Gene Discovery in the Threatened Elkhorn Coral: 454 Sequencing of the Acropora palmata Transcriptome

BACKGROUND: Cnidarians, including corals and anemones, offer unique insights into metazoan evolution because they harbor genetic similarities with vertebrates beyond that found in model invertebrates and retain genes known only from non-metazoans. Cataloging genes expressed in Acropora palmata, a foundation-species of reefs in the Caribbean and western Atlantic, will advance our understanding of the genetic basis of ecologically important traits in corals and comes at a time when sequencing efforts in other cnidarians allow for multi-species comparisons. RESULTS: A cDNA library from a sample enriched for symbiont free larval tissue was sequenced on the 454 GS-FLX platform. Over 960,000 reads were obtained and assembled into 42,630 contigs. Annotation data was acquired for 57% of the assembled sequences. Analysis of the assembled sequences indicated that 83-100% of all A. palmata transcripts were tagged, and provided a rough estimate of the total number genes expressed in our samples (~18,000-20,000). The coral annotation data contained many of the same molecular components as in the Bilateria, particularly in pathways associated with oxidative stress and DNA damage repair, and provided evidence that homologs of p53, a key player in DNA repair pathways, has experienced selection along the branch separating Cnidaria and Bilateria. Transcriptome wide screens of paralog groups and transition/transversion ratios highlighted genes including: green fluorescent proteins, carbonic anhydrase, and oxidative stress proteins; and functional groups involved in protein and nucleic acid metabolism, and the formation of structural molecules. These results provide a starting point for study of adaptive evolution in corals. CONCLUSIONS: Currently available transcriptome data now make comparative studies of the mechanisms underlying coral's evolutionary success possible. Here we identified candidate genes that enable corals to maintain genomic integrity despite considerable exposure to genotoxic stress over long life spans, and showed conservation of important physiological pathways between corals and bilaterians

The origin of multicellularity in cyanobacteria

Background: Cyanobacteria are one of the oldest and morphologically most diverse prokaryotic phyla on our planet. The early development of an oxygen-containing atmosphere approximately 2.45 - 2.22 billion years ago is attributed to the photosynthetic activity of cyanobacteria. Furthermore, they are one of the few prokaryotic phyla where multicellularity has evolved. Understanding when and how multicellularity evolved in these ancient organisms would provide fundamental information on the early history of life and further our knowledge of complex life forms. Results: We conducted and compared phylogenetic analyses of 16S rDNA sequences from a large sample of taxa representing the morphological and genetic diversity of cyanobacteria. We reconstructed ancestral character states on 10,000 phylogenetic trees. The results suggest that the majority of extant cyanobacteria descend from multicellular ancestors. Reversals to unicellularity occurred at least 5 times. Multicellularity was established again at least once within a single-celled clade. Comparison to the fossil record supports an early origin of multicellularity, possibly as early as the “Great Oxygenation Event” that occurred 2.45 - 2.22 billion years ago. Conclusions: The results indicate that a multicellular morphotype evolved early in the cyanobacterial lineage and was regained at least once after a previous loss. Most of the morphological diversity exhibited in cyanobacteria today —including the majority of single-celled species— arose from ancient multicellular lineages. Multicellularity could have conferred a considerable advantage for exploring new niches and hence facilitated the diversification of new lineages

Direct use of spent mushroom substrate from Pleurotus pulmonarius as a readily delignified feedstock for cellulase production

The feasibility of spent mushroom substrate (SMS) as an alternative fermentation feedstock for cellulase production has been demonstrated in this work. Utilization of SMS as a substrate has been attempted widely due to its high cellulose content and readily available in smaller particle size. On top of that, the availability of delignified SMS by the action of Pleurotus pulmonarius during mushroom cultivation offers another benefit to its use whereby no chemical pretreatment would be required prior to fermentation. The recovery of crude laccase and manganese peroxidase from delignified SMS were found to be 3 and 1.4 U/g, respectively. Further to this, the cellulase production from SMS by Trichoderma asperellum UPM 1 under solid state fermentation was optimized by applying central composite design, resulted in increment of 1.4-fold in CMCase (171.21 U/g) and 1.5-fold in β-glucosidase (6.83 U/g), with the optimum temperature of 27.5 °C, initial moisture content 81% and initial pH of fermentation 4.5. Therefore, this study showed that the direct utilization of SMS is feasible for promising cellulase production by T. asperellum UPM 1

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Not AvailableThe production of cellulase by Trichoderma reesei RUT C-30 under solid-state fermentation (SSF) on wheat bran and cellulose was optimized employing a two stage statistical design of experiments. Optimization of process parameters resulted in a 3.2-fold increase in CMCase production to 959.53 IU/gDS. The process was evaluated at pilot scale in tray fermenters and yielded 457 IU/gDS using the lab conditions and indicating possibility for further improvement. The cellulase could effectively hydrolyze alkali pretreated sorghum stover and addition of Aspergillus niger β-glucosidase improved the hydrolytic efficiency 174%, indicating the potential to use this blend for effective saccharification of sorghum stover biomass. The enzymatic hydrolysate of sorghum stover was fermented to ethanol with ∼80% efficiency.Not Availabl

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Not AvailableThe conversion of lignocellulosic biomass to ethanol involves three major unit operations such as pretreatment, hydrolysis and fermentation. Each unit operation involves processing of biomass with changes in its structure, and release of fermentable and other sugars and lignin degrading compounds. The evaluation of biomass conversion processes through material balance is fundamentally crucial in its commercialization. This gives an idea about the transfer of biomass from one phase to another and hence eventually of the efficiency of the total process. In the present study, material balance has been evaluated in each unit operations for sorghum biomass to ethanol conversion. An account of carbohydrates in the native as well as pretreated sorghum biomass, the release of fermentable sugars and the conversion of sugars to ethanol was maintained and analysed. Ethanol yield of 91.94 g per kg sorghum was achieved without any detoxification and washing of pretreated biomass after mild acid pretreatment followed by enzymatic hydrolysis and fermentation.Not Availabl

High-solids loading processing for an integrated lignocellulosic biorefinery: Effects of transport phenomena and rheology – A review

This review aims to present an analysis and discussion on the processing of lignocellulosic biomass in terms of biorefinery concept and circular bioeconomy operating at high solids lignocellulosic (above 15% [w/w]) at the pretreatment, enzymatic hydrolysis stage, and fermentation strategy for an integrated lignocellulosic bioprocessing. Studies suggest high solids concentration enzymatic hydrolysis for improved sugars yields and methods to overcome mass transport constraints. Rheological and computational fluid dynamics models of high solids operation through evaluation of mass and momentum transfer limitations are presented. Also, the review paper explores operational feeding strategies to obtain high ethanol concentration and conversion yield, from the hydrothermal pretreatment and investigates the impact of mass load over the operational techniques. Finally, this review contains a brief overview of some of the operations that have successfully scaled up and implemented high-solids enzymatic hydrolysis in terms of the biorefinery concept