Anna A. Ogienko

Genetically modified (GM) plants have revolutionized agriculture for more than three decades. The production of a GM plants is a complex, multi-stage process. Several key methods are available for generating GM plants. The choice of transformation method depends on the type of plant (dicotyledonous or monocotyledonous), the objective (large-scale production versus studying a specific gene in particular cells or tissues), and whether stable or transient transformation is desired. Following successful transformation, the next step is the regeneration of a whole plant from a single cell in tissue culture, which is a labor-intensive and time-consuming process. Currently, numerous genes that confer desirable traits have been identified. These traits include stress tolerance, herbicide and pest resistance, and improved consumer qualities (such as flavor, appearance, shelf life, and nutritional value). In this review, we describe the main methods for producing GM plants and provide examples of trait genes utilized in agricultural biotechnology. Despite the fact that GM plants represent one of the most significant biotechnological advances, they also remain among the most contentious issues in contemporary food safety and agricultural policy. Here, we discuss the advantages and disadvantages of using GM plants for humans.

Drosophila has provided a highly attractive model system for studying various tissue- and stage-specific processes as well as their pathologies, including a range of human diseases. The existence of a large number of diverse Gal4 drivers to precisely control the expression patterns of UAS transgenes simplifies such studies. However, the choice of driver is always critical, as its possible ectopic expression in non-target cells and tissues can directly impact the results. Therefore, it is very important to thoroughly characterize both the molecular nature and expression pattern of each Gal4 driver line. Here, we aim to fill such gaps regarding the AB1-Gal4 driver, which is typically used to express UAS transgenes in larval salivary glands. In this fly line, the P{GawB} enhancer trap construct encoding the Gal4 protein resides within overlapping evolutionary conserved spastin (spas) and Mitochondrial Rho (Miro) genes. Both these genes are expressed in a number of tissues, including the central nervous system (CNS), and their human orthologs are associated with neurodegenerative diseases. Consistently, we demonstrate that, in third-instar larvae, the expression pattern of AB1-Gal4 is also not restricted to salivary glands. We detect its activity in a subset of Elav-positive neurons in the CNS, including motor neurons, as well as in specific photoreceptor cells in eye discs.

In vitro models are of great importance in advancing our understanding of human diseases, especially complex disorders with unknown etiologies like inflammatory bowel diseases (IBD). One of the key IBD features is the increased intestinal permeability. The disruption of the intestinal barrier can occur due to a destructive inflammatory response involving intestinal cell death. Alternatively, proteins that form tight junctions (TJ) fail to form function complexes and promote epithelial barrier disruption. The mechanisms behind this process are not fully understood. Thus, in vitro models that facilitate studying the intestinal barrier and its molecular components are of particular importance in the context of IBD. There are in vitro and ex vivo models that can be used to recapitulate some aspects of IBD. Among these are intestinal explants, crypts, and epithelial 3D-organoids. Here we describe some practical limitations of isolated crypts, gut tissue explants, and intestinal organoids as models in epithelial barrier biology, and TJ in particular. Our findings demonstrate that only 3D intestinal organoids formed from single cells are suitable to study barrier permeability in vitro, as primary crypt-derived organoids do not retain epithelial integrity due to cell death. Importantly, 3D organoids raised in culture conditions may fail to recapitulate inflammatory and barrier phenotypes of the source mouse model. To study the features of the inflamed epithelium, ex vivo intestinal explants and crypts were employed. We show here that isolated crypts do not preserve native TJ structure in a long-term experimental setting and tend to disintegrate in the unsupported culture environment. However, intestinal explants were stable in culture conditions for about 24 hours and demonstrated their applicability for short-term living tissue imaging and fluorescence recovery after photobleaching (FRAP). Thus, a combination of 3D organoids and intestinal explants provides a more accurate experimental platform to understand the intestinal epithelial barrier.

Lifespan is a complex quantitative trait involving genetic and non-genetic factors as well as the peculiarities of ontogenesis. As with all quantitative traits, lifespan shows considerable variation within populations and between individuals. Drosophila, a favourite object of geneticists, has greatly advanced our understanding of how different forms of variability affect lifespan. This review considers the role of heritable genetic variability, phenotypic plasticity and stochastic variability in controlling lifespan in Drosophila melanogaster. We discuss the major historical milestones in the development of the genetic approach to study lifespan, the breeding of long-lived lines, advances in lifespan QTL mapping, the environmental factors that have the greatest influence on lifespan in laboratory maintained flies, and the mechanisms, by which individual development affects longevity. The interplay between approaches to study ageing and lifespan limitation will also be discussed. Particular attention will be paid to the interaction of different types of variability in the control of lifespan.

The nucleolus is a significant nuclear organelle that is primarily known for its role in ribosome biogenesis. However, emerging evidence suggests that the nucleolus may have additional functions. Particularly, it is involved in the organization of the three-dimensional structure of the genome. The nucleolus acts as a platform for the clustering of repressed chromatin, although this process is not yet fully understood, especially in the context of Drosophila. One way to study the regions of the genome that cluster near the nucleolus in Drosophila demands the identification of a reliable nucleolus-localizing signal (NoLS) motif(s) that can highly specifically recruit the protein of interest to the nucleolus. Here, we tested a series of various NoLS motifs from proteins of different species, as well as some of their combinations, for the ability to drive the nucleolar localization of the chimeric H2B-GFP protein. Several short motifs were found to effectively localize the H2B-GFP protein to the nucleolus in over 40% of transfected Drosophila S2 cells. Furthermore, it was demonstrated that NoLS motifs derived from Drosophila proteins exhibited greater efficiency compared to that of those from other species.

