Transport of ammonium and nitrate in saturated porous media incorporating physiobiotransformations and bioclogging

The vertical transport of nitrates from fertilizer application and wastewater irrigation through the subsurface and saturated zone is of major concern to assess the vulnerability of groundwater contamination. The present study addresses the transport of nitrogenous fertilizers such as ammonium and nitrate in the presence of organic carbon (acetate) in a one-dimensional soil column under saturated conditions, considering the effect of adsorption and biotransformation. The soil had a neutral pH range and was classified as loamy sand, with a 0.89% organic carbon content. Batch studies revealed that sorption occurred in the order of ammonium > acetate > nitrate following a Freundlich isotherm model. Mixed heterotrophic native soil bacteria for aerobic nitrification and anoxic denitrification were developed, and the growth kinetic parameters were simulated using a Haldane inhibition model for nitrification and a Monod inhibition model for denitrification. Results from biotransformation studies suggested that denitrification was the predominant process, with significant bacterial growth and clogging of pores occurring monotonously reaching a stationary phase by 12 days. Pore-clogging phenomenon not only reduces the permeability of the soil by 5 orders of magnitude but also increases the contact time of the contaminant with the soil microbe and thereby delays the transport process and decreases the effluent ammonium and nitrate concentrations. A tailing breakthrough in a leaching study illustrates that water flux variation (0.153 and 0.509 cm/min) did not influence the transport of solutes, rather irreversible chemical bonding retains more ammonium than nitrate in the soil matrix.     

Moderate heat stress induces state transitions in Arabidopsis thaliana

The effect of temperature on the photosynthetic machinery is crucial for the fundamental understanding of plant physiology and the bioengineering of heat-tolerant varieties. In our study, Arabidopsis thaliana was exposed to mild (40°C), short-term heat stress in the dark to evaluate the heat-triggered phosphorylation and migration of light harvesting complex (LHC) II in both wild-type (wt) and mutant lacking STN7 kinase. The 77K emission spectra revealed an increase in PSI relative to PSII emission similar to increases observed in light-induced state I to state II transitions in wt but not in stn7 mutant. Immunoblotting results indicated that the major LHCII was phosphorylated at threonine sites under heat stress in wt plants but not in the mutant. These results support the proposition that mild heat stress triggers state transitions in the dark similar to light-induced state transitions, which involve phosphorylation of LHCII by STN7 kinase. Pre-treatment of Arabidopsis leaves with inhibitor DBMIB, altered the extent of LHCII phosphorylation and PSI fluorescence emission suggests that activation of STN7 kinase may be dependent on Cyt b(6)/f under elevated temperatures in dark. Furthermore, fast Chl a transient of temperature-exposed leaves of wt showed a decrease in the F(v)/F(m) ratio due to both an increase in F(o) and a decrease in F(m). In summary, our findings indicate that a mild heat treatment (40°C) induces state transitions in the dark resulting in the migration of phosphorylated LHCII from the grana to the stroma region.     

Spacing of integrin ligands influences signal transduction in endothelial cells

The physical attributes of the extracellular matrix play a key role in endothelium function by modulating the morphology and phenotype of endothelial cells. Despite the recognized importance of matrix-cell interactions, it is currently not known how the arrangement of adhesive ligands affects the morphology, signal transduction processes, and migration of endothelial cells. We aimed to study how endothelial cells respond to the average spatial arrangement of integrin ligands. We designed functionalized silicon surfaces with average spacing ranging from nanometers to micrometers of the peptide arginine-glycine-aspartic acid (RGD). We found that endothelial cells adhered to and spread on surfaces independently of RGD-to-RGD spacing. In contrast, organization within focal adhesions (FAs) was extremely sensitive to ligand spacing, requiring a nanoscaled average RGD spacing of 44 nm to form lipid raft domains at FAs. The localized membrane organization strongly correlated with the signaling efficiencies of integrin activation and regulated vascular endothelial growth factor (VEGF)-induced signaling events. Importantly, this modulation in signal transduction directly affected the migratory ability of endothelial cells. We conclude that endothelial cells sense nanoscaled variations in the spacing of integrin ligands, which in turn influences signal transduction processes. Average RGD spacing similar to that found in fibronectin leads to lipid raft accumulation at FAs, enhances sensitivity to VEGF stimulation, and controls migration in endothelial cells.     

