Flexibility of active center affects thermostability and activity of Penicillium canescens xylanase E.

Xylanases are used in several industrial applications, such as feed additives, the bleaching of pulp and paper, and the production of bread, food, and drinks. Xylanases are required to remain active after heat treatment at 80-90 °C for 30 s to several minutes due to the conditions of feed pelleting. Also, xylanases need to be active at 60-70 °C for several hours while bleaching of pulp and paper or manufacturing of bread, food, and drinks is performed. Xylanases of the glycoside hydrolase family GH10 are good candidates for application in such processes because of their high thermostability and, in particular, as feed additives because of their insensitivity to protein inhibitors in cereal feeds. In the study, the thermostability of GH10 xylanase E from Penicillium canescens was improved to reach a half-inactivation period of 2 min at 80 °C compared to 21 s for the wild-type enzyme (WT). Enzymatic activity was increased by 22-48 % at 40-70 °C, which improved the action of the enzyme as a feed additive in the gastric system of animals and during bleaching of pulp and paper. Molecular dynamics simulations demonstrated lower flexibility of the tertiary structure of the engineered enzyme at elevated temperatures compared to WT. The residues W113, Q116, W313, and W321 in the (-1) and (-2) subsites for the substrate binding were less flexible. In the simulations, the engineered enzyme had a comparable content of α-helixes, 310-helixes, ß-sheets, and ß-bridges as WT, but a lower content of coils and a higher content of ß-turns.

The role of intracellular ß-glucosidase in cellulolytic response induction in filamentous fungus Penicillium verruculosum.

In this study, CRISPR/Cas9 genome editing was used to knockout the bgl2 gene encoding intracellular ß-glucosidase filamentous fungus Penicillium verruculosum. This resulted in a dramatic reduction of secretion of cellulolytic enzymes. The study of P. verruculosum Δbgl2 found that the transcription of the cbh1 gene, which encodes cellobiohydrolase 1, was impaired when induced by cellobiose and cellotriose. However, the transcription of the cbh1 gene remains at level of the host strain when induced by gentiobiose. This implies that gentiobiose is the true inducer of the cellulolytic response in P. verruculosum, in contrast to Neurospora crassa where cellobiose acts as an inducer.

Recombinant Oxidase from Armillaria tabescens as a Potential Tool for Aflatoxin B1 Degradation in Contaminated Cereal Grain.

Forage grain contamination with aflatoxin B1 (AFB1) is a global problem, so its detoxification with the aim of providing feed safety and cost-efficiency is still a relevant issue. AFB1 degradation by microbial enzymes is considered to be a promising detoxification approach. In this study, we modified an previously developed Pichia pastoris GS115 expression system using a chimeric signal peptide to obtain a new recombinant producer of extracellular AFB1 oxidase (AFO) from Armillaria tabescens (the yield of 0.3 g/L), purified AFO, and selected optimal conditions for AFO-induced AFB1 removal from model solutions. After a 72 h exposure of the AFB1 solution to AFO at pH 6.0 and 30 °C, 80% of the AFB1 was degraded. Treatments with AFO also significantly reduced the AFB1 content in wheat and corn grain inoculated with Aspergillus flavus. In grain samples contaminated with several dozen micrograms of AFB1 per kg, a 48 h exposure to AFO resulted in at least double the reduction in grain contamination compared to the control, while the same treatment of more significantly (~mg/kg) AFB1-polluted samples reduced their contamination by ~40%. These findings prove the potential of the tested AFO for cereal grain decontamination and suggest that additional studies to stabilize AFO and improve its AFB1-degrading efficacy are required.

Some Structural Elements of Bacterial Protein MF3 That Influence Its Ability to Induce Plant Resistance to Fungi, Viruses, and Other Plant Pathogens.

