Complex carbohydrates of plants are the main food sources animals and microbes, serve as promising renewable feedstock for biofuel biomaterial production. Carbohydrate active enzymes (CAZymes) most important complex carbohydrate metabolism. With an increasing number plant plant-associated microbial genomes metagenomes being sequenced, there is urgent need automatic tools genomic data mining CAZymes. We developed dbCAN web server in 2012 to provide a public service automated CAZyme annotation...

Abstract Background MicroRNAs are important regulators of gene expression at the post-transcriptional level and play an role in many biological processes. Due to it is great interest quantitatively determine their different settings. Results We describe a PCR method for quantification microRNAs based on single reverse transcription reaction all combined with real-time two, microRNA-specific DNA primers. Primer annealing temperatures were optimized by adding tail primers could be designed...

MicroRNAs are small but biologically important RNA molecules. Although different methods can be used for quantification of microRNAs, quantitative PCR is regarded as the reference that to validate other methods. Several commercial qPCR assays available they often come at a high price and sequences primers not disclosed. An alternative manually design this work tedious and, hence, practical larger number targets. I have developed software miRprimer automatic method miR-specific RT-qPCR, which...

Abstract Transgenic cassava (Manihot esculenta Crantz, cv MCol22) plants with a 92% reduction in cyanogenic glucoside content tubers and acyanogenic (<1% of wild type) leaves were obtained by RNA interference to block expression CYP79D1 CYP79D2, the two paralogous genes encoding first committed enzymes linamarin lotaustralin synthesis. About 180 independent lines obtained. Only few these depleted respect tubers. In agreement this observation, girdling experiments demonstrated that...

The first committed steps in the biosynthesis of two cyanogenic glucosides linamarin and lotaustralin cassava are conversion l-valine andl-isoleucine, respectively, to corresponding oximes. Two full-length cDNA clones that encode cytochromes P-450 catalyzing these reactions have been isolated. 85% identical, share 54% sequence identity CYP79A1 from sorghum, assigned CYP79D1 CYP79D2. Functional expression has achieved using methylotrophic yeast,<i>Pichia pastoris</i>. amount isolated 1 liter...

Carbohydrate-active enzymes are found in all organisms and participate key biological processes. These classified 274 families the CAZy database but sequence diversity within each family makes it a major task to identify new members provide basis for prediction of enzyme function. A fast reliable method de novo annotation genes encoding carbohydrate-active is conserved peptides curated followed by matching interest as demonstrated glycosyl hydrolase lytic polysaccharide monooxygenase...

Abstract The content of the cyanogenic glucoside dhurrin in sorghum (Sorghum bicolor L. Moench) varies depending on plant age and growth conditions. cyanide potential is highest shortly after onset germination. At this stage, nitrogen application has no effect content, whereas older plants, induces an increase. all stages, correlates well with activity two biosynthetic enzymes, CYP79A1 CYP71E1, protein mRNA level for enzymes. During development, lower than suggesting that catalyzes...

The rab17 gene from maize is transcribed in late embryonic development and responsive to abscisic acid water stress embryo vegetative tissues. In vivo footprinting transient transformation of were performed embryos tissues characterize the cis ‐elements involved regulation gene. By footprinting, protein binding was observed nine elements promoter, which correspond five putative ABREs (abscisic elements) four other sequences. footprints indicated that distinct proteins interact with these two...

Lytic polysaccharide monooxygenases are important enzymes for the decomposition of recalcitrant biological macromolecules such as plant cell wall and chitin polymers. These were originally designated glycoside hydrolase family 61 carbohydrate-binding module 33 but now classified auxiliary activities 9, 10 11 in CAZy database. To obtain a systematic analysis divergent families lytic we used Peptide Pattern Recognition to divide 5396 protein sequences resembling from AA9 (1828 proteins), AA10...

Aspergillus hancockii sp. nov., classified in subgenus Circumdati section Flavi, was originally isolated from soil peanut fields near Kumbia, the South Burnett region of southeast Queensland, Australia, and has since been found occasionally other substrates locations Australia. It is phylogenetically phenotypically related most closely to A. leporis States M. Chr., but differs conidial colour, minor features particularly metabolite profile. When cultivated on rice as an optimal substrate,...

