Whole transcriptome analysis of a reversible neurodegenerative process in Drosophila reveals potential neuroprotective genes

Endometrial Receptivity Analysis (ERA): data versus opinions

This article summarises and contextualises the accumulated basic and clinical data on the ERA test and addresses specific comments and opinions presented by the opponent as part of an invited debate. Progress in medicine depends on new technologies and concepts that translate to practice to solve long-standing problems. In a key example, combining RNA sequencing data (transcriptomics) with artificial intelligence (AI) led to a clinical revolution in personalising disease diagnosis and fostered the concept of precision medicine. The reproductive field is no exception. Translation of endometrial transcriptomics to the clinic yielded an objective definition of the limited time period during which the maternal endometrium is receptive to an embryo, known as the window of implantation (WOI). The WOI is induced by the presence of exogenous and/or endogenous progesterone (P) after proper oestradiol (E2) priming. The window lasts 30-36 hours and, depending on the patient, occurs between LH + 6 and LH + 9 in natural cycles or between P + 4 and P + 7 in hormonal replacement therapy (HRT) cycles. In approximately 30% of IVF cycles in which embryo transfer is performed blindly, the WOI is displaced and embryo-endometrial synchrony is not achieved. Extending this application of endometrial transcriptomics, the endometrial receptivity analysis (ERA) test couples next-generation sequencing (NGS) to a computational predictor to identify transcriptomic signatures for each endometrial stage: proliferative (PRO), pre-receptive (PRE), receptive (R) and post-receptive (POST). In this way, personalised embryo transfer (pET) may be possible by synchronising embryo transfer with each patient's WOI. Data are the only way to confront arguments sustained in opinions and/or misleading concepts; it is up to the reader to make their own conclusions regarding its clinical utility.

Drosophila melanogaster White Mutant w1118 Undergo Retinal Degeneration

Key scientific discoveries have resulted from genetic studies of Drosophila melanogaster, using a multitude of transgenic fly strains, the majority of which are constructed in a genetic background containing mutations in the white gene. Here we report that white mutant flies from w1118 strain undergo retinal degeneration. We observed also that w1118 mutants have progressive loss of climbing ability, shortened life span, as well as impaired resistance to various forms of stress. Retinal degeneration was abolished by transgenic expression of mini-white+ in the white null background w1118 . We conclude that beyond the classical eye-color phenotype, mutations in Drosophila white gene could impair several biological functions affecting parameters like mobility, life span and stress tolerance. Consequently, we suggest caution and attentiveness during the interpretation of old experiments employing white mutant flies and when planning new ones, especially within the research field of neurodegeneration and neuroprotection. We also encourage that the use of w1118 strain as a wild-type control should be avoided.

Transcriptional responses of detoxification genes to four plant allelochemicals in Aphis gossypii

Aphis gossypii Glover (Hemiptera: Aphididae) can damage a variety of agricultural crops, so it is very important for cotton aphids to evolve adaptive mechanisms to various allelochemicals from host plants. Our results aim to provide a fundamental and rich resource for exploring aphid functional genes in A. gossypii. A transcriptome data set and five expression profile data sets of A. gossypii samples were analyzed by Illumina sequencing platform. In total, 53,763,866 reads were assembled into 1,963,516 contigs and 28,555 unigenes. Compared with the control, 619 genes were significantly up- or downregulated in the treatment group by 2-tridecanone. There were 516, 509, and 717 of differential expression genes in tannic acid, quercetin, and gossypol treatment groups, respectively. Furthermore, there were 4 of 54 putative cytochrome P450 genes and 1 of 7 putative carboxylesterases downregulated in all treatment groups by four plant allelochemicals. When aphids fed on 2-tridecanone, tannic acid, and quercetin, only one P450 gene was upregulated. These results show that plant allelochemical stress can induce differential gene expression in A. gossypii. The differential response information of gene expression based on a large-scale sequence would be useful to reveal molecular mechanisms of adaptation for A. gossypii to plant allelochemicals.