The ability of the MF3 protein from Pseudomonas fluorescens to protect plants by inducing their resistance to pathogenic fungi, bacteria, and viruses is well confirmed both in greenhouses and in the field; however, the molecular basis of this phenomenon remains unexplored. To find a relationship between the primary (and spatial) structure of the protein and its target activity, we analyzed the inducing activity of a set of mutants generated by alanine scanning and an alpha-helix deletion (ahD) in the part of the MF3 molecule previously identified by our group as a 29-amino-acid peptide working as the inducer on its own. Testing the mutants' inducing activity using the "tobacco-tobacco mosaic virus" pathosystem revealed that some of them showed an almost threefold (V60A and V62A) or twofold (G51A, L58A, ahD) reduction in inducing activity compared to the wild-type MF3 type. Interestingly, these mutations demonstrated close proximity in the homology model, probably contributing to MF3 reception in a host plant.

Development of dual reporter vector system for estimating translational activity of regulatory elements.

BACKGROUND: For the needs of modern biotechnology, a quantitative approach to the control of regulatory elements at all stages of gene expression has long become indispensable. Such a control regime is impossible without a quantitative analysis of the role of each regulatory element or pattern used. Therefore, it seems important to modify and develop the accuracy, reproducibility, and availability of methods for quantifying the contribution of each regulatory code to the implementation of genetic information. RESULTS: A new vector system for transient expression in plants is described; this system is intended for quantitative analysis of the contribution of regulatory elements to transcription and translation efficiencies. The proposed vector comprises two expression cassettes carrying reporter genes (of the Clostridium thermocellum thermostable lichenase and E. coli ß-glucuronidase) under the control of different promoters. Herewith we also propose a new method for quantification of the effect of tested regulatory elements on expression, which relies on assessment of the enzyme activities of reporter proteins taking into account the transcription of their genes. CONCLUSIONS: In our view, this approach makes it possible to precisely determine the amounts of reporter proteins and their transcripts at all stages of expression. The efficiency of the proposed system has been validated by the analysis of the roles of known translation enhancers at the stages of transcription and translation.

Expression and Refolding of the Plant Chitinase From Drosera capensis for Applications as a Sustainable and Integrated Pest Management.

Recently, the study of chitinases has become an important target of numerous research projects due to their potential for applications, such as biocontrol pest agents. Plant chitinases from carnivorous plants of the genus Drosera are most aggressive against a wide range of phytopathogens. However, low solubility or insolubility of the target protein hampered application of chitinases as biofungicides. To obtain plant chitinase from carnivorous plants of the genus Drosera in soluble form in E.coli expression strains, three different approaches including dialysis, rapid dilution, and refolding on Ni-NTA agarose to renaturation were tested. The developed « Rapid dilution ¼ protocol with renaturation buffer supplemented by 10% glycerol and 2M arginine in combination with the redox pair of reduced/oxidized glutathione, increased the yield of active soluble protein to 9.5 mg per 1 g of wet biomass. A structure-based removal of free cysteines in the core domain based on homology modeling of the structure was carried out in order to improve the soluble of chitinase. One improved chitinase variant (C191A/C231S/C286T) was identified which shows improved expression and solubility in E. coli expression systems compared to wild type. Computational analyzes of the wild-type and the improved variant revealed overall higher fluctuations of the structure while maintaining a global protein stability. It was shown that free cysteines on the surface of the protein globule which are not involved in the formation of inner disulfide bonds contribute to the insolubility of chitinase from Drosera capensis. The functional characteristics showed that chitinase exhibits high activity against colloidal chitin (360 units/g) and high fungicidal properties of recombinant chitinases against Parastagonospora nodorum. Latter highlights the application of chitinase from D. capensis as a promising enzyme for the control of fungal pathogens in agriculture.

Desmoplastic Neurotropic Melanoma Presenting as Pilonidal Sinus: A Rare Clinical Association.

