The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing

DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall very low number of sites with any detectable level of DNA methylation, occurring at significant levels in only 303-3432 cytosines out of the ∼7.5 million total cytosines in the genome depending on the replicate. Furthermore, a knockout of the DNMA enzyme leads to no overall decrease in DNA methylation. Of the identified sites, significant methylation is only detected at 11 sites in all four of the methylomes analyzed. Targeted bisulfite PCR sequencing and computational analysis demonstrate that the methylation profile does not change during development and that these 11 cytosines are most likely false positives generated by protection from bisulfite conversion due to their location in hairpin-forming palindromic DNA sequences. Our data therefore provide evidence that there is no significant DNA methylation in Dictyostelium before fruiting body formation and identify a reproducible experimental artifact from bisulfite sequencing. © 2023 The Author(s). Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics

How does shading mitigates the water deficit in young Hymenaea courbaril L. plants?

Information on tolerance to isolated or combined abiotic stresses is still scarce for tree species, although such stresses are normal in nature. The interactive effect of light availability and water stress has been reported for some native tree species in Brazil but has not been widely investigated. To test the hypothesis that shading can mitigate the stressful effect of water deficit on the photosynthetic and antioxidant metabolism and on the growth of young Hymenaea courbaril L. plants, we evaluated the following two water regimes: a) continuous irrigation – control (I) - 75% field capacity. and b) water deficit (S), characterized by irrigation suspension associated the two following periods of evaluation: P0 - when the photosynthetic rate of plants subjected to irrigation suspension reached values ​​close to zero, with the seedlings being re-irrigated at that moment, and REC - when the photosynthetic rate of the re-irrigated plants of each shading levels reached values ​​similar to those of plants in the control treatment, totaling four treatments: IP0, SP0, IREC, and SREC. The plants of these four treatments were cultivated under the four following shading levels: 0, 30, 50, and 70%, constituting 16 treatments. Intermediate shading of 30 and 50% mitigates the water deficit and accelerates the recovery of H. courbaril. Water deficit associated with cultivation without shading (0%) should not be adopted in the cultivation or transplantation of H. courbaril. After the resumption of irrigation in the REC, the other characteristics presented a recovery under all cultivation conditions. Key message: Intermediate shading of 30 and 50% mitigates the water deficit and accelerates the recovery of H. courbaril

Influence of the balanced scorecard on the science and innovation performance of Latin American universities

This is an Accepted Manuscript of an article published by Taylor & Francis in Knowledge Management Research & Practice on 2019, available online: http://www.tandfonline.com/10.1080/14778238.2019.1569488[EN] Pressure on the education system to meet society's needs has led some universities to adopt organisational performance measurement systems as strategic control tools. One of the most commonly used systems in business is the balanced scorecard (BSC). For Latin American universities, the urgent task of increasing the quantity and quality of research and innovation has led these universities to update their essential processes. A suitable control system is necessary to ensure the effectiveness of these new policies. Based on strategic management theory, this study focuses on the implementation of a BSC method in Latin American public universities. The aim of this study is to determine the influence of BSC implementation on universities? research and innovation performance. The results reveal similar patterns of indicators to measure performance in public universities. Furthermore, these indicators develop favourably following implementation of the BSC.Peris-Ortiz, M.; García-Hurtado, D.; Devece Carañana, CA. (2019). Influence of the balanced scorecard on the science and innovation performance of Latin American universities. Knowledge Management Research & Practice. 17(4):373-383. https://doi.org/10.1080/14778238.2019.1569488S373383174Agostino, D., & Arnaboldi, M. (2012). Design issues in Balanced Scorecards: The «what» and «how» of control. European Management Journal, 30(4), 327-339. doi:10.1016/j.emj.2012.02.001Al-Ashaab, A., Flores, M., Doultsinou, A., & Magyar, A. (2011). A balanced scorecard for measuring the impact of industry–university collaboration. Production Planning & Control, 22(5-6), 554-570. doi:10.1080/09537287.2010.536626Ankrah, S., & AL-Tabbaa, O. (2015). Universities–industry collaboration: A systematic review. 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Limited Transplantation of Antigen-Expressing Hematopoietic Stem Cells Induces Long-Lasting Cytotoxic T Cell Responses

