Microfluidic study of effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength in the flowing and no-flowing microchannels

Journal of Industrial Microbiology & Biotechnology - Biofilm accumulation in porous media can cause pore plugging and change many of the physical properties of porous media. Engineering...     

Biosorption of copper by yeasts

Summary The ability to accumulate copper from aqueous solutions was determined with different yeast species. Yeast cells did not show any significant differences in process kinetics. The uptake was very fast and was influenced by environmental factors. The metal-accumulating capacity differed among the tested strains. The yeastsCandida tropicalis andPichia guilliermondii were chosen for extensive research. Cells of the stationary growth phase were able to adsorb a high amount of copper. The uptake capacity decreased with increasing biomass concentration. Copper adsorption obeyed the Freundlich isotherm. Optimal pH range was between 5 and 7. The biomass could be used repeatedly for biosorption after desorption by mineral acids.     

Seedling emergence and summer survival after direct seeding for woodland restoration on old fields in south‐western Australia

Restoration opportunities provided by an emerging carbon market have largely focused on large‐scale woodland restoration projects. Gondwana Link is one such project operating in a 1000‐km corridor in south‐western Australia. We identified environmental factors affecting the success of woody‐species restoration at a dry‐woodland Gondwana Link site, Peniup, by relating the emergence and survival of 1522 seedlings to abiotic and biotic variables, including soil conditions and weed cover. We found soil conditions were highly variable across the site and, together with the dry Mediterranean‐climate summer, affected seedling emergence and summer survival. Seedling emergence was higher in sandy soils, but summer survival was higher in clay soils. Most of the seedlings that emerged and survived the summer were in either the Fabales or Myrtaceae family. We concluded that attempts to analyse restoration outcomes that do not consider how the influence of primary abiotic and biotic factors changes over time may mask the mechanisms driving seedling establishment.     

The substrate radical of Escherichia coli oxygen-independent coproporphyrinogen III oxidase HemN

During porphyrin biosynthesis the oxygen-independent coproporphyrinogen III oxidase (HemN) catalyzes the oxidative decarboxylation of the propionate side chains of rings A and B of coproporphyrinogen III to form protoporphyrinogen IX. The enzyme utilizes a 5'-deoxyadenosyl radical to initiate the decarboxylation reaction, and it has been proposed that this occurs by stereo-specific abstraction of the pro-S-hydrogen atom at the beta-position of the propionate side chains leading to a substrate radical. Here we provide EPR-spectroscopic evidence for intermediacy of the latter radical by observation of an organic radical EPR signal in reduced HemN upon addition of S-adenosyl-L-methionine and the substrate coproporphyrinogen III. This signal (g(av) = 2.0029) shows a complex pattern of well resolved hyperfine splittings from at least five different hydrogen atoms. The radical was characterized using regiospecifically labeled (deuterium or 15N) coproporphyrinogen III molecules. They had been generated from a multienzyme mixture and served as efficient substrates. Reaction of HemN with coproporphyrinogen III, perdeuterated except for the methyl groups, led to the complete loss of resolved proton hyperfine splittings. Substrates in which the hydrogens at both alpha- and beta-positions, or only at the beta-positions of the propionate side chains, or those of the methylene bridges, were deuterated showed that there is coupling with hydrogens at the alpha-, beta-, and methylene bridge positions. Deuterium or 15N labeling of the pyrrole nitrogens without labeling the side chains only led to a slight sharpening of the radical signal. Together, these observations clearly identified the radical signal as substrate-derived and indicated that, upon abstraction of the pro-S-hydrogen atom at the beta-position of the propionate side chain by the 5'-deoxyadenosyl radical, a comparatively stable delocalized substrate radical intermediate is formed in the absence of electron acceptors. The observed hyperfine constants and g values show that this coproporphyrinogenyl radical is allylic and encompasses carbon atoms 3', 3, and 4.     

Assessment of genetic diversity and mating system of Acacia cyclops restoration and remnant populations

Acacia cyclops, or Ngaamarur, is a common coastal shrub or small tree of the southwest of Western Australia and South Australia used for restoration in these landscapes and elsewhere. Knowledge of genetic diversity and mating systems of restoration populations is often lacking but can help inform likely restoration success. We compared genetic diversity and mating system parameters at three restoration populations of A. cyclops to nearby remnant reference populations. Mean levels of genetic diversity in restoration populations (Na = 1.806, Ne = 1.560, He = 0.270, Ho = 0.359) were not significantly different from those in the reference populations (Na = 1.833, Ne = 1.574, He = 0.269, Ho = 0.352) suggesting diverse seed collections were made for restoration. Allelic genetic divergence among restoration and reference populations was low (D_ST ≤ 0.04) suggesting that seeds were of local provenance. Mating system parameters were similar among restoration (t_m = 0.989, t_m–t_s = 0.010, r_pm = 0.392) and reference populations (t_m = 0.868, t_m–t_s = 0.039, r_pm = 0.410), suggesting functionality of the mating system and restitution of generalist insect pollinator services in restored populations at 7, 10, and 12 years after planting. Lower levels of heterozygosity in progeny compared to adults suggest post‐germination or late‐acting selection against inbred seedlings. Evidence for selection and seedling attrition further emphasizes the benefits of collections from many individuals in well‐connected outcrossed source populations. Overall, results suggest available local genetic diversity was captured and restoration populations have mating systems equivalent to those of reference populations.     