BACKGROUND Pilonidal Sinus (PNS) is a small cutaneous orifice in the intergluteal region; symptoms include pain and swelling. Disparately, desmoplastic neurotropic melanoma (DNM) accounts for 1% of all melanomas and mostly occurs in the head and neck region. Because its appearance is generally benign, it typically comes to surgical attention only at an advanced stage or after recurrence. A perineural involvement occurs in 30-40% of the cases and is accompanied by symptoms such as paresthesia, paresis, and/or paralysis. To the best of our knowledge, the association between PNS and DNM has not been described in the literature before. Here, we present a patient with PNS that was diagnosed with DNM. CASE REPORT A 31-year-old healthy man presented with coccydynia and sacral cyst that had been present for about a year. While the initial diagnosis was of a PNS, after excision and biopsy, the pathology changed to PNS with DNM. The patient underwent a work-up for distant metastasis, which was negative. Wide local excision (WLE) with sentinel lymph node biopsy (SLNB) was also performed. CONCLUSIONS Due to the malignant potential of PNS, we support the routine of pathological examination of excised specimens. Once DNM is diagnosed, work-up for distant metastasis and further treatment with WLE as well as SLNB are recommended. The current report describes an association between PNS and DNM. While coccydynia may have been caused by the PNS or the melanoma, the presence of the PNS helped with an earlier diagnosis of the melanoma. Further research on the possible causative relationship between the conditions is required.

Screening for Melanoma and Other Skin Cancer Shows a Higher Early Melanoma Incidence: Social Educational Program "Life Fear-Free".

BACKGROUND: The screening program Life Fear-Free (LFF) aimed at early diagnosis of cutaneous melanoma (CM) was introduced in Samara, Chelyabinsk, Yekaterinburg, and Krasnodar (Russia) in 2019. OBJECTIVES: To analyze the impact of the program on early CM and non-melanoma skin cancer (NMSC) detection. METHODS: According to the social educational campaign, people were informed about CM risk factors and symptoms and were invited for skin examination. The program planned to involve 3200 participants in total. Participants with suspicious lesions were invited for excisional biopsy. RESULTS: 3143 participants, including 75.4% women, were examined for skin lesions. The average age of the participants was 43.7 years. Mostly skin phototypes II and III were registered (48.2% and 41.0%, respectively); 3 patients had CM, 15 had basal cell carcinoma, and 1 had Bowen's disease, which were confirmed histologically. All detected melanomas had Breslow's thickness of 1 mm. CONCLUSION: The participants showed high interest in early skin cancer detection programs. The incidence rate of CM and NMSCs among the program participants was higher than in general public. The early disease grade was proven for the detected CMs and NMSCs. The study has shown that it is important to continue such programs.

Exosomes in the phloem and xylem of woody plants.

MAIN CONCLUSION: Exosomes in the secondary phloem and secondary xylem of angiosperms and gymnosperms have physiological roles in the storage and transport of endoglucanases. Knowledge of plant extracellular vesicles (EVs) is limited by their presence in the apoplastic fluid of seeds and leaves. The contents of plant EVs and their biological functions are unclear. The aim of the present study was to expand our knowledge of EVs in woody plants. Sample splits were prepared from branch and stem samples from angiosperms and gymnosperms after cryomechanical destruction with liquid nitrogen. The study methods included scanning electron (SEM), atomic force microscopy (AFM), endoglucanase activity measurement. EVs visualized on the internal layers of the cell walls proved to be exosomes according to their diameter (65-145 nm). SEM revealed cup-shaped structures characteristic of exosomes in a dry state. Plant exosomes in the form of globules in the native state were visualized for the first time by AFM. Exosomes were present both in the active and dormant cambium. Erosion zones were observed at the sites of exosome localization. The activity of endo-1,4-ß-glucanase was detected in Picea xylem, while the RNA level was very low, suggesting that endo-1,4-ß-glucanases were preserved in the exosomes. There are grounds to assert that endo-1,4-ß-glucanases delivered by exosomes participated in pit cavity formation in the S1 layer of xylary fibres. A possible mechanism of endo-1,4-ß-glucanase action in the biosynthesis of the secondary wall is proposed. These results demonstrate that the physiological role of the exosomes in the phloem and xylem is the storage and transport of endo-1,4-ß-glucanases participating in cell wall remodeling in woody plants. Present study expands our knowledge about plant exosomes.

