Identification of putative serum glycoprotein biomarkers for human lung adenocarcinoma by multilectin affinity chromatography and LC-MS/MS

Glycoproteins in human serum play fundamental roles in many biological processes, and also have clinical value as biomarkers for disease progression and treatment. In this study, we isolated glycoproteins from the sera of three healthy individuals and three lung adenocarcinoma patients using multilectin affinity chromatography. The recovered glycoproteins were subjected to treatment with peptide-N-glycosidase F (PNGase F) and in-gel digestion by trypsin. Tryptic peptides were analyzed by nano-LC coupled to ESI-MS/MS and the MS/MS spectra were processed by Bioworks 3.2 and an in-house bioinformatics tool, ProtAn. Approximately 90% of the proteins identified contained more than one potential glycosylation site. Comparison of the serum glycoproteome of healthy and adenocarcinoma individuals revealed 38 cancer-selective proteins. Among them, 60% have previously been reported as low abundance proteins in human sera. We identified several cancer-selective proteins that have been previously characterized as potential indicators of lung cancer in serum or plasma, including haptoglobin (HP), inter-alpha-trypsin inhibitor heavy chain 4 (ITI-H4), complement C3 precursor, and leucine-rich alpha-2-glycoprotein. In addition, plasma kallikrein (KLKB1) and inter-alpha-trypsin inhibitor heavy chain 3 (ITI-H3) were identified as being potentially elevated in the lung cancer group, and were validated by Western blot analysis. Furthermore, approximately 18 kDa plasma kallirein protein fragment was detected at high levels in 25 out of 28 adenocarcinoma patients, while one of the eight normal individuals showed moderate positive. The results suggest that KLKB1 represents a potential candidate serum biomarker of lung cancer.     

Biofilm stratification during simultaneous nitrification and denitrification (SND) at a biocathode

The aeration of the cathode compartment of bioelectrochemical systems (BESs) was recently shown to promote simultaneous nitrification and denitrification (SND). This study investigates the cathodic metabolism under different operating conditions as well as the structural organization of the cathodic biofilm during SND. Results show that a maximal nitrogen removal efficiency of 86.9 ± 0.5%, and a removal rate of 3.39 ± 0.08 mg N L⁻¹ h⁻¹ could be achieved at a dissolved oxygen (DO) level of 5.73 ± 0.03 mg L⁻¹ in the catholyte. The DO levels used in this study are higher than the thresholds previously reported as detrimental for denitrification. Analysis of the cathodic half-cell potential during batch tests suggested the existence of an oxygen gradient within the biofilm while performing SND. FISH analysis corroborated this finding revealing that the structure of the biofilm included an outer layer occupied by putative nitrifying organisms, and an inner layer where putative denitrifying organisms were most dominant. To our best knowledge this is the first time that nitrifying and denitrifying microorganisms are simultaneously observed in a cathodic biofilm.     

Increasing manganese peroxidase production and biodecolorization of triphenylmethane dyes by novel fungal consortium

A fungal consortium-SR consisting of Trametes sp. SQ01 and Chaetomium sp. R01 was developed for decolorizing three kinds of triphenylmethane dyes, which were decolorized by individual fungi with low efficiencies. The fungal consortium-SR produced 1.3 U ml(-1) of manganese peroxidase, 5.5 times higher than that produced by the monoculture of Trametes sp. SQ01, and decolorized Crystal Violet, Coomassie Brilliant Blue G250 (CBB G250) and Cresol Red. The fungal consortium-SR had a decolorization rate of 63-96%, much higher than that of the monoculture of strain SQ01 (38-72%). In consortium-SR, the higher efficiencies of decolorization of Crystal Violet and CBB G250 were obtained when they added to the culture after 4d of mixed cultivation rather than at the beginning of cultivation. Cresol Red was the exception. It is suggested that the consortium-SR has great potential for decolorizing triphenylmethane dyes.     

Beauveria bassiana (Balsamo) Vuillemin as an endophyte in tissue culture banana (Musa spp.)

