A sawdust-derived soil conditioner promotes plant growth and improves water-holding capacity of different types of soils

Sawdust, a bulky waste generated by wood processing industries, has very few profitable and ecofriendly uses and poses a problem of proper disposal. Treatment with the fungusVolvariella volvaceae and a dilute solution of urea converted sawdust from a phytoinhibitory material to a phytostimulatory soil conditioner. In different types of soils, the soil conditioner increased the moisture retention and facilitated the cohesive interaction of particles. Analyses of the major biopolymers of sawdust after fungal treatment indicated that levels of cellulose, hemicellulose and lignin decreased; however, these changes did not account for the plant growth stimulatory property attained by this material.     

Cationic amphiphiles induce fusion of acidic liposomes

Decylamine, dodecylamine and tetradecylamine induced aggregation and fusion of acidic liposomes at concentrations of about 1 mM, 75 μM and 75 μM, respectively. Aggregation was assayed as increase in turbidity. Fusion was assayed as intermixing of membranes and contents, and was observed in the electron-microscope to form large liposomes. Only at higher concentrations did these amphiphiles induce massive leakage of the liposomes' contents. Similar effects were caused by hexadecylpyridinium bromide (CP) and hexadecyltrimethylammonium bromide (CTAB). The trivalent cation 4-dodecyldiethylenetriamine and the more hydrophobic amphiphile, trioctylmethylammonium chloride, induced fusion at concentrations of about 10–20 μM. Octylamine and heptylamine induced size increase at mM concentrations. They induced membrane intermixing but little or no content intermixing. Thus, these amphiphiles seem to promote size increase either by transfer of lipid or mainly by ‘cracking and annealing’.     

The enzymatic activity of lysyl oxidas-like-2 (LOXL2) is not required for LOXL2-induced inhibition of keratinocyte differentiation

Lysyl oxidase-like-2 (LOXL2) induces tumor progression and fibrosis. It also inhibits the differentiation of keratinocytes promoting development of squamous cell carcinomas. Stimulation of HaCaT skin keratinocytes with exogenous LOXL2 or overexpression of LOXL2 in these cells inhibits their differentiation as manifested by inhibition of calcium or vitamin D-induced involucrin expression. The inhibition was abrogated by the LOXL2 function-blocking monoclonal antibody AB0023 as well as by an anti-LOXL2 polyclonal antibody. Surprisingly, a point-mutated form of LOXL2 (LOXL2(Y689F)) lacking enzymatic activity, as well as a LOXL2 deletion mutant lacking the entire catalytic domain, also inhibited calcium or vitamin D-induced up-regulation of involucrin expression, suggesting that the enzymatic activity of LOXL2 is not required for this activity. This conclusion was supported by experiments that showed that β-aminoproprionitrile, an irreversible competitive inhibitor of the enzymatic activity of all lysyl oxidases, is unable to abolish the LOXL2-induced inhibition of HaCaT cell differentiation. The activity of LOXL2(Y689F) required the presence of the fourth scavenger receptor-cysteine-rich (SRCR) domain of LOXL2, which is also the binding target of AB0023. Epitope-tagged LOXL2(Y689F) was internalized at 37 °C by HaCaT cells. The internalization was inhibited by AB0023 and by competition with unlabeled LOXL2, suggesting that these cells may express a LOXL2 receptor. Our results suggest that agents that inhibit the enzymatic activity of LOXL2 may not suffice to inhibit completely the effects of LOXL2 on complex processes that involve altered states of cellular differentiation.     

N-terminal extended conjugates of the agonists and antagonists of both bradykinin receptor subtypes: structure-activity relationship, cell imaging using ligands conjugated with fluorophores and prospect for functionally active cargoes

Peptide agonists and antagonists of both bradykinin (BK) B(1) and B(2) receptors (B(1)R, B(2)R) are known to tolerate to a certain level N-terminal sequence extensions. Using this strategy, we produced and characterized the full set of fluorescent ligands by extending both agonists and antagonist peptides at both receptor subtypes with 5(6)-carboxyfluorescein (CF) and the ε-aminocaproyl (ε-ACA) optional spacer. Alternatively, kinin receptor ligands were extended with another carboxylic acid cargo (chlorambucil, biotinyl, pentafluorocinnamoyl, AlexaFluor-350 (AF350), ferrocenoyl, cetirizine) or with fluorescein isothiocyanate. N-terminal extension always reduced receptor affinity, more importantly for bulkier substituents and more so for the agonist version compared to the antagonist. This loss was generally alleviated by the presence of the spacer and modulated by the species of origin for the receptor. We report and review the pharmacological properties of these N-terminally extended peptides and the use of fluorophore-conjugated ligands in imaging of cell receptors and of angiotensin converting enzyme (ACE) in intact cells. Antagonists (B(1)R: B-10376: CF-ε-ACA-Lys-Lys-[Hyp(3), CpG(5), D-Tic(7), CpG(8)]des-Arg(9)-BK; B(2)R: B-10380: CF-ε-ACA-D-Arg-[Hyp(3), Igl(5), D-Igl(7), Oic(8)]-BK and fluorescein-5-thiocarbamoyl (FTC)-B-9430) label the plasma membrane of cells expressing the cognate receptors. The B(2)R agonists CF-ε-ACA-BK, AF350-ε-ACA-BK and FTC-B-9972 are found in endosomes and model the endosomal degradation of BK in a complementary manner. The uneven surface fluorescence associated to the B(1)R agonist B-10378 (CF-ε-ACA-Lys-des-Arg(9)-BK) is compatible with a particular form of agonist-induced receptor translocation. CF-ε-ACA-BK binds to the carboxydipeptidase ACE with an affinity identical to that of BK. Metal- or drug-containing cargoes further show the prospect of ligands that confer special signaling to kinin receptors.     