Static laser speckle contrast analysis for noninvasive burn diagnosis using a camera-phone imager.

Laser speckle contrast analysis (LASCA) is an established optical technique for accurate widefield visualization of relative blood perfusion when no or minimal scattering from static tissue elements is present, as demonstrated, for example, in LASCA imaging of the exposed cortex. However, when LASCA is applied to diagnosis of burn wounds, light is backscattered from both moving blood and static burn scatterers, and thus the spatial speckle contrast includes both perfusion and nonperfusion components and cannot be straightforwardly associated to blood flow. We extract from speckle contrast images of burn wounds the nonperfusion (static) component and discover that it conveys useful information on the ratio of static-to-dynamic scattering composition of the wound, enabling identification of burns of different depth in a porcine model in vivo within the first 48 h postburn. Our findings suggest that relative changes in the static-to-dynamic scattering composition of burns can dominate relative changes in blood flow for burns of different severity. Unlike conventional LASCA systems that employ scientific or industrial-grade cameras, our LASCA system is realized here using a camera phone, showing the potential to enable LASCA-based burn diagnosis with a simple imager.

Accurate, fully-automated NMR spectral profiling for metabolomics.

Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile"-i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR) spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person's metabolic profile. Given a 1D 1H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid), BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF), defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error), in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively-with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in clinical settings. BAYESIL is accessible at http://www.bayesil.ca.

MetaboAnalyst 3.0--making metabolomics more meaningful.

MetaboAnalyst (www.metaboanalyst.ca) is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. First introduced in 2009, MetaboAnalyst has experienced more than a 50X growth in user traffic (>50 000 jobs processed each month). In order to keep up with the rapidly increasing computational demands and a growing number of requests to support translational and systems biology applications, we performed a substantial rewrite and major feature upgrade of the server. The result is MetaboAnalyst 3.0. By completely re-implementing the MetaboAnalyst suite using the latest web framework technologies, we have been able substantially improve its performance, capacity and user interactivity. Three new modules have also been added including: (i) a module for biomarker analysis based on the calculation of receiver operating characteristic curves; (ii) a module for sample size estimation and power analysis for improved planning of metabolomics studies and (iii) a module to support integrative pathway analysis for both genes and metabolites. In addition, popular features found in existing modules have been significantly enhanced by upgrading the graphical output, expanding the compound libraries and by adding support for more diverse organisms.

HMDB 3.0--The Human Metabolome Database in 2013.

The Human Metabolome Database (HMDB) (www.hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. Since its first release in 2007, the HMDB has been used to facilitate research for nearly 1000 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 3.0) has been significantly expanded and enhanced over the 2009 release (version 2.0). In particular, the number of annotated metabolite entries has grown from 6500 to more than 40,000 (a 600% increase). This enormous expansion is a result of the inclusion of both 'detected' metabolites (those with measured concentrations or experimental confirmation of their existence) and 'expected' metabolites (those for which biochemical pathways are known or human intake/exposure is frequent but the compound has yet to be detected in the body). The latest release also has greatly increased the number of metabolites with biofluid or tissue concentration data, the number of compounds with reference spectra and the number of data fields per entry. In addition to this expansion in data quantity, new database visualization tools and new data content have been added or enhanced. These include better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps. This article describes these enhancements to the HMDB, which was previously featured in the 2009 NAR Database Issue. (Note to referees, HMDB 3.0 will go live on 18 September 2012.).

Chromosomal aberrations in adenomatoid hyperplasia of palatal minor salivary gland.