CHO cells are most commonly used for the synthesis of recombinant proteins in biopharmaceutical production. When stable producer cell lines are obtained, the locus of transgene integration into the genome has a great influence on the level of its expression. Therefore, the identification of genomic loci ensuring a high level of protein production is very important. Here, we used the TRIP assay to study the influence of the local chromatin environment on the activity of transgenes in CHO cells. For this purpose, reporter constructs encoding eGFP under the control of four promoters were stably integrated into the genome of CHO cells using the piggyBac transposon. Each individual transgene contained a unique tag, a DNA barcode, and the resulting polyclonal cell population was cultured for almost a month without any selection. Next, using the high-throughput sequencing, genomic localizations of barcodes, as well as their abundances in the population and transcriptional activities were identified. In total, ~640 transgenes more or less evenly distributed across all chromosomes of CHO cells were characterized. More than half of the transgenes were completely silent. The most active transgenes were identified to be inserted in gene promoters and 5’ UTRs. Transgenes carrying Chinese hamster full-length promoter of the EF-1α gene showed the highest activity. Transgenes with a truncated version of the same promoter and with the mouse PGK gene promoter were on average 10 and 19 times less active, respectively. In total, combinations of genomic loci of CHO cells and transgene promoters that together provide different levels of transcriptional activity of the model reporter construct were described.

Compared to transcription initiation, much less is known about transcription termination. In particular, large-scale mutagenesis studies have, so far, primarily concentrated on promoter and enhancer, but not terminator sequences. Here, we used a massively parallel reporter assay (MPRA) to systematically analyze the influence of short (8 bp) sequence variants (mutations) located downstream of the polyadenylation signal (PAS) on the steady-state mRNA level of the upstream gene, employing an eGFP reporter and human HEK293T cells as a model system. In total, we evaluated 227,755 mutations located at different overlapping positions within +17..+56 bp downstream of the PAS for their ability to regulate the reporter gene expression. We found that the positions +17..+44 bp downstream of the PAS are more essential for gene upregulation than those located more distal to the PAS, and that the mutation sequences ensuring high levels of eGFP mRNA expression are extremely T-rich. Next, we validated the positive effect of a couple of mutations identified in the MPRA screening on the eGFP and luciferase protein expression. The most promising mutation increased the expression of the reporter proteins 13-fold and sevenfold on average in HEK293T and CHO cells, respectively. Overall, these findings might be useful for further improving the efficiency of production of therapeutic products, e.g., recombinant antibodies.

The spatio-temporal regulation of gene expression determines the fate and function of various cells and tissues and, as a consequence, the correct development and functioning of complex organisms. Certain mechanisms of gene activity regulation provide adequate cell responses to changes in environmental factors. Aside from gene expression disorders that lead to various pathologies, alterations of expression of particular genes were shown to significantly decrease or increase the lifespan in a wide range of organisms from yeast to human. Drosophila fruit fly is an ideal model system to explore mechanisms of longevity and aging due to low cost, easy handling and maintenance, large number of progeny per adult, short life cycle and lifespan, relatively low number of paralogous genes, high evolutionary conservation of epigenetic mechanisms and signalling pathways, and availability of a wide range of tools to modulate gene expression in vivo. Here, we focus on the organization of the evolutionarily conserved signaling pathways whose components significantly influence the aging process and on the interconnections of these pathways with gene expression regulation.

There is an urgent need for new drugs to overcome the challenge of the ever-growing drug resistance towards tuberculosis. A new, highly efficient anti-tuberculosis drug, Perchlozone (thioureidoiminomethylpyridinium perchlorate, Pz), is only available in an oral dosage form, though injectable forms and inhalation solutions could be better alternatives, offering higher bioavailability. To produce such forms, nano- and micro-particles of APIs would need to be prepared as dispersions with carriers. We use this case study to illustrate the principles of selecting solvents and excipients when preparing such formulations. We justify the choice of water–THF (19.1 wt % THF) as solvent and mannitol as carrier to prepare formulations of Pz—a poorly soluble compound—that are suitable for injection or inhalation. The formulations could be prepared by conventional freeze-drying in vials, making the proposed method suitable for industrial scaling. A similar strategy for selecting the organic solvent and the excipient can be applied to other compounds with low water solubility.

Collective cell migration is a complex process that happens during normal development of many multicellular organisms, as well as during oncological transformations. In Drosophila oogenesis, a small set of follicle cells originally located at the anterior tip of each egg chamber become motile and migrate as a cluster through nurse cells toward the oocyte. These specialized cells are referred to as border cells (BCs) and provide a simple and convenient model system to study collective cell migration. The process is known to be complexly regulated at different levels and the product of the slow border cells (slbo) gene, the C/EBP transcription factor, is one of the key elements in this process. However, little is known about the regulation of slbo expression. On the other hand, the ubiquitously expressed transcription factor GAGA, which is encoded by the Trithorax-like (Trl) gene was previously demonstrated to be important for Drosophila oogenesis. Here, we found that Trl mutations cause substantial defects in BC migration. Partially, these defects are explained by the reduced level of slbo expression in BCs. Additionally, a strong genetic interaction between Trl and slbo mutants, along with the presence of putative GAGA binding sites within the slbo promoter and enhancer, suggests the direct regulation of this gene by GAGA. This idea is supported by the reduction in the slbo-Gal4-driven GFP expression within BC clusters in Trl mutant background. However, the inability of slbo overexpression to compensate defects in BC migration caused by Trl mutations suggests that there are other GAGA target genes contributing to this process. Taken together, the results define GAGA as another important regulator of BC migration in Drosophila oogenesis.