Beauveria bassiana is considered a virulent pathogen against the banana weevil Cosmopolites sordidus. However, current field application techniques for effective control against this pest remain a limitation and an alternative method for effective field application needs to be investigated. Three screenhouse experiments were conducted to determine the ability of B. bassiana to form an endophytic relationship with tissue culture banana (Musa spp.) plants and to evaluate the plants for possible harmful effects resulting from this relationship. Three Ugandan strains of B. bassiana (G41, S204 and WA) were applied by dipping the roots and rhizome in a conidial suspension, by injecting a conidial suspension into the plant rhizome and by growing the plants in sterile soil mixed with B. bassiana-colonized rice substrate. Four weeks after inoculation, plant growth parameters were determined and plant tissue colonization assessed through re-isolation of B. bassiana. All B. bassiana strains were able to colonize banana plant roots, rhizomes and pseudostem bases. Dipping plants in a conidial suspension achieved the highest colonization with no negative effect on plant growth or survival. Beauveria bassiana strain G41 was the best colonizer (up to 68%, 79% and 41% in roots, rhizome and pseudostem base, respectively) when plants were dipped. This study demonstrated that, depending on strain and inoculation method, B. bassiana can form an endophytic relationship with tissue culture banana plants, causing no harmful effects and might provide an alternative method for biological control of C. sordidus.     

Nitrogen dynamics in two antarctic streams

The many glacier meltwater streams of southern Victoria Land flow through catchments where life forms are almost entirely microbial. Allochthonous inputs of nitrogen from two study streams near McMurdo Sound were derived mostly from the melting glaciers (ca. 100–200 mg N m^–3) with some originating from N₂-fixation by heterocystous cyanobacteria (max. 939 mg N m^–2 year^–1). Thirty to fifty per cent of the glacier derived N was dissolved organic N and a major proportion of this was identified as urea N which was utilised by the rich algal and cyanobacterial mats in the streams. A nutrient budget for Fryxell Stream was estimated, quantifying uptake of urea-N and dissolved inorganic N and the release of dissolved organic (non urea) and particulate N by the stream communities. An index of in-stream nitrogen processing, the Net Uptake Length Constant in these streams was compared with that from temperate climates and was found to be similar. Despite the influence of low temperatures on microbial activity (mean daily water temperature = 5 °C) nutrient removal rates from these antarctic streams are high because of the large standing stock of microbial biomass there.     

Identification of toxicological biomarkers of di(2‐ethylhexyl) phthalate in proteins secreted by HepG2 cells using proteomic analysis

The effects of di(2‐ethylhexyl) phthalate (DEHP) on proteins secreted by HepG2 cells were studied using a proteomic approach. HepG2 cells were exposed to various concentrations of DEHP (0, 2.5, 5, 10, 25, 50, 100, and 250 μM) for 24 or 48 h. 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl tetrazolium bromide (MTT) and comet assays were then conducted to determine the cytotoxicity and genotoxicity of DEHP, respectively. The MTT assay showed that 10 μM DEHP was the maximum concentration that did not cause cell death. In addition, the DNA damage in HepG2 cells exposed to DEHP was found to increase in a dose‐ and time‐dependent fashion. Proteomic analysis using two different pI ranges (4–7 and 6–9) and large size 2‐DE revealed the presence of 2776 protein spots. A total of 35 (19 up‐ and 16 down‐regulated) proteins were identified as biomarkers of DEHP by ESI‐MS/MS. Several differentiated protein groups were also found. Proteins involved in apoptosis, transportation, signaling, energy metabolism, and cell structure and motility were found to be up‐ or down‐regulated. Among these, the identities of cystatin C, Rho GDP inhibitor, retinol binding protein 4, gelsolin, DEK protein, Raf kinase inhibitory protein, triose phosphate isomerase, cofilin‐1, and haptoglobin‐related protein were confirmed by Western blot assay. Therefore, these proteins could be used as potential biomarkers of DEHP and human disease associated with DEHP.     