Adenomatoid hyperplasia of minor salivary glands is rare, idiopathic, and benign, and typically presents as a tumour-like mass in the hard or soft palate. Its exact nature is not clear and histological examination usually shows an excess of normal-appearing minor salivary glands. To our knowledge, cytogenetic analysis of it in a minor salivary gland of the palate has not previously been reported. We present the cytogenetic analysis of adenomatoid hyperplasia in the hard palate of a 52-year-old woman.

Differential metabolite profiles and salinity tolerance between two genetically related brown-seeded and yellow-seeded Brassica carinata lines.

Brassica carinata (Ethiopian mustard) has previously been identified as a potential crop species suitable for marginal land in the North American prairies due to its relatively high salt tolerance. Two genetically related B. carinata lines with brown-seeded (BS) and yellow-seeded (YS) phenotypes were assessed for their tolerance to sodium sulfate. Specifically, each line was greenhouse-grown under 0, 50 and 100mM of salt, and analyzed after four weeks and eight weeks of treatment. Generally, the height of the BS line was greater than the YS line under both salt treatments, indicating enhanced salt tolerance of the BS line. NMR-based metabolite profiling and PCA analyses indicated a more pronounced shift in key stem metabolites after four weeks of treatment with the YS line compared to the BS line. For example, tryptophan and formate levels increased in the YS line after four weeks of 100mM salt treatment, while proline and threonine levels varied uniquely compared to other metabolites of the lines. Together, the data indicate that the brown-seeded line has greater sodium tolerance than the yellow-seed line, provide clues to the biochemical underpinnings for the phenotypic variation, and highlight the utility of B. carinata as a biorefinery crop for saline land.

METAGENassist: a comprehensive web server for comparative metagenomics.

With recent improvements in DNA sequencing and sample extraction techniques, the quantity and quality of metagenomic data are now growing exponentially. This abundance of richly annotated metagenomic data and bacterial census information has spawned a new branch of microbiology called comparative metagenomics. Comparative metagenomics involves the comparison of bacterial populations between different environmental samples, different culture conditions or different microbial hosts. However, in order to do comparative metagenomics, one typically requires a sophisticated knowledge of multivariate statistics and/or advanced software programming skills. To make comparative metagenomics more accessible to microbiologists, we have developed a freely accessible, easy-to-use web server for comparative metagenomic analysis called METAGENassist. Users can upload their bacterial census data from a wide variety of common formats, using either amplified 16S rRNA data or shotgun metagenomic data. Metadata concerning environmental, culture, or host conditions can also be uploaded. During the data upload process, METAGENassist also performs an automated taxonomic-to-phenotypic mapping. Phenotypic information covering nearly 20 functional categories such as GC content, genome size, oxygen requirements, energy sources and preferred temperature range is automatically generated from the taxonomic input data. Using this phenotypically enriched data, users can then perform a variety of multivariate and univariate data analyses including fold change analysis, t-tests, PCA, PLS-DA, clustering and classification. To facilitate data processing, users are guided through a step-by-step analysis workflow using a variety of menus, information hyperlinks and check boxes. METAGENassist also generates colorful, publication quality tables and graphs that can be downloaded and used directly in the preparation of scientific papers. METAGENassist is available at http://www.metagenassist.ca.

MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis.

First released in 2009, MetaboAnalyst (www.metaboanalyst.ca) was a relatively simple web server designed to facilitate metabolomic data processing and statistical analysis. With continuing advances in metabolomics along with constant user feedback, it became clear that a substantial upgrade to the original server was necessary. MetaboAnalyst 2.0, which is the successor to MetaboAnalyst, represents just such an upgrade. MetaboAnalyst 2.0 now contains dozens of new features and functions including new procedures for data filtering, data editing and data normalization. It also supports multi-group data analysis, two-factor analysis as well as time-series data analysis. These new functions have also been supplemented with: (i) a quality-control module that allows users to evaluate their data quality before conducting any analysis, (ii) a functional enrichment analysis module that allows users to identify biologically meaningful patterns using metabolite set enrichment analysis and (iii) a metabolic pathway analysis module that allows users to perform pathway analysis and visualization for 15 different model organisms. In developing MetaboAnalyst 2.0 we have also substantially improved its graphical presentation tools. All images are now generated using anti-aliasing and are available over a range of resolutions, sizes and formats (PNG, TIFF, PDF, PostScript, or SVG). To improve its performance, MetaboAnalyst 2.0 is now hosted on a much more powerful server with substantially modified code to take advantage the server's multi-core CPUs for computationally intensive tasks. MetaboAnalyst 2.0 also maintains a collection of 50 or more FAQs and more than a dozen tutorials compiled from user queries and requests. A downloadable version of MetaboAnalyst 2.0, along detailed instructions for local installation is now available as well.