Structure of developmental gene regulatory networks from the perspective of cell fate-determining genes

The core of gene regulatory networks (GRNs) is formed by transcription factors (TF) and cis-regulatory modules (CRMs) present in their downstream genes. GRNs have a modular structure in which complex circuitries link TFs to CRMs to generate specific transcriptional outputs. (1) Of particular interest are those GRNs including cell fate-determining genes, as they constitute developmental switches which activity is necessary and sufficient to promote particular cellular fates. Most of the genetic analysis of developmental processes deals with the composition and structure of GRNs acting upstream of cell fate-determining genes, as they are best suited for genetic analysis and molecular deconstruction. More recently, the application of a variety of in vivo, computational and genome-wide approaches is allowing the identification and functional analysis of GRNs acting downstream of cell fate-determining genes. In this review we discuss several examples of GRNs acting upstream and downstream of cell fate-determining genes, including other TFs which activity pervade across both regulatory networks.

The Spalt Transcription Factors Generate the Transcriptional Landscape of the Drosophila melanogaster Wing Pouch Central Region

The Drosophila genes spalt major (salm) and spalt-related (salr) encode Zn-finger transcription factors regulated by the Decapentaplegic (Dpp) signalling pathway in the wing imaginal disc. The function of these genes is required for cell survival and proliferation in the central region of the wing disc, and also for vein patterning in the lateral regions. The identification of direct Salm and Salr target genes, and the analysis of their functions, are critical steps towards understanding the genetic control of growth and patterning of the Drosophila wing imaginal disc by the Dpp pathway. To identify candidate Salm/Salr target genes, we have compared the expression profile of salm/salr knockdown wing discs with control discs in microarray experiments. We studied by in situ hybridization the expression pattern of the genes whose mRNA levels varied significantly, and uncovered a complex transcription landscape regulated by the Spalt proteins in the wing disc. Interestingly, candidate Salm/Salr targets include genes which expression is turned off and genes which expression is positively regulated by Salm/Salr. Furthermore, loss-of-function phenotypic analysis of these genes indicates, for a fraction of them, a requirement for wing growth and patterning. The identification and analysis of candidate Salm/Salr target genes opens a new avenue to reconstruct the genetic structure of the wing, linking the activity of the Dpp pathway to the development of this epithelial tissue.

How signalling pathways regulate the formation of organs with a precise size and pattern of differentiation is a fundamental question in developmental genetics. One classical example of the link between signalling and organ development is the regulation of wing disc development by the Decapentaplegic/BMP (Dpp) signalling pathway in Drosophila. A key outcome of this pathway is the transcriptional activation of the spalt major (salm) and spalt related (salr) genes, both encoding transcription factors. In this manner, the identification of Salm/Salr target genes is a critical step towards the understanding of the mode of action of these proteins and the genetic logic underlying the regulation of wing development by the Dpp signalling pathway. In order to identify these target genes, we used expression microarrays, in situ hybridization and phenotypic analysis. We identified an unexpected complexity in the transcriptional landscape of the wing disc that includes genes positively and negatively regulated by Salm/Salr. These findings have major implications for the reconstruction of the genetic hierarchy initiated by the Dpp pathway and leading to the formation of a wing with a correct size and pattern, because some of the genes we identified could explain particular aspects of the sal mutant phenotype.

Do the genes of the innate immune response contribute to neuroprotection in Drosophila?

A profound debate exists on the relationship between neurodegeneration and the innate immune response in humans. Although it is clear that such a relation exists, the causes and consequences of this complex association remain to be determined in detail. Drosophila is being used to investigate the mechanisms involved in neurodegeneration, and all genomic studies on this issue have generated gene catalogues enriched in genes of the innate immune response. We review the data reported in these publications and propose that the abundance of immune genes in studies of neurodegeneration reflects at least two phenomena: (i) some proteins have functions in both immune and nervous systems, and (ii) immune genes might also be of neuroprotective value in Drosophila. This review opens this debate in Drosophila, which could thus be used as an instrumental model to elucidate this question.

