Emerging biotechnological potentials of DyP-type peroxidases in remediation of lignin wastes and phenolic pollutants: a global assessment (2007–2019)

Dye decolourizing peroxidase (DyP) is an emerging biocatalyst with enormous bioremediation and biotechnological potentials. This study examined the global trend of research related to DyP through a bibliometric analysis. The search term ‘dye decolourizing peroxidase’ or ‘DyP-type peroxidase’ was used to retrieve published articles between 2007 and 2019 from the Web of Science (WoS) and Scopus databases. A total of 62 articles were published within the period, with an annual growth rate of 17·6%. The highest research output was observed in 2015, which accounted for about 13% of the total output in 12 years. Germany published the highest number of articles (n = 10, 16·1%) with a total citation of 478. However, the lowest number of published articles among the top 10 countries was observed in India and Korea (n = 2, 3·2%). Research collaboration was low (collaboration index = 4·08). In addition to dye decolourizing peroxidase(s) and DyP-type peroxidase(s) (n = 33, 53·23%), the top authors keywords and research focus included lignin and lignin degradation (n = 10, 16·1 %). More so, peroxidase (n = 59, 95·2%), amino acid sequence (n = 27, 46·8%), lignin (n = 24, 38·7%) and metabolism (n = 23, 37·1%) were highly represented in keywords-plus. The most common conceptual framework from this study include characterization, lignin degradation and environmental proteomics. Apart from the inherent efficient dye-decolourizing properties, this study showed that DyP has emerging biotechnological potentials in lignin degradation and remediation of phenolic environmental pollutants, which at the moment are under explored globally.     

Metabolic pools associated with monoterpene biosynthesis in higher plants

Partial degradations of (+)-isothujone biosynthesised in Tanacetum vulgare after feeding IPP-[4-¹⁴C], DMAPP-[4-¹⁴C] or 3,3-dimethylacrylate-[Me-¹⁴C], and of geraniol and (+)-pulegone formed in Pelargonium graveolens and Mentha pulegium respectively after uptake of 3,3-dimethylacrylate-[Me-¹⁴C], indicated that none of these metabolites was a direct source of the part of the monoterpene skeleton derived hypothetically from DMAPP. Uptake of glucose-[U¹⁴C] into P. graveolens led, in contrast, to both IPP and DMAPP-derived moieties of geraniol being extensively labelled. Feeding of l-valine-[U-¹⁴C] and l-leucine-[U-¹⁴C] to all three plants resulted in negligible incorporation of tracer into monoterpenes. A soluble enzyme system prepared from foliage of T. vulgare that had been exposed to CO₂-[¹⁴C] for 20 days converted isotopically-normal IPP into GPP with the DMAPP-derived portion containing essentially all (>98%) of the radioactivity present. These observations and those previously obtained from feeding experiments with other [¹⁴C]-labelled precursors on the same plant species are consistent with the occurrence of two metabolic pools of intermediates for monoterpene biosynthesis, one of which is probably protein-bonded.     

Context based mixture model for cell phase identification in automated fluorescence microscopy

Background  

Automated identification of cell cycle phases of individual live cells in a large population captured via automated fluorescence microscopy technique is important for cancer drug discovery and cell cycle studies. Time-lapse fluorescence microscopy images provide an important method to study the cell cycle process under different conditions of perturbation. Existing methods are limited in dealing with such time-lapse data sets while manual analysis is not feasible. This paper presents statistical data analysis and statistical pattern recognition to perform this task.     

Tobamovirus evolution: gene overlaps, recombination, and taxonomic implications

Tobamoviruses, mostly isolated from solanaceous plants, may represent ancient virus lineages that have codiverged with their hosts. Recently completed nucleotide sequences of six nonsolanaceous tobamoviruses allowed assessment of the codivergence hypothesis and support a third subgroup within tobamoviruses. The genomic sequences of 12 tobamoviruses and the partial sequences of 11 others have been analyzed. Comparisons of the predicted protein sequences revealed three clusters of tobamoviruses, corresponding to those infecting solanaceous species (subgroup 1), those infecting cucurbits and legumes (subgroup 2), and those infecting crucifers. The orchid-infecting odontoglossum ringspot tobamovirus was associated with subgroup 1 genomes by its coat and movement protein sequences, but with the crucifer-pathogenic tobamoviruses by the remainder of its genome, suggesting that it is the progeny of a recombinant. For four of five genomic regions, subgroup 1 and 3 genomes were equidistant from a subgroup 2 genome chosen for comparison, suggesting uniform rates of evolution. A phylogenetic tree of plant families based on the tobamoviruses they harbor was congruent with that based on rubisco sequences but had a different root, suggesting that codivergence was tempered by rare events of viruses of one family colonizing another family. The proposed subgroup 3 viruses probably have an origin of virion assembly in the movement protein gene, a large (25-codon) overlap of movement and coat protein open reading frames, and a comparably shorter genome. Codon-position- dependent base compositions and codon prevalences suggested that the coat protein frame of the overlap region was ancestral. Bootstrapped parsimony analysis of the nucleotides in the overlap region and of the sequences translated from the -1 frame (the subgroup 3 movement protein frame) of this region produced trees inconsistent with those deduced from other regions. The results are consistent with a model in which a no or short overlap organization was ancestral. Despite encoding of subgroup 2 and 3 movement protein C-termini by nonhomologous nucleotides, weak similarities between their amino acid sequences suggested convergent sequence evolution.      

3D cell nuclei segmentation based on gradient flow tracking

Background  

Reliable segmentation of cell nuclei from three dimensional (3D) microscopic images is an important task in many biological studies. We present a novel, fully automated method for the segmentation of cell nuclei from 3D microscopic images. It was designed specifically to segment nuclei in images where the nuclei are closely juxtaposed or touching each other. The segmentation approach has three stages: 1) a gradient diffusion procedure, 2) gradient flow tracking and grouping, and 3) local adaptive thresholding.     

Biosynthesis of chiral α- and β-pinenes in pinus species

C-3 of (+) and (?)-α-pinene and of (?)-β-pinene biosynthesized in several Pinus species was derived from C-2 of mevalonate; and the hydrogen at C-5 in all the isomers was derived from that at C-6 in nerol. This pattern is consistent with two routes for bicyclization of the acyclic biosynthetic precursor: one leads to (?)-β-pinene and the other to (+)-α-pinene of opposite absolute configuration. (?)-α-Pinene probably results from subsequent isomerisation of the (?)-β-isomer, and (very small) amounts of (+)-β-pinene result from similar (unfavoured thermodynamically) isomerisation of the (+)-α-isomer.     

Bioluminescence imaging reveals inhibition of tumor cell proliferation by Alzheimer's amyloid β protein

Background  

Cancer and Alzheimer's disease (AD) are two seemingly distinct diseases and rarely occur simultaneously in patients. To explore molecular determinants differentiating pathogenic routes towards AD or cancer, we investigate the role of amyloid β protein (Aβ) on multiple tumor cell lines that are stably expressing luciferase (human glioblastoma U87; human breast adenocarcinoma MDA-MB231; and mouse melanoma B16F).