Connecting Proline and γ-Aminobutyric Acid in Stressed Plants through Non-Enzymatic Reactions

The accumulation of proline (Pro) in plants exposed to biotic/abiotic stress is a well-documented and conserved response in most vegetal species. Stress conditions induce the overproduction of reactive oxygen species which can lead to cellular damage. In vitro assays have shown that enzyme inactivation by hydroxyl radicals (^·OH) can be avoided in presence of Pro, suggesting that this amino acid could act as an ^·OH scavenger. We applied Density Functional Theory coupled with a polarizable continuum model to elucidate how Pro reacts with ^·OH. In this work we suggest that Pro reacts favourably with ^·OH by H–abstraction on the amine group. This reaction produces the spontaneous decarboxylation of Pro leading to the formation of pyrrolidin-1-yl. In turn, pyrrolidin-1-yl can easily be converted to Δ¹-pyrroline, the substrate of the enzyme Δ¹-pyrroline dehydrogenase, which produces γ-aminobutyric acid (GABA). GABA and Pro are frequently accumulated in stressed plants and several protective roles have been assigned to these molecules. Thereby we present an alternative non-enzymatic way to synthetize GABA under oxidative stress. Finally this work sheds light on a new beneficial role of Pro accumulation in the maintenance of photosynthetic activity.     

Use of FabV-Triclosan Plasmid Selection System for Efficient Expression and Production of Recombinant Proteins in Escherichia coli

Maintenance of recombinant plasmid vectors in host bacteria relies on the presence of selection antibiotics in the growth media to suppress plasmid -free segregants. However, presence of antibiotic resistance genes and antibiotics themselves is not acceptable in several applications of biotechnology. Previously, we have shown that FabV-Triclosan selection system can be used to select high and medium copy number plasmid vectors in E. coli. Here, we have extended our previous work and demonstrated that expression vectors containing FabV can be used efficiently to express heterologous recombinant proteins in similar or better amounts in E. coli host when compared with expression vectors containing β-lactamase. Use of small amount of non-antibiotic Triclosan as selection agent in growth medium, enhanced plasmid stability, applicability in various culture media, and compatibility with other selection systems for multiple plasmid maintenance are noteworthy features of FabV-Triclosan selection system.     

Egyptian tortoise conservation: A community‐based,field research program developed from a study on a captive population

Local community participation and ex situ conservation has the potential to assist the recovery of the endangered Egyptian tortoise, Testudo kleinmanni. We initiated an in situ community‐based conservation and research program from a captive population of T. kleinmanni. We used a captive population of the Egyptian tortoise to train a member of the local community as a research technician and used his indigenous tracking skills and knowledge of the area to collect activity and dietary data on 28 captive tortoises. We overcame problems with illiteracy by creating a data sheet based on symbols and numbers. This data sheet allowed us to use the indigenous knowledge of various people from the community, and employ them in the future. Our local community approach to data collection, in conjunction with a craft program, made the conservation of the Egyptian tortoise more rewarding to the local community by providing a more sustainable form of income than collecting animals for the pet trade. Our multidimensional approach (local community participation as research technicians, craft program, and trust building) for gaining local support eventually led to the rediscovery of wild Egyptian tortoises in North Sinai, which was significant, as this species was presumed extinct in Egypt. We have now shifted our focus to in situ conservation, using the research and local capacity building template developed from this captive population study. Our template can be used by zoos and conservation organizations with small budgets and collections of native species in natural habitats to create similar captive research programs that can be applied to in situ conservation. Zoo Biol 26:397–406, 2007. © 2007 Wiley‐Liss, Inc.     

Growth Factor and Th2 Cytokine Signaling Pathways Converge at STAT6 to Promote Arginase Expression in Progressive Experimental Visceral Leishmaniasis

