Degradation of pruning wastes by Phanerochaete sordida growing in SSF: Ultrastructural,chemical, and enzymatic studies

A solid standard fermentation (SSF) with the fungus Phanerochaete sordida in a medium with Nephrolepis cordifolia (entire pinnae separated from the rachis) and Laurus nobilis (fragmented leaves) was performed over 92 days to study the degradation of leaves with histological, chemical, and enzymatic methods. The fungus entered the leaves early, through the stomata in N. cordifolia and L. nobilis, and also through mechanical cuts that had been made in the latter. The initial attack affected the mesophyll in both plant species, and the phloem in L. nobilis. The vascular bundle of N. cordifolia was protected by a sheath of cells with thick lignified walls. The collenchyma cell walls situated near the principal vein in L. nobilis swelled during the initial stages of enzymatic action, but reduced their thickness afterwards, mainly in regions of contact with the hyphae. At the end of the experiment, no species had leaves with mesophyll. In L. nobilis, phloem was also lacking, and a partial and heterogeneous attack on the xylem became evident. The histological changes are compared with the enzymatic activities and the chemical composition of the culture media, describing the stages of fungal colonization.     

Influence of the carbon source on the growth and lignocellulolytic enzyme production by Morchella esculenta strains

Growth and lignocellulolytic enzymes production by two Morchella esculenta strains (BAFC 1728 and BEL 124) growing in solid state fermentation using different lignocellulosic materials along 58 days was characterized. Both strains were able to grow on the three substrates: wheat bran, wheat bran plus corn starch, and rolled oat. The growth was characterized by measuring chitin content, reducing sugars, pH, dry weight loss, and extractable proteins, such parameters varied substantially with substrate and strain used. The maximum rate of growth in both strains was observed between 5 and 28 days. Regarding enzyme production, as a general trend strain BAFC 1728 produced the highest titres. The most evident difference was observed in laccase production by this strain on wheat bran, which exceeded that observed in strain BEL 124 by tenfold (7.45 U g⁻¹).     

Evaluation of Argentinean white rot fungi for their ability to produce lignin-modifying enzymes and decolorize industrial dyes

The decolorizing capacity of 26 white rot fungi from Argentina was investigated. Extracellular production of ligninolytic enzymes by mycelium growing on solid malt extract/glucose medium supplemented with different dyes (Malachite Green, Azure B, Poly R-478, Anthraquinone Blue, Congo Red and Xylidine), dye decolorization and the relationship between these two processes were studied. Only ten strains decolorized all the dyes, all ten strains produced laccase, lignin peroxidase and manganese peroxidase on solid medium. However, six of the strains could not decolorize any of the dyes; all six strains tested negative for lignin peroxidase, and produced less than 0.05 U/g agar of manganese peroxidase. Comparing the isolates with the well-known dye-degrader Phanerochaete chrysosporium, a new fungus was identified: Coriolus versicolor f. antarcticus, potentially a candidate for use in biodecoloration processes. Eighteen day-old cultures of this fungus were able to decolorize in an hour 28%, 30%, 43%, 88% and 98% of Xylidine (24 mg/l), Poly R-478 (75 mg/l), Remazol Brilliant Blue R (9 mg/l), Malachite Green (6 mg/l) and Indigo Carmine (23 mg/l), respectively. Laccase activity was 0.13 U/ml, but neither lignin peroxidase nor manganese peroxidase were detected in the extracellular fluids for that day of incubation.     

Degradation of poplar wood by Fomes sclerodermeus: production of ligninolytic enzymes in sawdust of poplar and cedar

Fomes sclerodermeus is a white-rot fungus. Its production of laccase, manganese peroxidase and lignin peroxidase on sawdust-based media was evaluated. No lignin peroxidase activity was measured in any media tested. The higher production of laccase and manganese peroxidase were found on media containing poplar sawdust. F. sclerodermeus was grown on wood blocks of poplar during six months. Dry weight losses of the blocks reached a mean value of 51%. The quantification of cellulose and lignin in the 6-months incubated blocks showed losses of up to 58 and 56% for cellulose and lignin, respectively. The decay examined under microscope revealed mycelium colonizing the lumen of vessel elements, cell wall thinning and entire degradation of the radial parenchyma.     

Production of laccase and manganese peroxidase by<Emphasis Type="Italic"> Fomes sclerodermeus</Emphasis> grown on wheat bran

The aim of this work was to study the growth and production of ligninolytic enzymes by Fomes sclerodermeus using a natural medium based on wheat bran as the principal substrate in a solid-state fermentation. Growth was monitored by measuring the chitin content in the substrate. The maximum rate of growth was observed between days 7 and 18. A 38% total dry-weight loss of the substrate was measured after 28 days of cultivation. Differential hydrolysis of the substrate revealed that cellulose was more extensively degraded than lignin. In the 28-day incubation period, the losses of cellulose and lignin were 38 and 15%, respectively. No lignin peroxidase activity was found in any of the media tested. The maximum manganese-dependent peroxidase activity recorded was 6.3 U g⁻¹ at 14 days, while the maximum laccase activity was 270 U g⁻¹ at 28 days post-inoculation. Addition of commonly used inducers such as copper or manganese did not produce a further increase in the enzyme activities, nor did addition of glucose, asparagine, or malt extract. Electronic Publication     

Combined effect of copper and initial pH of the culture on production of laccase and manganese peroxidase by Stereum hirsutum (Willd) Pers

Stereum hirsutum is a white-rot fungus which produces laccase and manganese peroxidase as part of its ligninolytic system. Maximal ligninases production (under the conditions studied) was obtained in the media containing 250 microM Cu++ along with a pH value of 5.5. The fitting of ligninase production to a linear equation showed negative interaction between increasing values of pH and concentration of copper.     