Habitat Use by Sonoran Desert Tortoises

ABSTRACT The distribution of desert tortoises (Gopherus agassizii) spans a wide range of biotic and abiotic conditions in the southwestern United States and northwestern Mexico, with physical and behavioral differences distinguishing tortoises inhabiting the Mojave Desert from those inhabiting the Sonoran Desert. Relative to tortoise populations in the Mojave Desert, populations in the Sonoran Desert have not been well-studied. To assess how habitat use of desert tortoises in the Sonoran Desert was influenced by topography, vegetation, geomorphology, and soil, we surveyed 40 randomly located 3-ha sites for presence of adult tortoises within a site-occupancy framework. We modeled both occupancy and detection probability as a function of environmental features, and compared those results with a logistic regression model that assumed detection probability was equal to 1. Results from both approaches agreed, suggesting that habitat selection of tortoises in the Sonoran Desert was influenced primarily by topographic and geomorphologic features rather than by vegetation. Specifically, tortoises were more likely to occupy sites that were steep (we detected tortoises on 29% of sites with mean slope <5° and 92% of sites with mean slope >15°) and predominantly east-facing (53% of sites with <5% of site facing E and 92% of sites with >20% facing E), and less likely to occupy north-facing slopes (100% of sites with <10% of site facing N and 14% of sites with >60% facing N). Our results contrast with patterns of habitat use in the Mojave Desert where tortoises primarily occupy valley bottoms. Habitat use of tortoises in Sonoran and Mojave Desert populations differ considerably, contributing to the mounting body of evidence suggesting that these geographically distinct populations may represent separate species.     

Systematic analysis of biochemical performance and the microbial community of an activated sludge process using ozone-treated sludge for sludge reduction

Two lab-scale bioreactors (reactors 1 and 2) were employed to examine the changes in biological performance and the microbial community of an activated sludge process fed with ozonated sludge for sludge reduction. During the 122 d operation, the microbial activities and community in the two reactors were evaluated. The results indicated that, when compared with the conventional reactor (reactor 1), the reactor that was fed with the ozonated sludge (reactor 2) showed good removal of COD, TN and cell debris, without formation of any excess sludge. In addition, the protease activity and intracellular ATP concentration of reactor 2 were increased when compared to reactor 1, indicating that reactor 2 had a better ability to digest proteins and cell debris. DGGE analysis revealed that the bacterial communities in the two reactors were different, and that the dissimilarity of the bacterial population was nearly 40%. Reactor 2 also contained more protozoa and metazoa, which could graze on the ozone-treated sludge debris directly.     

Biogeography and diversification of colletid bees (Hymenoptera: Colletidae): emerging patterns from the southern end of the world

Aim The evolutionary history of bees is presumed to extend back in time to the Early Cretaceous. Among all major clades of bees, Colletidae has been a prime example of an ancient group whose Gondwanan origin probably precedes the complete break‐up of Africa, Antarctica, Australia and South America, because modern lineages of this family occur primarily in southern continents. In this paper, we aim to study the temporal and spatial diversification of colletid bees to better understand the processes that have resulted in the present southern disjunctions. Location Southern continents. Methods We assembled a dataset comprising four nuclear genes of a broad sample of Colletidae. We used Bayesian inference analyses to estimate the phylogenetic tree topology and divergence times. Biogeographical relationships were investigated using event‐based analytical methods: a Bayesian approach to dispersal–vicariance analysis, a likelihood‐based dispersal–extinction–cladogenesis model and a Bayesian model. We also used lineage through time analyses to explore the tempo of radiations of Colletidae and their context in the biogeographical history of these bees. Results Initial diversification of Colletidae took place at the Late Cretaceous (≥ 70 Ma). Several (6–14) lineage exchanges between Australia and South America via Antarctica during the Late Cretaceous and Eocene epochs could explain the disjunctions observed between colletid lineages today. All biogeographical methods consistently indicated that there were multiple lineage exchanges between South America and Australia, and these approaches were valuable in exploring the degree of uncertainty inherent in the ancestral reconstructions. Biogeographical and dating results preclude an explanation of Scrapterinae in Africa as a result of vicariance, so one dispersal event is assumed to explain the disjunction in relation to Euryglossinae. The net diversification rate was found to be highest in the recent history of colletid evolution. Main conclusions The biogeography and macroevolutionary history of colletid bees can be explained by a combination of Cenozoic vicariance and palaeoclimatic changes during the Neogene. The austral connection and posterior break‐up of South America, Antarctica and Australia resulted in a pattern of disjunct sister lineages. Increased biome aridification coupled with floristic diversification in the southern continents during the Neogene may have contributed to the high rates of cladogenesis in these bees in the last 25–30 million years.