Zebrafish caspase-3: molecular cloning, characterization, crystallization and phylogenetic analysis

Apoptosis plays an important role in maintaining the normal function of various tissues and organs in different species. Caspase-3 is a terminal caspases which plays an important role in the execution of apoptosis in all vertebrates. It was cloned from zebra fish embryos and its properties were identified through Western blotting and biological activity. In the cells over-expressing caspase-3, Western blotting with an anti-His-tag antibody confirmed the presence of caspase-3 in the three bands that were proposed to correspond to the precursor form (33 kDa), the mature forms processed at the prodomain alone (29 kDa, large subunit) and small sub unit (13 kD). Fish kidney cells were transiently co-transfected with the beta-galactosidase reporter gene and either vector alone (mock), pZCASP3His (caspase-3) or pZCASP3His mutant (caspase-3 mutant). After 72 h following transfection of fish kidney cells, 35% of cells transfected with the zebra fish caspase-3 construct, pZCASP3His, showed apoptotic morphology when compared with cells transfected with the mock vector or an expression construct (pZCASP3His mutant) encoding the caspase-3 mutant lacking Cys. The fusion proteins were expressed in Escherichia coli, isolated from cell lysates by nickel-affinity column chromatography, and cleaved with thrombin. A thrombin cleavage recognition site was positioned at the fusion junction to release the caspase-3 from the fusion protein. Phylogenetic analysis showed that the cloned zebra fish caspase was a member of the caspase-3 subfamily with approximately 60% identity with caspase-3 from Xenopus, chicken and mammals. We have obtained structural information by X-ray crystallography. Orthorhombic crystals of the caspase-3 that diffracted to 1.8 A were obtained in a mixture of 0.1 M imidazole (pH 6.0) and 0.4 M NaOAc (pH 7.0 -7.5), containing 30% glycerol. The space group is C222 with cell dimensions of a = 36.07 A, b = 38.80 A, c = 135.20 A.     

Quantifying the impact of above‐ and belowground higher trophic levels on plant and herbivore performance by modeling1

Growing empirical evidence suggests that aboveground and belowground multitrophic communities interact. However, investigations that comprehensively explore the impacts of above‐ and belowground third and higher trophic level organisms on plant and herbivore performance are thus far lacking. We tested the hypotheses that above‐ and belowground higher trophic level organisms as well as decomposers affect plant and herbivore performance and that these effects cross the soil–surface boundary. We used a well‐validated simulation model that is individual‐based for aboveground trophic levels such as shoot herbivores, parasitoids, and hyperparasitoids while considering belowground herbivores and their antagonists at the population level. We simulated greenhouse experiments by removing trophic levels and decomposers from the simulations in a factorial design. Decomposers and above‐ and belowground third trophic levels affected plant and herbivore mortality, root biomass, and to a lesser extent shoot biomass. We also tested the effect of gradual modifications of the interactions between different trophic level organisms with a sensitivity analysis. Shoot and root biomass were highly sensitive to the impact of the fourth trophic level. We found effects that cross the soil surface, such as aboveground herbivores and parasitoids affecting root biomass and belowground herbivores influencing aboveground herbivore mortality. We conclude that higher trophic level organisms and decomposers can strongly influence plant and herbivore performance. We propose that our modelling framework can be used in future applications to quantitatively explore the possible outcomes of complex above‐ and belowground multitrophic interactions under a range of environmental conditions and species compositions.     

