Transcription factor expression landscape in Drosophila embryonic cell lines

Background: Transcription factor (TF) proteins are a key component of the gene regulatory networks that control cellular fates and function. TFs bind DNA regulatory elements in a sequence-specific manner and modulate target gene expression through combinatorial interactions with each other, cofactors, and chromatin-modifying proteins. Large-scale studies over the last two decades have helped shed light on the complex network of TFs that regulate development in Drosophila melanogaster. Results: Here, we present a detailed characterization of expression of all known and predicted Drosophila TFs in two well-established embryonic cell lines, Kc167 and S2 cells. Using deep coverage RNA sequencing approaches we investigate the transcriptional profile of all 707 TF coding genes in both cell types. Only 103 TFs have no detectable expression in either cell line and 493 TFs have a read count of 5 or greater in at least one of the cell lines. The 493 TFs belong to 54 different DNA-binding domain families, with significant enrichment of those in the zf-C2H2 family. We identified 123 differentially expressed genes, with 57 expressed at significantly higher levels in Kc167 cells than S2 cells, and 66 expressed at significantly lower levels in Kc167 cells than S2 cells. Network mapping reveals that many of these TFs are crucial components of regulatory networks involved in cell proliferation, cell–cell signaling pathways, and eye development. Conclusions: We produced a reference TF coding gene expression dataset in the extensively studied Drosophila Kc167 and S2 embryonic cell lines, and gained insight into the TF regulatory networks that control the activity of these cells. © The Author(s) 2024

Transcriptome profile in Drosophila Kc and S2 embryonic cell lines

Drosophila melanogaster cell lines are an important resource for a range of studies spanning genomics, molecular genetics, and cell biology. Amongst these valuable lines are Kc167 (Kc) and Schneider 2 (S2) cells, which were originally isolated in the late 1960s from embryonic sources and have been used extensively to investigate a broad spectrum of biological activities including cell-cell signaling and immune system function. Whole-genome tiling microarray analysis of total RNA from these two cell types was performed as part of the modENCODE project over a decade ago and revealed that they share a number of gene expression features. Here, we expand on these earlier studies by using deep-coverage RNA-sequencing approaches to investigate the transcriptional profile in Kc and S2 cells in detail. Comparison of the transcriptomes reveals that ∼75% of the 13,919 annotated genes are expressed at a detectable level in at least one of the cell lines, with the majority of these genes expressed at high levels in both cell lines. Despite the overall similarity of the transcriptional landscape in the two cell types, 2,588 differentially expressed genes are identified. Many of the genes with the largest fold change are known only by their CG designations, indicating that the molecular control of Kc and S2 cell identity may be regulated in part by a cohort of relatively uncharacterized genes. Our data also indicate that both cell lines have distinct hemocyte-like identities, but share active signaling pathways and express a number of genes in the network responsible for dorsal-ventral patterning of the early embryo. © The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America

Projeções de consumo de madeira com fins energéticos para secagem de grãos na região de Guarapuava, PR.

O objetivo principal deste artigo foi avaliar a capacidade potencial da indústria madeireira em atender às necessidades da secagem dos grãos produzidos na região de Guarapuava em florestas plantadas de eucalipto voltadas à produção de energia a partir de sua biomassa. Sob a ótica metodológica, a pesquisa caracterizou-se pela natureza aplicada, enfoque quantitativo e caráter explicativo e por estar fundamentada nos princípios de cadeias produtivas e de demanda derivada. Os resultados indicaram que normalmente os plantios energéticos de eucalipto na região apresentam produtividade de 40 m³/ha/ano. Os grãos de milho, soja, trigo e cevada passam por processos de secagem na região. Utiliza-se 0,0574 m³ de madeira de eucalipto para secar uma tonelada de milho, 0,0218 m³ por tonelada de soja, 0,0224 m³ por tonelada de trigo e 0,0258 m³ por tonelada de cevada. Estimou-se que, entre os anos de 2012 e 2022, a área total necessária para atender a secagem desses grãos pode variar entre 1.947 e 4.800 ha, com média entre 177 ha e 436,4 ha, conforme o cenário analisado. Os resultados indicam a necessidade da integração dos plantios florestais de eucalipto às cadeias produtivas agrícolas, visando ao atendimento das necessidades de secagem de grãos da região. Palavras-chave: Produção florestal; energia da biomassa; secagem de grãos

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

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