Host arginase 1 (arg1) expression is a significant contributor to the pathogenesis of progressive visceral leishmaniasis (VL), a neglected tropical disease caused by the intracellular protozoan Leishmania donovani. Previously we found that parasite-induced arg1 expression in macrophages was dependent on STAT6 activation. Arg1 expression was amplified by, but did not require, IL-4, and required de novo synthesis of unknown protein(s). To further explore the mechanisms involved in arg1 regulation in VL, we screened a panel of kinase inhibitors and found that inhibitors of growth factor signaling reduced arg1 expression in splenic macrophages from hamsters with VL. Analysis of growth factors and their signaling pathways revealed that the Fibroblast Growth Factor Receptor 1 (FGFR-1) and Insulin-like Growth Factor 1 Receptor (IGF-1R) and a number of downstream signaling proteins were activated in splenic macrophages isolated from hamsters infected with L. donovani. Recombinant FGF-2 and IGF-1 increased the expression of arg1 in L. donovani infected hamster macrophages, and this induction was augmented by IL-4. Inhibition of FGFR-1 and IGF-1R decreased arg1 expression and restricted L. donovani replication in both in vitro and ex vivo models of infection. Inhibition of the downstream signaling molecules JAK and AKT also reduced the expression of arg1 in infected macrophages. STAT6 was activated in infected macrophages exposed to either FGF-2 or IGF-1, and STAT6 was critical to the FGFR-1- and IGF-1R-mediated expression of arg1. The converse was also true as inhibition of FGFR-1 and IGF-1R reduced the activation of STAT6 in infected macrophages. Collectively, these data indicate that the FGFR/IGF-1R and IL-4 signaling pathways converge at STAT6 to promote pathologic arg1 expression and intracellular parasite survival in VL. Targeted interruption of these pathological processes offers an approach to restrain this relentlessly progressive disease.     

Immune response of mice exposed to cis-diamminedichloroplatinum

Summary The effects of cis-diamminedichloroplatinum (CDDP) on lymphoid organs and the immune response of young and older adult mice were studied histologically and by functionally assessing the activity of various subpopulations of immune cells. Young adult mice (6–8 weeks old) treated with 2 mg/kg CDDP mounted an enhanced splenic plaque-forming cell (PFC) response to both sheep erythrocytes, a helper T-cell-dependent antigen (HD), and pneumococcal polysaccharide type III a helper T-cell-independent antigen (HI). Older adult mice (18–22 weeks old) treated in the same way exhibited an equally enhanced PFC response to HD antigen and even a more pronounced response to HI antigen. Treatment of mice with 12 mg/kg CDDP resulted in immunosuppression. Thymus, lymph nodes, and spleen of animals treated with the higher dose of CDDP showed a marked cell depletion from both T and B areas, confirming that the immunosuppression was due to an indiscriminate elimination of both T and B lymphocytes. The immunosuppression and the cell depletion from lymphoid organs were more pronounced in younger mice. Thus, the effects of CDDP on the lymphoid organs and the immune response depend both on the age of the animals and on the dose of the drug. CDDP given in small doses enhances the PFC response, whereas a reduced PFC response is obtained following high-dose treatment. Abbreviations used: CDDP, cis-diamminedichloroplatinum; PFC, plaque-forming cell; HD, helper T-cell dependent; HI, helper T cell-independent; SIII, pneumococcal polysaccharide type III; SRBC, sheep red blood cells; TNP, trinitrophenyl; KLH, keyhole limpet hemocyanin; TNBS, 2, 4, 6-trinitrobenzene sulfonic acid; BBS, borate-buffered saline     

An S188V Mutation Alters Substrate Specificity of Non-Stereospecific α-Haloalkanoic Acid Dehalogenase E (DehE)

The non-stereospecific α-haloalkanoic acid dehalogenase E (DehE) degrades many halogenated compounds but is ineffective against β-halogenated compounds such as 3-chloropropionic acid (3CP). Using molecular dynamics (MD) simulations and site-directed mutagenesis we show here that introducing the mutation S188V into DehE improves substrate specificity towards 3CP. MD simulations showed that residues W34, F37, and S188 of DehE were crucial for substrate binding. DehE showed strong binding ability for D-2-chloropropionic acid (D-2CP) and L-2-chloropropionic acid (L-2CP) but less affinity for 3CP. This reduced affinity was attributed to weak hydrogen bonding between 3CP and residue S188, as the carboxylate of 3CP forms rapidly interconverting hydrogen bonds with the backbone amide and side chain hydroxyl group of S188. By replacing S188 with a valine residue, we reduced the inter-molecular distance and stabilised bonding of the carboxylate of 3CP to hydrogens of the substrate-binding residues. Therefore, the S188V can act on 3CP, although its affinity is less strong than for D-2CP and L-2CP as assessed by K_m. This successful alteration of DehE substrate specificity may promote the application of protein engineering strategies to other dehalogenases, thereby generating valuable tools for future bioremediation technologies.     

