The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

3.2.3. Hydroformylation 2467 3.2.4. Dimerization 2468 3.2.5. Oxidative Cleavage and Ozonolysis 2469 3.2.6. Metathesis 2470 4. Terpenes 2472 4.1. Pinene 2472 4.1.1. Isomerization: R-Pinene 2472 4.1.2. Epoxidation of R-Pinene 2475 4.1.3. Isomerization of R-Pinene Oxide 2477 4.1.4. Hydration of R-Pinene: R-Terpineol 2478 4.1.5. Dehydroisomerization 2479 4.2. Limonene 2480 4.2.1. Isomerization 2480 4.2.2. Epoxidation: Limonene Oxide 2480 4.2.3. Isomerization of Limonene Oxide 2481 4.2.4. Dehydroisomerization of Limonene and Terpenes To Produce Cymene 2481

Chemical Routes for the Transformation of Biomass into Chemicals

Biotechnological potential of agro-industrial residues. I: sugarcane bagasse

Production of liquid biofuels, such as bioethanol, has been advocated as a sustainable option to tackle the problems associated with rising crude oil prices, global warming and diminishing petroleum reserves. Second-generation bioethanol is produced from lignocellulosic feedstock by its saccharification, followed by microbial fermentation and product recovery. Agricultural residues generated as wastes during or after processing of agricultural crops are one of such renewable and lignocellulose-rich biomass resources available in huge amounts for bioethanol production. These agricultural residues are converted to bioethanol in several steps which are described here. This review enlightens various steps involved in production of the second-generation bioethanol. Mechanisms and recent advances in pretreatment, cellulases production and second-generation ethanol production processes are described here.

/pdf/lignocellulosic-agriculture-wastes-as-biomass-feedstocks-for-2ki8xu9b01.pdf

Lignocellulosic agriculture wastes as biomass feedstocks for second-generation bioethanol production: concepts and recent developments

In humans, microbial cells (including bacteria, archaea, and fungi) greatly outnumber host cells. Candida albicans is the most prevalent fungal species of the human microbiota; this species asymptomatically colonizes many areas of the body, particularly the gastrointestinal and genitourinary tracts of healthy individuals. Alterations in host immunity, stress, resident microbiota, and other factors can lead to C. albicans overgrowth, causing a wide range of infections, from superficial mucosal to hematogenously disseminated candidiasis. To date, most studies of C. albicans have been carried out in suspension cultures; however, the medical impact of C. albicans (like that of many other microorganisms) depends on its ability to thrive as a biofilm, a closely packed community of cells. Biofilms are notorious for forming on implanted medical devices, including catheters, pacemakers, dentures, and prosthetic joints, which provide a surface and sanctuary for biofilm growth. C. albicans biofilms are intrinsically resistant to conventional antifungal therapeutics, the host immune system, and other environmental perturbations, making biofilm-based infections a significant clinical challenge. Here, we review our current knowledge of biofilms formed by C. albicans and closely related fungal species.

/pdf/candida-albicans-biofilms-and-human-disease-4oyjga11bp.pdf

Candida albicans Biofilms and Human Disease.

Mixed culture solid substrate fermentation of Trichoderma reesei with Aspergillus niger on sugar cane bagasse

Ammonia-treated bagasse with 80%(w/w) moisture content was subjected to mixed-culture solid-substrate fermentation (SSF) with Trichoderma reesei LM-UC4 and Aspergillus phoenicis QM 329, in flask or pot fermenters, for cellulase production. Significantly higher activities of all the enzymes of the cellulase complex were achieved in 4 days of mixed-culture SSF than in single-culture (T. reesei) SSF. The highest filter-paper-cellulase and β-glucosidase activities seen in mixed-culture SSF were 18.7 and 38.6 IU/g dry wt, respectively, representing approx. 3- and 6-fold increases over the activities attained in single-culture SSF. The mixed-culture SSF process also converted about 46% of the cellulose and hemicellulose to reducing sugars and enriched the product with 13% fungal protein. The biomass productivity, 0.29 gl(-1).h, and enzyme productivity, 28.0 IU I(-1).h, were about twice as high in the mixed-culture than in the single-culture.

https://link.springer.com/content/pdf/10.1007/BF00367112.pdf

Cellulase production by mixed fungi in solid-substrate fermentation of bagasse.

Trichoderma reesei LM-UC4 and its mutant LM-UC4E1 were co-cultured with Aspergillus phoenicis QM329 for cellu-lase production on bagasse by mixed culture solid substrate fermentation. A mutual synergism was observed between the parent Trichoderma strain and the Aspergillus, resulting in enhanced combined biomass production and corresponding increased in cellulase, endoglucanase and b-glucosidase activities. Such synergism was absent with the mutant Trichoderma strain suggesting that in the hypermutation the ability for cooperative interaction with other microbes was lost.

Production of cellulase on sugar cane bagasse by fungal mixed culture solid substrate fermentation

The biofilm phenotype is an increasingly important concept in mycological research. Recently, there has been a developing interest in whether Aspergillus species are truly able to form biofilms or not. Industrial mycologists have long been aware of biofilms and their benefit in fermentation processes, whereas clinically their role is uncertain. This review provides an update on the impact that Aspergillus biofilms have medically and industrially, and will discuss biofilm development, and our current understanding of its molecular basis. The role of exopolymeric substance and how this substance relates to antimicrobial recalcitrance will also be discussed.

Aspergillus biofilms: clinical and industrial significance.

Cellulolytic and hemicellulolytic enzymes were produced on extracted sweet sorghum silage by mixed culture solid substrate fermentation with Trichoderma reesei LM-1 (a Peruvian mutant) and Aspergillus niger ATCC 10864. Optimal cellulose and xylanase levels of 4 IU/g dry weight (DW) and 180 IU/g DW, respectively, were achieved in 120 h-fermentation when T. reesei, inoculated at 0 h, was followed by the inoculation of A. niger at 48 h.

Marcel Gutiérrez-Correa

Papers

Mixed culture solid substrate fermentation of Trichoderma reesei with Aspergillus niger on sugar cane bagasse

Cellulase production by mixed fungi in solid-substrate fermentation of bagasse.

Production of cellulase on sugar cane bagasse by fungal mixed culture solid substrate fermentation

Aspergillus biofilms: clinical and industrial significance.

Mixed culture solid substrate fermentation for cellulolytic enzyme production