Characterization of the B2 receptor and activity of bradykinin analogs in SHP-77 cell line by Cytosensor microphysiometer

The Cytosensor microphysiometer device (Molecular Devices, Sunnyvale, CA) is capable of measuring the rate at which cells acidify their environment in response to ligand–receptor binding. By measuring the extracellular acidification response (ECAR) we characterized some aspects of ligand–B₂ receptor interaction in SHP-77 cell line. SHP-77 cells maximally acidified their environment within 30 s after the exposure to bradykinin (BK) or the BK agonist, B9972, with the maximum effect seen at a ligands concentration of 1 μM. Fetal bovine serum (FBS) modulated the binding of BK or B9972, showing that B9972 is a partial agonist. In addition, the binding of BK agonist or antagonist to the B₂ receptor showed different ECAR and different interaction with other intracellular and plasma membrane proteins. Our microphysiometrical results showed that two parameters, antagonist binding affinity (pD₂) and antagonist potency (pIC₅₀) are required to characterize BK antagonist activity for the B₂ receptor in the SHP-77 cell line. The previously used parameter of B₂ antagonist activity, pA₂, had high variation and poor correlation with the inhibition of SHP-77 cell growth in vitro and suppression of tumor growth when SHP-77 cells were injected to mice. Our results permit us to conclude that BK agonists and antagonists differ in their interactions with the B₂ receptor and consequently elicit different cell responses. Based on our results, we have developed a new microphysiometrical assay for analyzing the activity of BK agonists and antagonist in SHP-77 cells, which may facilitate the discovery of new potent anticancer drugs.     

Interferon-γ-induced increased sensitivity ofHER2/neu-overexpressing tumor cells to lymphokine-activated killer cell lysis: importance of ICAM-1 in binding and post-binding events

Treatment ofHER2/neu-overexpressing target cells with interferon (IFN) (200–2000 U/ml for 3 days) markedly enhances their sensitivity to lymphokine-activated killer (LAK) cell lysis. Increased sensitivity is associated with an up-regulation of intercellular adhesion molecule ICAM-1 determinants and a down-regulation ofHER2/neu expression. In the present study, we show that exposure to another cytokine, tumor necrosis factor (200 U/ml for 3 days), also decreasedHER2/neu expression but had no effect on LAK cell lysis and ICAM-1 expression. This suggests that down-regulation of oncogene expression is not sufficient by itself to induce an enhanced sensitivity to LAK cell lysis. IFN-induced enhanced lysis was associated with an increased binding between effectors and targets, and antibodies to ICAM-1 as well as its counter-receptor LFA-1, blocked the increased binding and lysis. Treatment with IFN still significantly enhanced lysis even when concanavalin A was added to the assay to induce maximal binding, indicating that a post-binding effect also participated in enhanced cytotoxicity. These post-binding alterations, were also sensitive to blocking with anti-ICAM-1 and anti-LFA-1 antibodies. Treatment with IFN also sensitized targets to lysis by T cells in the presence of lectin but had no effect on the relative resistance of HER2⁺ cells to lysis mediated by perforin or TNF. Together these data demonstrate the importance of ICAM-1 determinants in binding and post-binding events in the IFN-induced increased lysis ofHER2/neu ⁺ targets.Supported by research funds of the Veteran's Administration, the California Institute for Cancer Research and Jonsson Cancer Center core grant CA 16042 funded by NIH     

Tracking the genetic imprints of lost Jewish tribes among the gene pool of Kuki-Chin-Mizo population of India

Background  

The Kuki-Chin-Mizo population comprising traditionally endogamous tribal groups residing in the state of Mizoram, India claim their descent from the ten lost tribes of Israel that were exiled by the Assyrians. To ascertain their oral history, we analysed DNA markers comprising 15 autosomal microsatellite markers, 5 biallelic and 20 microsatellite markers on Y-chromosome and the maternally inherited mitochondrial DNA sequence variations on 414 individuals belonging to 5 tribal communities from Mizoram (Hmar, Kuki, Mara, Lai and Lusei). The genetic profiles obtained were compared either with populations sharing Jewish ancestry or with local populations along the probable route of migration of the Jewish ancestry claimant Mizoram tribes.     

Articles selected by Faculty of 1000: plant comparative mitochondrial genomics; open source proteomics database; identifying disease-associated enzymes; predicting microRNA targets; genome annotation using polymorphisms

Background

Phylogenetic analysis of human complete mitochondrial DNA sequences has largely contributed to resolving phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this haplogroup to precisely characterize the lineages and unravel their intricate phylogeny.

Results

The phylogenetic tree constructed from sequencing information of twenty four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the formulation of a new lineage M30, distinguished by the presence of 12007 transition, and comprises of the recently defined M18 and a potential new sub-lineage possessing substitution at 16223 and 16300. M30 further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage M* with HVSI sequence 16223,16325. No new substitutions were found in M25 and the M3 mt DNA genome could only be tentatively rooted by 16126 mutation. M4 and M*(16251, 16267) lineages could not be resolved distinctly.

Conclusions

This study describes seven new basal mutations and fourteen lineages that substantially contribute to the present understanding of superhaplogroup M. The phylogenetic tree supported by median-joining network helps in distinctly identifying the genetic relation between different M lineages that could not be achieved solely by control region sequence information. Although high control region diversity has been reported in the different M lineages distributed in India, complete sequencing of M* and defined lineages suggests that these mt DNA genomes emerged from a limited number of branches arising from the M trunk.