Rates of DNA sequence evolution are not sex-biased in Drosophila melanogaster and D. simulans

To determine whether male- or female-biased mutation rates have affected the molecular evolution of Drosophila melanogaster and D. simulans, we calculated the male-to-female ratio of germline cell divisions ([symbol: see text]) from germline generation data and the male-to-female ratio of mutation rate ([symbol: see text]) by comparing chromosomal levels of nucleotide divergence. We found that the ratio of germline cell divisions changes from indicating a weak female bias to indicating a weak male bias as the age of reproduction increases. The range of [symbol: see text] values that we observed, however, does not lead us to expect much, if any, difference in mutation rate between the sexes. Silent and intron nucleotide divergence were compared between nine loci on the X chromosome and nine loci on the second and third chromosomes. The average levels of nucleotide divergence were not significantly different across the chromosomes, although both silent and intron sites show a trend toward slightly more divergence on the X. These results indicate a lack of sex- or chromosome-biased molecular evolution in D. melanogaster and D. simulans.      

The performance of using dried blood spot specimens for HIV-1 viral load testing: A systematic review and meta-analysis

BackgroundAccurate routine HIV viral load testing is essential for assessing the efficacy of antiretroviral treatment (ART) regimens and the emergence of drug resistance. While the use of plasma specimens is the standard for viral load testing, its use is restricted by the limited ambient temperature stability of viral load biomarkers in whole blood and plasma during storage and transportation and the limited cold chain available between many health care facilities in resource-limited settings. Alternative specimen types and technologies, such as dried blood spots, may address these issues and increase access to viral load testing; however, their technical performance is unclear. To address this, we conducted a meta-analysis comparing viral load results from paired dried blood spot and plasma specimens analyzed with commonly used viral load testing technologies.Methods and findingsStandard databases, conferences, and gray literature were searched in 2013 and 2018. Nearly all studies identified (60) were conducted between 2007 and 2018. Data from 40 of the 60 studies were included in the meta-analysis, which accounted for a total of 10,871 paired dried blood spot:plasma data points. We used random effects models to determine the bias, accuracy, precision, and misclassification for each viral load technology and to account for between-study variation. Dried blood spot specimens produced consistently higher mean viral loads across all technologies when compared to plasma specimens. However, when used to identify treatment failure, each technology compared best to plasma at a threshold of 1,000 copies/ml, the present World Health Organization recommended treatment failure threshold. Some heterogeneity existed between technologies; however, 5 technologies had a sensitivity greater than 95%. Furthermore, 5 technologies had a specificity greater than 85% yet 2 technologies had a specificity less than 60% using a treatment failure threshold of 1,000 copies/ml. The study’s main limitation was the direct applicability of findings as nearly all studies to date used dried blood spot samples prepared in laboratories using precision pipetting that resulted in consistent input volumes.ConclusionsThis analysis provides evidence to support the implementation and scale-up of dried blood spot specimens for viral load testing using the same 1,000 copies/ml treatment failure threshold as used with plasma specimens. This may support improved access to viral load testing in resource-limited settings lacking the required infrastructure and cold chain storage for testing with plasma specimens.

Lara Vojnov and co-workers report on the use of dried blood spots for HIV viral load testing.     

Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival

Background

Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this study was to identify general and clinical-dependent biomarker genes and biological processes of three complementary events: lifetime, overall and progression-free glioblastoma survival.

Methods

A novel analytical strategy was developed to identify general associations between the biomarkers and glioblastoma, and associations that depend on cohort groups, such as race, gender, and therapy. Gene network inference, cross-validation and functional analyses further supported the identified biomarkers.

Results

A total of 61, 47 and 60 gene expression profiles were significantly associated with lifetime, overall, and progression-free survival, respectively. The vast majority of these genes have been previously reported to be associated with glioblastoma (35, 24, and 35 genes, respectively) or with other cancers (10, 19, and 15 genes, respectively) and the rest (16, 4, and 10 genes, respectively) are novel associations. Pik3r1, E2f3, Akr1c3, Csf1, Jag2, Plcg1, Rpl37a, Sod2, Topors, Hras, Mdm2, Camk2g, Fstl1, Il13ra1, Mtap and Tp53 were associated with multiple survival events. Most genes (from 90 to 96%) were associated with survival in a general or cohort-independent manner and thus the same trend is observed across all clinical levels studied. The most extreme associations between profiles and survival were observed for Syne1, Pdcd4, Ighg1, Tgfa, Pla2g7, and Paics. Several genes were found to have a cohort-dependent association with survival and these associations are the basis for individualized prognostic and gene-based therapies. C2, Egfr, Prkcb, Igf2bp3, and Gdf10 had gender-dependent associations; Sox10, Rps20, Rab31, and Vav3 had race-dependent associations; Chi3l1, Prkcb, Polr2d, and Apool had therapy-dependent associations. Biological processes associated glioblastoma survival included morphogenesis, cell cycle, aging, response to stimuli, and programmed cell death.

Conclusions

Known biomarkers of glioblastoma survival were confirmed, and new general and clinical-dependent gene profiles were uncovered. The comparison of biomarkers across glioblastoma phases and functional analyses offered insights into the role of genes. These findings support the development of more accurate and personalized prognostic tools and gene-based therapies that improve the survival and quality of life of individuals afflicted by glioblastoma multiforme.