Experimental study of solute transport and extraction by a single root in soil

The fate of ¹⁴C-2,4,6-trinitrotoluene ([U-¹⁴C]TNT) in soil/plant systems was studied using onion (Allium cepa L.) plants with only a single root. It was found that the single roots grew exponentially and that the rate of water uptake of the onion plants increased exponentially, as well. The concentration of [U-¹⁴C] in the roots at first increased and then appeared to reach a steady state, while the [U-¹⁴C] concentration in the leaves was found to increase linearly with time. The [U-¹⁴C] concentration in the rhizosphere increased gradually, while in the bulk soil it decreased slowly. The accumulation of [U-¹⁴C] in the rhizosphere is likely to difference between movement into the rhizosphere (through advective mass flow of soil water by root uptake) and its uptake into the roots. The distribution of ¹⁴C in the soil/plant system was found to be 60–85% in the soil solid phase, 7–11% in the soil liquid phase, <1% in the soil air phase, <1% in the root compartment, and <0.01% in the leaf compartment. The maximum RCF (root concentration factor) value for TNT and its derivates was found to be about 20, and the maximum TSCF (transpiration stream concentration factor) was 0.18. These values can be changed by a variety of factors in soil-plant systems     

The effect of synthesis media on the properties of substituted polyaniline/chitosan composites

Substituted polyaniline/chitosan (sPANI/Ch) composites were chemically synthesized in H₂SO₄ and CH₃COOH synthesis media. Structural and physical properties of the composites were characterized by using FTIR, SEM, TGA, UV–vis, XRD techniques, and conductivity measurements. The effect of synthesis media on morphology, thermal stability, conductivity, and crystalline properties was investigated. Chemical interactions between substituted polyanilines and chitosan were explained using FTIR spectra results. The different morphological surfaces were observed in SEM images of the composites. The size of the substituted polyaniline/chitosan (sPANI/Ch) composites was in nanoscale, and the composites synthesized in acetic acid media showed smaller structures than those of H₂SO₄ media and pure chitosan. It was interpreted from XRD results that the composites have amorphous structure and the PNEANI/Ch–CH₃COOH composite has the highest crystallinity.     

The Roles of Melatonin and Vitamin E Plus Selenium in Prevention of Oxidative Stress Induced by Naloxone-Precipitated Withdrawal in Heroin-Addicted Rats

The therapeutic effects of melatonin or vitamin E plus Se (vE + Se) on the restrain of the heroin withdrawal-induced oxidative stress were studied. For this, rats were divided into ten groups. The rats were injected by fixed or variable doses of heroin for 16 consecutive days, and naloxone was given 1 h after the last heroin injection. One hour after naloxone administration, some groups were treated with melatonin or vE + Se. After 1 h this, blood samples were taken, and the levels of malondialdehyde (MDA) and reduced glutathione (GSH) in whole blood, ascorbic acid, α-tocopherol, retinol, β-carotene, nitrite, nitrate, and ceruloplasmin levels in the serum were measured. Our findings showed that, naloxone administration precipitated the heroin withdrawal. This also increased the level of MDA and decreased the levels of GSH in blood. Melatonin or vE + Se administration prevented the rise in MDA levels and increased the GSH levels. On the other hand, there were some significant differences between α-tocopherol, retinol, β-carotene, nitrite, nitrate, and ceruloplasmin levels of experimental groups. Results of present study showed that heroin withdrawal increased the lipid peroxidation and depressed endogenous antioxidative systems. Additionally, melatonin or vE + Se administrations prevented lipid peroxidation and augmented endogenous antioxidant defense systems.     

Insecticidal Metabolites from the Rhizomes of Veratrum album against Adults of Colorado Potato Beetle,Leptinotarsa decemlineata