Functional prediction of carbohydrate-active enzymes is difficult due to low sequence identity. However, similar often share a few short motifs, e.g., around the active site, even when overall sequences are very different. To exploit this notion for functional enzymes, we developed simple algorithm, peptide pattern recognition (PPR), that can divide proteins into groups set conserved sequences. When method was used on 118 glycoside hydrolase 5 with 9% average pairwise identity and...

Poultry processing plants and slaughterhouses produce huge quantities of feathers hair/bristle waste annually. These keratinaceous wastes are highly resistant to degradation. Onygena corvina, a non-pathogenic fungus, grows specifically on feathers, hooves, horn, hair in nature. Hence, the proteases secreted by O. corvina interesting view their potential relevance for industrial decomposition wastes. We sequenced assembled genome used method called peptide pattern recognition identify 73...

Background MicroRNAs are small, non-coding RNA molecules that regulate gene expression at the post-transcriptional level and play an important role in control of developmental physiological processes. In particular, developing brain contains impressive diversity microRNAs. Most microRNA profiling studies have been performed human or rodents relatively limited knowledge exists other mammalian species. The domestic pig is considered to be excellent, alternate, large mammal model for...

Elucidation of fungal biomass degradation is important for understanding the turnover biological materials in nature and has implications industrial conversion. In recent years there been an increasing interest elucidating role thermophilic fungi characterization their industrially useful enzymes. present study we investigated cellulolytic potential 16 from three ascomycete orders Sordariales, Eurotiales Onygenales zygomycete order Mucorales thus covering all that include thermophiles....

New lysine decarboxylases, combined with the simultaneous cell-treatment and bioconversion processes have great potential in large-scale production of cadaverine.

Objective: Cardiac hypertrophy is induced by a number of stimuli and can lead to cardiomyopathy heart failure. Present knowledge suggests that cell-cycle regulatory proteins take part in hypertrophy. We have investigated if the D-type cyclins are involved cardiac Methods: The expression activity associated kinases cardiomyocytes were studied during angiotensin II- pressure overload-induced rats (Rattus norvegicus) isolated, neonatal cardiomyocytes. Expression was manipulated...

The vision of the European common research programme for 2014-2020, called Horizon 2020, is to create a smarter, more sustainable and inclusive society. However, this global endeavor, which important mycologists all over world because it includes special role fungi fungal products. After ten years on industrial scale conversion biowaste, conclusion that most efficient gentle way converting recalcitrant lignocellulosic materials into high value products purposes, through use enzymes....

The cellulose-degrading fungal enzymes are glycoside hydrolases of the GH families and lytic polysaccharide monooxygenases. entanglement hydrolase functions makes it difficult to predict enzymatic activity based on their sequence. In present study we further developed method Peptide Pattern Recognition an automatic approach not only find all genes encoding monooxygenases in genomes but also function genes. functional annotation is important feature as provides a direct route from primary...

Fungus-growing termites rely on mutualistic fungi of the genus Termitomyces and gut microbes for plant biomass degradation. Due to a certain degree symbiont complementarity, this tripartite symbiosis has evolved as complex bioreactor, enabling decomposition nearly any polymer, likely contributing success one main decomposers in Old World. In study, we evaluated which polymers are decomposed enzymes active during process two major genera fungus-growing termites. We found diversity at...

The aim of this study was to elucidate the evolution enzyme secretome early lineage fungi contribute resolving basal part Fungal Kingdom and pave way for industrial evaluation their unique enzymes. By combining results advanced sequence analysis with mass spectrometry phylogenetic trees, we provide evidence that plant cell wall degrading enzymes higher share a common ancestor from aerobic ancient fungi. Sequence (HotPep, confirmed by dbCAN-HMM models) enabled prediction function directly...

The catalytic domain of glucoamylases G1 and G2 from Aspergillus niger is produced in vitro high yield by limited proteolysis using either subtilisin Novo or Carlsberg. Purification affinity chromatography on an acarbose-Sepharose column followed ion-exchange HiLoad Q-Sepharose leads to separation a number structurally closely related forms domain. cleavage occurs primarily between Val-470 Ala-471 as indicated C-terminal sequencing, whereas the N-terminus intact. Subtilisin Carlsberg,...