Global gene expression shift during the transition from early neural development to late neuronal differentiation in Drosophila melanogaster

Regulation of transcription is one of the mechanisms involved in animal development, directing changes in patterning and cell fate specification. Large temporal data series, based on microarrays across the life cycle of the fly Drosophila melanogaster, revealed the existence of groups of genes which expression increases or decreases temporally correlated during the life cycle. These groups of genes are enriched in different biological functions. Here, instead of searching for temporal coincidence in gene expression using the entire genome expression data, we searched for temporal coincidence in gene expression only within predefined catalogues of functionally related genes and investigated whether a catalogue's expression profile can be used to generate larger catalogues, enriched in genes necessary for the same function. We analyzed the expression profiles from genes already associated with early neurodevelopment and late neurodifferentiation, at embryonic stages 16 and 17 of Drosophila life cycle. We hypothesized that during this interval we would find global downregulation of genes important for early neuronal development together with global upregulation of genes necessary for the final differentiation of neurons. Our results were consistent with this hypothesis. We then investigated if the expression profile of gene catalogues representing particular processes of neural development matched the temporal sequence along which these processes occur. The profiles of genes involved in patterning, neurogenesis, axogenesis or synaptic transmission matched the prediction, with largest transcript values at the time when the corresponding biological process takes place in the embryo. Furthermore, we obtained catalogues enriched in genes involved in temporally matching functions by performing a genome-wide systematic search for genes with their highest expression levels at the corresponding embryonic intervals. These findings imply the use of gene expression data in combination with known biological information to predict the involvement of functionally uncharacterized genes in particular biological events.

Ecological adaption analysis of the cotton aphid (Aphis gossypii) in different phenotypes by transcriptome comparison

Background

The cotton aphid, Aphis gossypii Glover, is a destructive insect pest worldwide; it directly or indirectly damages (virus transmission) 300 species of host plants. Knowledge of their ecologically adaptive mechanisms at the molecular level may provide an essential and urgent method to effectively control this pest. However, no transcriptome information is available for the cotton aphid and sequence data are scarce. Therefore, we obtained transcriptome data.

Results

To facilitate such a study, two cotton aphid transcriptomes at different growth stages of cotton, seedling and summer, were sequenced. A total of 161,396 and 66,668 contigs were obtained and assembled into 83,671 and 42,438 transcripts, respectively. After combining the raw date for both transcriptomes, the sequences were reassembled into 66,695 transcripts, and 52,160 were annotated based on BLASTX analyses. Comparison of the transcriptomes revealed that summer presented less challenges for the cotton aphids than the seedling stage of cotton. In total, 58 putative heat shock protein genes and 66 candidate cytochrome p450 genes were identified with BLASTX.

Conclusions

Our results form a basis for exploring the molecular mechanisms of ecological adaption in the cotton aphid. Our study also provides a baseline for the exploration of abiotic stress responses. In addition, it provides large-scale sequence information for further studies on this species.

First Transcriptome and Digital Gene Expression Analysis in Neuroptera with an Emphasis on Chemoreception Genes in Chrysopa pallens (Rambur)

Background

Chrysopa pallens (Rambur) are the most important natural enemies and predators of various agricultural pests. Understanding the sophisticated olfactory system in insect antennae is crucial for studying the physiological bases of olfaction and also could lead to effective applications of C. pallens in integrated pest management. However no transcriptome information is available for Neuroptera, and sequence data for C. pallens are scarce, so obtaining more sequence data is a priority for researchers on this species.

Results

To facilitate identifying sets of genes involved in olfaction, a normalized transcriptome of C. pallens was sequenced. A total of 104,603 contigs were obtained and assembled into 10,662 clusters and 39,734 singletons; 20,524 were annotated based on BLASTX analyses. A large number of candidate chemosensory genes were identified, including 14 odorant-binding proteins (OBPs), 22 chemosensory proteins (CSPs), 16 ionotropic receptors, 14 odorant receptors, and genes potentially involved in olfactory modulation. To better understand the OBPs, CSPs and cytochrome P450s, phylogenetic trees were constructed. In addition, 10 digital gene expression libraries of different tissues were constructed and gene expression profiles were compared among different tissues in males and females.

Conclusions

Our results provide a basis for exploring the mechanisms of chemoreception in C. pallens, as well as other insects. The evolutionary analyses in our study provide new insights into the differentiation and evolution of insect OBPs and CSPs. Our study provided large-scale sequence information for further studies in C. pallens.