group had no influence on the genotoxic activity. Fluorinated compounds exhibited higher genotoxicity regardless of the presence of CH3 at C-2 or NO2 at C-4 or C-5. However, in compounds 11 (2-CH3; 4-NO2; N-CH2OHCH2Cl) and 12 (2-CH3; 4-NO2; N-CH2OHCH2F), the fluorine atom had no influence on genotoxicity. This study contributes to the future search for new and safer prototypes and provide.     

Nectar Production and Floral Characteristics of Tropaeolum majus L. Grown in Ambient and Elevated Carbon Dioxide

Tropaeolum majus (nasturtiums) were grown from seed in growthcabinets, under 380 and 750 ppmv CO₂. Elevated CO₂significantlyincreased nectar secretion rate, both in flowers milked of nectardaily and in once sampled, 3-d-old flowers. Elevated CO₂didnot affect time to flowering, total number of flowers produced,pollen to ovule ratio, or the total or individual concentrationsof nectar amino acids. The dry weight and longevity of individualflowers was also unchanged. Nectar sugar content was unchangedby elevated CO₂in a subset of flowers used to assess the 3-d-oldnectar volume. This subset did not show the same increase innectar volume under elevated CO₂as the full set, resulting inthe concentration of sugars remaining unchanged. Overall, thequantity rather than the quality of the nectar changed underelevated CO₂while flower characteristics remained constant,implying that the identity of pollinators may remain the samewhile foraging behaviour (e.g. number of visits per plant, distancetravelled) may change in the future. Copyright 1999 Annals ofBotany Company Tropaeolum majus, nasturtiums, elevated CO₂, nectar, phenology, floral characteristics, amino acids, pollinator-plant interactions.