The Acid-Dependent and Independent Effects of Lactobacillus acidophilus CL1285, Lacticaseibacillus casei LBC80R,and Lacticaseibacillus rhamnosus CLR2 on Clostridioides difficile R20291

Clostridioides difficile infections (CDI) result from antibiotic use and cause severe diarrhea which is life threatening and costly. A specific probiotic containing Lactobacillus acidophilus CL1285, Lacticaseibacillus casei LBC80R, and Lacticaseibacillus rhamnosus CLR2 has demonstrated a strong inhibitory effect on the growth of several nosocomial C. difficile strains by production of antimicrobial metabolites during fermentation. Though there are several lactobacilli shown to inhibit C. difficile growth by processes relying on acidification, this probiotic has demonstrated potency for CDI prevention among hospitalized patients. Here, we describe the acid-dependent and independent mechanisms by which these strains impair the cytotoxicity of a hypervirulent strain, C. difficile R20291 (CD). These bacteria were co-cultured in a series of experiments under anaerobic conditions in glucose-rich and no-sugar medium to inhibit or stimulate CD toxin production, respectively. In glucose-rich medium, there was low CD toxin production, but sufficient amounts to cause cytotoxic damage to human fibroblast cells. In co-culture, there was acidification by the lactobacilli resulting in growth inhibition as well as ≥ 99% reduced toxin A and B production and no observable cytotoxicity. In the absence of glucose, CD produced much more toxin. In co-culture, the lactobacilli did not acidify the medium and CD growth was unaffected; yet, the amount of detected toxin A and B was decreased by 20% and 41%, respectively. Despite the high concentration of toxin, cells exposed to the supernatant from the co-culture were able to survive. These results suggest that in addition to known acid-dependent effects, the combination of L. acidophilus CL1285, L. casei LBC80R, and L. rhamnosus CLR2 can interfere with CD pathogenesis without acidification: (1) reduced toxin A and B production and (2) toxin neutralization. This might explain the strain specificity of this probiotic in potently preventing C. difficile-associated diarrhea in antibiotic-treated patients compared with other probiotic formulae.

     

Structure-activity analysis of niclosamide reveals potential role for cytoplasmic pH in control of mammalian target of rapamycin complex 1 (mTORC1) signaling

Mammalian target of rapamycin complex 1 (mTORC1) signaling is frequently dysregulated in cancer. Inhibition of mTORC1 is thus regarded as a promising strategy in the treatment of tumors with elevated mTORC1 activity. We have recently identified niclosamide (a Food and Drug Administration-approved antihelminthic drug) as an inhibitor of mTORC1 signaling. In the present study, we explored possible mechanisms by which niclosamide may inhibit mTORC1 signaling. We tested whether niclosamide interferes with signaling cascades upstream of mTORC1, the catalytic activity of mTOR, or mTORC1 assembly. We found that niclosamide does not impair PI3K/Akt signaling, nor does it inhibit mTORC1 kinase activity. We also found that niclosamide does not interfere with mTORC1 assembly. Previous studies in helminths suggest that niclosamide disrupts pH homeostasis of the parasite. This prompted us to investigate whether niclosamide affects the pH balance of cancer cells. Experiments in both breast cancer cells and cell-free systems demonstrated that niclosamide possesses protonophoric activity in cells and in vitro. In cells, niclosamide dissipated protons (down their concentration gradient) from lysosomes to the cytosol, effectively lowering cytoplasmic pH. Notably, analysis of five niclosamide analogs revealed that the structural features of niclosamide required for protonophoric activity are also essential for mTORC1 inhibition. Furthermore, lowering cytoplasmic pH by means other than niclosamide treatment (e.g. incubation with propionic acid or bicarbonate withdrawal) recapitulated the inhibitory effects of niclosamide on mTORC1 signaling, lending support to a possible role for cytoplasmic pH in the control of mTORC1. Our data illustrate a potential mechanism for chemical inhibition of mTORC1 signaling involving modulation of cytoplasmic pH.     