The dried rhizomes of Veratrum album were individually extracted with CHCl₃, acetone, and NH₄OH/benzene to test the toxic effects against the Colorado potato beetle, Leptinotarsa decemlineata, which is an important agricultural pest. Fifteen compounds in various amounts were isolated from the extracts using column and thin‐layer chromatography. The chemical structures of 14 compounds were characterized as octacosan‐1‐ol ( 1 ), β‐sitosterol ( 2 ), stearic acid ( 3 ), diosgenin ( 4 ), resveratrol ( 5 ), wittifuran X ( 6 ), oxyresveratrol ( 7 ), β‐sitosterol 3‐O‐β‐D ‐glucopyranoside ( 8 ), diosgenin 3‐O‐α‐L ‐rhamnopyranosyl‐(1→2)‐β‐D ‐glucopyronoside ( 9 ), oxyresveratrol 3‐O‐β‐D ‐glucopyranoside ( 10 ), jervine ( 11 ), pseudojervine ( 13 ), 5,6‐dihydro‐1‐hydroxyjervine ( 14 ), and saccharose ( 15 ) using UV, IR, MS, ¹H‐ and ¹³C‐NMR, and 2D‐NMR spectroscopic methods. However, the chemical structure of 12 , an oligosaccharide, has not fully been elucidated. Compounds 4, 6, 9 , and 10 were isolated from V. album rhizomes for the first time in the current study. The toxic effects of three extracts (acetone, CHCl₃, and NH₄OH/benzene) and six metabolites, 2, 2 + 4, 5, 7, 8 , and 11 , were evaluated against the Colorado potato beetle. The assay revealed that all three extracts, and compounds 7, 8 , and 11 exhibited potent toxic effects against this pest. This is the first report on the evaluation of the toxic effects of the extracts and secondary metabolites of V. album rhizomes against L. decemlineata. Based on these results, it can be concluded that the extracts can be used as natural insecticides.     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

α-SNAP Interferes with the Zippering of the SNARE Protein Membrane Fusion Machinery

Neuronal exocytosis is mediated by soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. Before fusion, SNARE proteins form complexes bridging the membrane followed by assembly toward the C-terminal membrane anchors, thus initiating membrane fusion. After fusion, the SNARE complex is disassembled by the AAA-ATPase N-ethylmaleimide-sensitive factor that requires the cofactor α-SNAP to first bind to the assembled SNARE complex. Using chromaffin granules and liposomes we now show that α-SNAP on its own interferes with the zippering of membrane-anchored SNARE complexes midway through the zippering reaction, arresting SNAREs in a partially assembled trans-complex and preventing fusion. Intriguingly, the interference does not result in an inhibitory effect on synaptic vesicles, suggesting that membrane properties also influence the final outcome of α-SNAP interference with SNARE zippering. We suggest that binding of α-SNAP to the SNARE complex affects the ability of the SNARE complex to harness energy or transmit force to the membrane.     

Delineating the Specific Influence of Virus Isoelectric Point and Size on Virus Adsorption and Transport through Sandy Soils

Many of the factors controlling viral transport and survival within the subsurface are still poorly understood. In order to identify the precise influence of viral isoelectric point on viral adsorption onto aquifer sediment material, we employed five different spherical bacteriophages (MS2, PRD1, Qβ, X174, and PM2) having differing isoelectric points (pI 3.9, 4.2, 5.3, 6.6, and 7.3 respectively) in laboratory viral transport studies. We employed conventional batch flowthrough columns, as well as a novel continuously recirculating column, in these studies. In a 0.78-m batch flowthrough column, the smaller phages (MS2, X174, and Qβ), which had similar diameters, exhibited maximum effluent concentration/initial concentration values that correlated exactly with their isoelectric points. In the continuously recirculating column, viral adsorption was negatively correlated with the isoelectric points of the viruses. A model of virus migration in the soil columns was created by using a one-dimensional transport model in which kinetic sorption was used. The data suggest that the isoelectric point of a virus is the predetermining factor controlling viral adsorption within aquifers. The data also suggest that when virus particles are more than 60 nm in diameter, viral dimensions become the overriding factor.     

Acid-bile, antibiotic resistance and inhibitory properties of propionibacteria isolated from Turkish traditional home-made cheeses

In this study, a total of 29 Propionibacterium spp. were isolated from traditional home-made Turkish cheese samples. As a result of the identification, isolates were identified as Propionibacterium freudenreichii subsp. freudenreichii (15 strains), Propionibacterium jensenii (12), and Propionibacterium thoenii (2). All isolates and 5 reference strains were examined for their abilities to survive at pH 2.0, 3.0, 4.0, 5.0 and in the presence of 0.06, 0.15 and 0.30% bile salts, their influence on the growth of food-borne and spoilage bacteria, as well as their sensitivity against 11 selected antibiotics. Only seven propionibacteria strains survived in both the acidic and bile salt environments. Propionibacterium spp. strains strongly inhibited growth of the Escherichia coli ATCC 11229 and Shigella sonnei Mu:57 strains (91%). All propionibacteria strains were sensitive to a majority of the antibiotics used in the investigations. Overall, dairy propionibacteria showed high antibacterial activity, resistance to pH 4.0, 5.0, high resistance to bile salts and will provide an alternative source to Lactobacillus and Bifidobacterium as probiotic culture.     