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

The analysis of single-cell genomics data presents several statistical challenges, and extensive efforts have been made to produce methods for the analysis of this data that impute missing values, address sampling issues and quantify and correct for noise. In spite of such efforts, no consensus on best practices has been established and all current approaches vary substantially based on the available data and empirical tests. The k-Nearest Neighbor Graph (kNN-G) is often used to infer the identities of, and relationships between, cells and is the basis of many widely used dimensionality-reduction and projection methods. The kNN-G has also been the basis for imputation methods using, e.g., neighbor averaging and graph diffusion. However, due to the lack of an agreed-upon optimal objective function for choosing hyperparameters, these methods tend to oversmooth data, thereby resulting in a loss of information with regard to cell identity and the specific gene-to-gene patterns underlying regulatory mechanisms. In this paper, we investigate the tuning of kNN- and diffusion-based denoising methods with a novel non-stochastic method for optimally preserving biologically relevant informative variance in single-cell data. The framework, Denoising Expression data with a Weighted Affinity Kernel and Self-Supervision (DEWÄKSS), uses a self-supervised technique to tune its parameters. We demonstrate that denoising with optimal parameters selected by our objective function (i) is robust to preprocessing methods using data from established benchmarks, (ii) disentangles cellular identity and maintains robust clusters over dimension-reduction methods, (iii) maintains variance along several expression dimensions, unlike previous heuristic-based methods that tend to oversmooth data variance, and (iv) rarely involves diffusion but rather uses a fixed weighted kNN graph for denoising. Together, these findings provide a new understanding of kNN- and diffusion-based denoising methods. Code and example data for DEWÄKSS is available at https://gitlab.com/Xparx/dewakss/-/tree/Tjarnberg2020branch.     

Femtosecond Laser Axotomy in Caenorhabditis elegans and Collateral Damage Assessment Using a Combination of Linear and Nonlinear Imaging Techniques

In this work highly localized femtosecond laser ablation is used to dissect single axons within a living Caenorhabditis elegans (C. elegans). We present a multimodal imaging methodology for the assessment of the collateral damage induced by the laser. This relies on the observation of the tissues surrounding the targeted region using a combination of different high resolution microscopy modalities. We present the use of Second Harmonic Generation (SHG) and Polarization Sensitive SHG (PSHG) to determine damage in the neighbor muscle cells. All the above is done using a single instrument: multimodal microscopy setup that allows simultaneous imaging in the linear and non-linear regimes and femtosecond-laser ablation.     

Reproductive characteristics that favor invasiveness in Leonotis nepetifolia (L.) R. Br.

Reproductive systems are life attributes important in defining the demography and genetic constitution of invasive alien species populations. We describe the phenology, floral behavior and floral visitors in Mexican populations of Leonotis nepetifolia considered invasive in America, Asia and Oceania. The mating system was determined through pollination experiments and, with a morphological analysis of flowers (outcrossing index, OCI) and pollen/ovule ratio, the breeding system was evaluated. Germination of 1 and 2-year-old seeds was tested to assess the potential characteristics of germination. Leonotis nepetifolia was reproductive for 7 months (June to December) and tended towards a specific season during autumn. Anthesis lasted 36 hr with protogyny and no hercogamy, with floral visitors of Apodiformes, Hymenoptera, Lepidoptera and Thysanoptera. Pollination experiments indicated a mixed mating system, whereas the OCI and the pollen/ovule ratio pointed towards a facultative xenogamous breeding system. Seed production was high (1,445 ± 132 seeds/plant); the seeds had potential longevity and were neutral photoblastic. One-year-old seeds germinated slightly later ( = 2.6 ± 0.11 days) than 2-year-old seeds ( = 1.9 ± 0.02 days), both synchronously (IS_1yr = 0.88 ± 0.03 and IS_2yr = 0.82 ± 0.02). Germination percentage for 1-year-old seeds was lower (55.33 ± 4.40%) than that of 2-year-old seeds (94.18 ± 0.59%), suggesting a potential longevity of the seeds in an optimal environment. Reproductive characteristics, such as wide reproductive period, mixed breeding system, copious seed production, seeds with potential longevity, and quick and synchronic germination in different light conditions, favor the invasive capacity of Leonotis nepetifolia.     

The Causal Effect of Market Priming on Trust: An Experimental Investigation Using Randomized Control

We report data from laboratory experiments where participants were primed using phrases related to markets and trade. Participants then participated in trust games with anonymous strangers. The decisions of primed participants are compared to those of a control group. We find evidence that priming for market participation affects positively the beliefs regarding the trustworthiness of anonymous strangers and increases trusting decisions.