Isopentenyl transferase gene expression offers the positive selection of marker-free transgenic plant of <Emphasis Type="Italic">Kalanchoe blossfeldiana</Emphasis>

The technologies allowing the production of transgenic plants without selectable marker genes, is of great interest in public and environmental safety. For generating such marker-free transgenic plants, possibility has been offered by Multi-Auto-Transformation [MAT] vector system, which combines positive selection, using the isopentenyl transferase (ipt) gene, with a site-specific recombination that generates marker-free plants. In this study Agrobacterium tumefaciens strain EHA105 harboring an ipt-type MAT vector, pMAT21, containing lacZ, gus genes and the removable cassette in the T-DNA region was used to produce marker-free transgenic Kalanchoe blossfeldiana Poelln., employing ipt gene as the selectable marker gene. Co-cultivated explants were cultured on hormone- and selective agent-free MS medium, and 85% of the regenerated shoots showed ipt-shooty phenotype with GUS expression. Forty-one morphologically normal shoots were produced during the subculture. More than ninety percent of the normal shoots were ipt ⁻, gus ⁻ but lacZ ⁺ as determined by PCR analyses. These results indicate that the ipt phenotype was clearly distinguishable from non-transgenic as well as transgenic marker-free shoots. This study opens interesting perspective for the generation of marker-free transgenic K. blossfeldiana with objective useful transgene.     

TGF-alpha as a candidate tumor antigen for renal cell carcinomas

Objectives  Patients with renal cell carcinomas (RCC) have few treatment options, underscoring the importance of developing new approaches such as immunotherapy. However, few tumor associated antigens (TAA), which can be targeted by immunotherapy, have been identified for this type of cancer. von Hippel-Lindau clear cell RCC (VHL^−/−RCC) are characterized by mutations in the VHL tumor suppressor gene. Loss of VHL function causes the overexpression of transforming growth factor (TGF)-α, leading us to hypothesize that TGF-α could be a potential TAA for immunotherapy of kidney cancer, which was evaluated in this study. Methods and results  We first confirmed the absent or weak expression of TGF-α in important normal tissues as well as its overexpression in 61% of renal tumors in comparison to autologous normal kidney tissues. In addition, we demonstrated the immunogenicity of TGF-α, by expanding many T cell lines specific for certain TGF-α peptides or the mature TGF-α protein, when presented by major histocompatibility complex (MHC) molecules on the surface of antigen-presenting cells. Interestingly, some of these TGF-α-specific T cells were polyfunctionals and secreted IFN-γ, TNF-α and IL-2. Conclusion  We have shown that TGF-α is a valid candidate TAA, which should allow the development of a targeted immunotherapy.     

The importance of including imperfect detection models in eDNA experimental design

Environmental DNA (eDNA) is DNA that has been isolated from field samples, and it is increasingly used to infer the presence or absence of particular species in an ecosystem. However, the combination of sampling procedures and subsequent molecular amplification of eDNA can lead to spurious results. As such, it is imperative that eDNA studies include a statistical framework for interpreting eDNA presence/absence data. We reviewed published literature for studies that utilized eDNA where the species density was known and compared the probability of detecting the focal species to the sampling and analysis protocols. Although biomass of the target species and the volume per sample did not impact detectability, the number of field replicates and number of samples from each replicate were positively related to detection. Additionally, increased number of PCR replicates and increased primer specificity significantly increased detectability. Accordingly, we advocate for increased use of occupancy modelling as a method to incorporate effects of sampling effort and PCR sensitivity in eDNA study design. Based on simulation results and the hierarchical nature of occupancy models, we suggest that field replicates, as opposed to molecular replicates, result in better detection probabilities of target species.