Plasmin activates epithelial Na+ channels by cleaving the gamma subunit

Proteolytic processing of epithelial sodium channel (ENaC) subunits occurs as channels mature within the biosynthetic pathway. The proteolytic processing events of the alpha and gamma subunits are associated with channel activation. Furin cleaves the alpha subunit ectodomain at two sites, releasing an inhibitory tract and activating the channel. However, furin cleaves the gamma subunit ectodomain only once. A second distal cleavage in the gamma subunit induced by other proteases, such as prostasin and elastase, is required to release a second inhibitory tract and further activate the channel. We found that the serine protease plasmin activates ENaC in association with inducing cleavage of the gamma subunit at gammaLys194, a site distal to the furin site. A gammaK194A mutant prevented both plasmin-dependent activation of ENaC and plasmin-dependent production of a unique 70-kDa carboxyl-terminal gamma subunit cleavage fragment. Plasmin-dependent cleavage and activation of ENaC may have a role in extracellular volume expansion in human disorders associated with proteinuria, as filtered plasminogen may be processed by urokinase, released from renal tubular epithelium, to generate active plasmin.     

Identification of Highly Methylated Genes across Various Types of B-Cell Non-Hodgkin Lymphoma

Epigenetic alterations of gene expression are important in the development of cancer. In this study, we identified genes which are epigenetically altered in major lymphoma types. We used DNA microarray technology to assess changes in gene expression after treatment of 11 lymphoma cell lines with epigenetic drugs. We identified 233 genes with upregulated expression in treated cell lines and with downregulated expression in B-cell lymphoma patient samples (n = 480) when compared to normal B cells (n = 5). The top 30 genes were further analyzed by methylation specific PCR (MSP) in 18 lymphoma cell lines. Seven of the genes were methylated in more than 70% of the cell lines and were further subjected to quantitative MSP in 37 B-cell lymphoma patient samples (diffuse large B-cell lymphoma (activated B-cell like and germinal center B-cell like subtypes), follicular lymphoma and Burkitt`s lymphoma) and normal B lymphocytes from 10 healthy donors. The promoters of DSP, FZD8, KCNH2, and PPP1R14A were methylated in 28%, 67%, 22%, and 78% of the 36 tumor samples, respectively, but not in control samples. Validation using a second series of healthy donor controls (n = 42; normal B cells, peripheral blood mononuclear cells, bone marrow, tonsils and follicular hyperplasia) and fresh-frozen lymphoma biopsies (n = 25), confirmed the results. The DNA methylation biomarker panel consisting of DSP, FZD8, KCNH2, and PPP1R14A was positive in 89% (54/61) of all lymphomas. Receiver operating characteristic analysis to determine the discriminative power between lymphoma and healthy control samples showed a c-statistic of 0.96, indicating a possible role for the biomarker panel in monitoring of lymphoma patients.     

Lactococcus lactis HemW (HemN) is a haem-binding protein with a putative role in haem trafficking

Lactococcus lactis cannot synthesize haem, but when supplied with haem, expresses a cytochrome bd oxidase. Apart from the cydAB structural genes for this oxidase, L. lactis features two additional genes, hemH and hemW (hemN), with conjectured functions in haem metabolism. While it appears clear that hemH encodes a ferrochelatase, no function is known for hemW. HemW-like proteins occur in bacteria, plants and animals, and are usually annotated as CPDHs (coproporphyrinogen III dehydrogenases). However, such a function has never been demonstrated for a HemW-like protein. We here studied HemW of L. lactis and showed that it is devoid of CPDH activity in vivo and in vitro. Recombinantly produced, purified HemW contained an Fe-S (iron-sulfur) cluster and was dimeric; upon loss of the iron, the protein became monomeric. Both forms of the protein covalently bound haem b in vitro, with a stoichiometry of one haem per monomer and a KD of 8?μM. In vivo, HemW occurred as a haem-free cytosolic form, as well as a haem-containing membrane-associated form. Addition of L. lactis membranes to haem-containing HemW triggered the release of haem from HemW in vitro. On the basis of these findings, we propose a role of HemW in haem trafficking. HemW-like proteins form a distinct phylogenetic clade that has not previously been recognized.     

Nuclear Legumain Activity in Colorectal Cancer

The cysteine protease legumain is involved in several biological and pathological processes, and the protease has been found over-expressed and associated with an invasive and metastatic phenotype in a number of solid tumors. Consequently, legumain has been proposed as a prognostic marker for certain cancers, and a potential therapeutic target. Nevertheless, details on how legumain advances malignant progression along with regulation of its proteolytic activity are unclear. In the present work, legumain expression was examined in colorectal cancer cell lines. Substantial differences in amounts of pro- and active legumain forms, along with distinct intracellular distribution patterns, were observed in HCT116 and SW620 cells and corresponding subcutaneous xenografts. Legumain is thought to be located and processed towards its active form primarily in the endo-lysosomes; however, the subcellular distribution remains largely unexplored. By analyzing subcellular fractions, a proteolytically active form of legumain was found in the nucleus of both cell lines, in addition to the canonical endo-lysosomal residency. In situ analyses of legumain expression and activity confirmed the endo-lysosomal and nuclear localizations in cultured cells and, importantly, also in sections from xenografts and biopsies from colorectal cancer patients. In the HCT116 and SW620 cell lines nuclear legumain was found to make up approximately 13% and 17% of the total legumain, respectively. In similarity with previous studies on nuclear variants of related cysteine proteases, legumain was shown to process histone H3.1. The discovery of nuclear localized legumain launches an entirely novel arena of legumain biology and functions in cancer.