Harnessing the ability of cytotoxic T lymphocytes (CTLs) to recognize and eradicate tumor or pathogen-infected cells is a critical goal of modern immune-based therapies. Although multiple immunization strategies efficiently induce high levels of antigen-specific CTLs, the initial increase is typically followed by a rapid contraction phase resulting in a sharp decline in the frequency of functional CTLs. We describe a novel approach to immunotherapy based on a transplantation of low numbers of antigen-expressing hematopoietic stem cells (HSCs) following nonmyeloablative or partially myeloablative conditioning. Continuous antigen presentation by a limited number of differentiated transgenic hematopoietic cells results in an induction and prolonged maintenance of fully functional effector T cell responses in a mouse model. Recipient animals display high levels of antigen-specific CTLs four months following transplantation in contrast to dendritic cell-immunized animals in which the response typically declines at 4–6 weeks post-immunization. Majority of HSC-induced antigen-specific CD8+ T cells display central memory phenotype, efficiently kill target cells in vivo, and protect recipients against tumor growth in a preventive setting. Furthermore, we confirm previously published observation that high level engraftment of antigen-expressing HSCs following myeloablative conditioning results in tolerance and an absence of specific cytotoxic activity in vivo. In conclusion, the data presented here supports potential application of immunization by limited transplantation of antigen-expressing HSCs for the prevention and treatment of cancer and therapeutic immunization of chronic infectious diseases such as HIV-1/AIDS

The Unconserved Groucho Central Region Is Essential for Viability and Modulates Target Gene Specificity

Groucho (Gro) is a Drosophila corepressor required by numerous DNA-binding repressors, many of which are distributed in gradients and provide positional information during development. Gro contains well-conserved domains at its N- and C-termini, and a poorly conserved central region that includes the GP, CcN, and SP domains. All lethal point mutations in gro map to the conserved regions, leading to speculation that the unconserved central domains are dispensable. However, our sequence analysis suggests that the central domains are disordered leading us to suspect that the lack of lethal mutations in this region reflects a lack of order rather than an absence of essential functions. In support of this conclusion, genomic rescue experiments with Gro deletion variants demonstrate that the GP and CcN domains are required for viability. Misexpression assays using these same deletion variants show that the SP domain prevents unrestrained and promiscuous repression by Gro, while the GP and CcN domains are indispensable for repression. Deletion of the GP domain leads to loss of nuclear import, while deletion of the CcN domain leads to complete loss of repression. Changes in Gro activity levels reset the threshold concentrations at which graded repressors silence target gene expression. We conclude that co-regulators such as Gro are not simply permissive components of the repression machinery, but cooperate with graded DNA-binding factors in setting borders of gene expression. We suspect that disorder in the Gro central domains may provide the flexibility that allows this region to mediate multiple interactions required for repression

Parasite fate and involvement of infected cells in the induction of CD4+ and CD8+ T cell responses to Toxoplasma gondii

During infection with the intracellular parasite Toxoplasma gondii, the presentation of parasite-derived antigens to CD4+ and CD8+ T cells is essential for long-term resistance to this pathogen. Fundamental questions remain regarding the roles of phagocytosis and active invasion in the events that lead to the processing and presentation of parasite antigens. To understand the most proximal events in this process, an attenuated non-replicating strain of T. gondii (the cpsII strain) was combined with a cytometry-based approach to distinguish active invasion from phagocytic uptake. In vivo studies revealed that T. gondii disproportionately infected dendritic cells and macrophages, and that infected dendritic cells and macrophages displayed an activated phenotype characterized by enhanced levels of CD86 compared to cells that had phagocytosed the parasite, thus suggesting a role for these cells in priming naïve T cells. Indeed, dendritic cells were required for optimal CD4+ and CD8+ T cell responses, and the phagocytosis of heat-killed or invasion-blocked parasites was not sufficient to induce T cell responses. Rather, the selective transfer of cpsII-infected dendritic cells or macrophages (but not those that had phagocytosed the parasite) to naïve mice potently induced CD4+ and CD8+ T cell responses, and conferred protection against challenge with virulent T. gondii. Collectively, these results point toward a critical role for actively infected host cells in initiating T. gondii-specific CD4+ and CD8+ T cell responses