Selectivity of a bromelain based enzymatic debridement agent: a porcine study.

BACKGROUND: Debridement of the burn eschar is a cornerstone of burn wound care. Rapid enzymatic debridement with a bromelain-based agent (Debriding Gel Dressing-DGD) has recently been investigated. The current study was designed to further investigate the selectivity of DGD to burned eschar in a larger number and more varied types of wounds. METHODS: A systematic animal experiment was conducted to determine the effects of DGD on normal, non-injured skin, burns, exposed dermis of donor sites, and skin punch biopsy wells. Partial thickness dermal burns and partial thickness skin graft donor sites were created on a pig and treated with a 4-h application of DGD or its control hydrating vehicle that does not have any activity except hydration. Punch biopsy samples were taken before and after treatment and microscopically assessed for evidence of tissue viability and its respective components thickness. RESULTS: Rapid dissolution of the burn eschar was noted in all DGD but not vehicle treated burns. There was no apparent damage to the underlying sub eschar dermis, donor sites, normal skin or punch biopsy wells after exposure to DGD. While the thickness of the treated tissues slightly increased due to edema, the increase in dermal thickness was similar after treatment with DGD or its vehicle. The increase in the cross section surface area of the treated punch biopsy wells was similar after treatment with DGD and its control vehicle. CONCLUSIONS: Exposure of the burn eschar to DGD results in its rapid dissolution. Exposure of normal skin or non-burned dermis to DGD has no effects demonstrating its selectivity to eschar.

Phase II, multicenter, uncontrolled trial of single-agent capecitabine in patients with non-clear cell metastatic renal cell carcinoma.

BACKGROUND: Although significant progress has been made for metastatic renal cell carcinoma (MRCC), very little progress has been achieved for non-clear cell MRCC. Thus, we performed a phase II, multicenter trial of capecitabine in patients with non-clear cell MRCC. PATIENTS AND METHODS: Adult patients with MRCC containing <50% of clear cells were eligible. All patients received oral capecitabine (1,250 mg/m) twice daily for 14 days, followed by 14 days of rest. Primary end point was objective response rate. On the basis of Chen and Ng 2-stage accrual design, maximum planned enrollment was 51 patients. This study is registered with ClinicalTrials.gov, NCT01182142. RESULTS: Fifty-one patients enrolled between February 2006 and January 2009. Most patients were men (72.5%), who had papillary RCC (76.5%), Memorial Sloan Kettering Cancer Center intermediate prognosis (86%), and had not been treated earlier (92%). The objective response rate was 26%. Two patients (4%) had a complete response. Stable disease was achieved in 24 (47%) patients. The median progression-free survival was 10.1 months [95% confidence interval (CI), 8.7-11.5], and overall survival was 18.3 months (95% CI, 15.5-21.1). The 1-year overall survival was 71% (95% CI, 63%-79%). Major grades 3 to 4, treatment-related toxicities included diarrhea (2%), esophageal mucosal inflammation (2%), hand-foot syndrome (4%), thrombocytopenia (9.8%), and neutropenia (8%). No patients were withdrawn because of laboratory abnormalities. CONCLUSIONS: Capecitabine has clinical activity in MRCC patients who have non-clear cell histology and a good or intermediate prognosis. Additional prospective randomized trial comparing capecitabine with placebo is required.