Immunohistochemical and immunocytochemical findings associated with Marek’s disease virus in naturally infected laying hens

We compared immunohistochemical (IHC) staining of tissue sections of liver, kidney, spleen, lung, proventriculus, sciatic nerve, bursa of Fabricius, brain, heart, intestine and skin; immunocytochemical (ICC) staining of peripheral blood samples and touch preparations of liver, spleen and kidney of laying hens naturally infected with Marek’s disease (MD) virus. We used one hundred and fifty 5-17-week-old commercial hens. IHC and ICC staining were performed using polymer-based techniques. IHC staining exhibited mostly free immunopositive reactions in tumor cells and in the cytoplasm of the parenchymal cells of liver, kidney, spleen and bursa of Fabricius. In the sciatic nerve, severe reactions were observed in the cytoplasm of plasma and MD cells in the lymphoproliferative areas. Pronounced staining was found in the lymphoid cells in the medulla of intrafollicular regions in the bursa of Fabricius. Although immunostaining was observed in the liver and spleen touch preparations, there was no staining in the kidneys and peripheral blood cell samples. The presence of virus in the tissue and peripheral blood samples and in touch preparations was compared immunohistochemically and immunocytochemically. IHC and ICC techniques were helpful for diagnosis of MD. Peripheral blood samples are inappropriate for field conditions and natural infections.     

Foraminifera,Radiolaria and Conodont assemblages from the Early Mississipian (late Tournaisian)/Early Pennsylvanian (early Bashkirian) blocks within the Mersin Mélange,southern Turkey: Biochronological and paleogeographical implications

The Mersin Mélange, a sedimentary complex in southern Turkey, includes blocks of various origins within a Late Cretaceous matrix. Two blocks in the Mersin Mélange are herein recognized to be of Carboniferous age. One block (the Kozan Block) is composed of alternating chert and mudstone, and includes radiolarian and conodont assemblages revealing a late Tournaisian (Early Mississippian) age. The other (Keven-West Block) consists of platform carbonate containing abundant foraminifera indicating Bashkirian (Early Pennsylvanian) age. These dates are so far the oldest obtained from the blocks within the Mersin Mélange. A correlation of the lithostratigraphies of blocks in the Mersin Mélange with the coeval Tauride sequences indicates that they correspond to the successions in the Beysehir-Hoyran Nappes. In these nappes, the late Tournaisian is characterized by radiolarian rich chert and mudstone of an open marine environment, whereas the Bashkirian succession represents a shallow water environment with Foraminifera-bearing limestone. The Tournaisian deepening can be ascribed to the opening of a deep marginal basin to the north of the Tauride Platform and uplifting of the northern Tauride-Anatolide Platform margin during the Late Mississippian and Early Pennsylvanian.A shallowing upward sequence started in the Tournaisian with a pelagic sequence followed by platform carbonates of Bashkirian age in the Beysehir-Hoyran Nappes, and could be related to a major glaciation event during late Visean–Serpukhovian resulting in a sea-level drop and deposition of platform carbonates in the Bashkirian. Given the stratigraphic properties of northerly originated nappe packages (Cataloturan, Hadim and Bolkardag) and parautochthonous/autochthonous sequences in Taurides, sedimentation on the Tauride-Anatolide Platform mainly terminated after the Moscovian, except in the Hadim Nappe with sedimentation in a very shallow sea conditions until the end of the Permian. A depositional break corresponding to the Kasimovian–Wordian time interval in these sequences in the Tauride-Anatolide Platform could be related to the effects of both late Paleozoic Gondwanan glaciation and a possible mantle plume occurrence evidenced by the geochemistry of lavas in the Mersin Mélange causing major uplift in the Northern NeoTehys Ocean. However; at the center of the plume, pelagic sequences (e.g., ribbon chert and pelagic limestone) were deposited associated with these lavas due to a progressive developing rift system during the Permian, based on previous studies.