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opencc-zeroMay 2023View details →

Rapid reduction of Paraoxonase expression followed by inactivation across semiaquatic mammals suggests adaptive benefit of gene loss

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of function; loss of protein function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages – Pon1 became a pseudogene at least six times independently in aquatic and semiaquatic mammals with clear genetic lesions, such as stop codons and frameshifts. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and blood plasma activity across four major aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We also observed in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing for accumulation of disrupting mutations. The recurrent and rapid loss of Pon1 even suggests that it is adaptive in aquatic mammals. Accordingly, we examined diving and dietary traits across pinniped species as potential driving forces of Pon1 loss. We found that loss is best correlated with diving activity and is likely the result of selective pressures associated with hypoxia and hypoxia-induced inflammation.

Annona squamosa Leaf Extract Inhibit Migration of Human Cervical Cancer Cells Through MMP-9 Expression

Figure 1. a.Annona squamosa leaf . b.Simplicia powder of Annona squamosa leaves Figure 2. Annona squamosa leaves ethanol    extract. Figure 3. FTIR spectrophotometer results of acetogenin compounds of Annona squamosa leaves extract Figure 4. The cytotoxic test of HeLa cells at 24 hours.  The combination of ASL (Annona squamosa leaf Extract) 12.5 mg/ml + cisplatin was very effective compared with  a single therapy.  *P < 0.05Figure 4. The cytotoxic test of HeLa cells at 24 hours.  The combination of ASL (Annona squamosa leaf Extract) 12.5 mg/ml + cisplatin was very effective compared with  a single therapy.  *P < 0.05 Figure 5. The percentage of living cells of HeLa cells were cultured with different concentrations of Annona squamosa leaf extract. Figure 6. The combination therapy of ASL with cisplatin reduced the expressions of MMP-9 in HeLa cells. a. A significant concentration for cytotoxicity was a concentration of 12.5 mg/mL ASL + 5 μg/mL Cisplatin. b. The number of MMP-9 positive cells. *P< 0.005. Figure 7. The combination therapy of ASL and Cisplatin inhibit cell migration. a. HeLa cells were treated with single cisplatin or in combination with ASL 12.5; 25, 50, and a single dose of ASL 75 mg/mL. b.  Percentage area of cells undergoing migration. *P<0.005.

Additional raw data in `Cell-type-specific co-expression inference from single cell RNA-sequencing data'.

This repository holds the additional raw data used to generate figures in the publication "Cell-type-specific co-expression inference from single cell RNA-sequencing data" (preprint version: <a href="http://source%20code%20repo%20for%20%60cell-type-specific%20co-expression%20inference%20from%20single%20cell%20rna-sequencing%20data%27./">https://www.biorxiv.org/content/10.1101/2022.12.13.520181v1</a>). Table of contents: <ul> <li>Figure_1B.rds:  <ul> <li>raw data of Figure 1B </li> <li>co-expression estimates of 500*499/2 gene pairs across 100 replicates for 7 methods under two settings of sequencing detph variations</li> </ul> </li> <li>Supplementary_Figure_1B.rds:  <ul> <li>raw data of Supplementary Figure 1B </li> <li>co-expression estimates of 500*499/2 gene pairs across 100 replicates for 7 methods under two settings of sequencing detph variations</li> </ul> </li> <li>Supplementary_Figure_2.rds:  <ul> <li>raw data of Supplementary Figure 2 </li> <li>empirical power evaluated for 4999 gene pairs and 6 methods</li> </ul> </li> <li>Figure_3B.rds:  <ul> <li>raw data of Figure 3B</li> <li>co-expression estimates of a network of 500 genes for 9 methods across 100 replicates</li> </ul> </li> <li>Additional_Raw_Data.xlsx <ul> <li>raw data of Figure 3A: (geometric mean expression levels, co-expression estimates) for 4999 gene pairs and 11 methods</li> <li>raw data of Figure 3C: running times for 11 methods</li> <li>raw data of Supplementary Figure 3: (geometric mean expression levels, co-expression estimates) for 4999 gene pairs and 11 methods under two settings of sequencing detph variations</li> </ul> </li> </ul>

curatedPCaData supplementary data table for differential gene expression analysis

This tab-separated plaintext file contains differential gene expression analyses reported for the curatedPCaData data resource publication.

Tapping to drumbeats in an online experiment changes our perception of time and expressiveness - Dataset

The dataset is a supplement to the study Tapping to drumbeats in an online experiment changes our perception of time and expressiveness on Psychological Research.

Tapping to drumbeats in an online experiment changes our perception of time and expressiveness - Stimuli

The video and audio material here are the experiment stimuli for the study Tapping to drumbeats in an online experiment changes our perception of time and expressiveness on Psychological Research.

opencc-by-4.0Jul 2023View details →

Data for GECCO2023 Paper "Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness"

Data for Paper "Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness" <ul> <li>instances.tar.xz contains 𝜌mnk-landscape instances</li> <li>metrics.csv contains the (C)PLOS-net metric-values</li> <li>performance.csv contains the performance of the different algorithms on each instance</li> <li>merged.csv contains the merged data from the 2 csv files above</li> </ul> Reference Arnaud Liefooghe, Gabriela Ochoa, Sébastien Verel, and Bilel Derbel. 2023. Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness. In Genetic and Evolutionary Computation Conference (GECCO ’23), July 15–19, 2023, Lisbon, Portugal. ACM, New York, NY, USA, 9 pages. <a href="https://doi.org/10.1145/3583131.3590474">https://doi.org/10.1145/3583131.3590474</a> Abstract The structure of local optima in multi-objective combinatorial optimization and their impact on algorithm performance are not yet properly understood. In this paper, we are interested in the representation of multi-objective landscapes and their multi-modality. More specifically, we revise and extend the network of Pareto local optimal solutions (PLOS-net), inspired by the well-established local optima network from single-objective optimization. We first define a compressed PLOS-net which allows us to enhance its perception while preserving the important notion of connectedness between local optima. We then study an alternative visualization of the (compressed) PLOS-net that focuses on good-quality solutions, improves the distinction between connected components in the network, and generalizes well to landscapes with more than 2 objectives. We finally define a number of network metrics that characterize the PLOS-net, some of them being strongly correlated with search performance. We visualize and experiment with small-size multi-objective nk-landscapes, and we disclose the effect of PLOS-net metrics against well-established multi-objective local search and evolutionary algorithms.

opencc-zeroJun 2023View details →

Oviposition behaviour is not affected by ultraviolet light in a butterfly with sexually-dimorphic expression of a UV-sensitive opsin

Animal vision is important for mediating multiple complex behaviours. In Heliconius butterflies, vision guides fundamental behaviours such as oviposition, foraging and mate choice. Colour vision in Heliconius involves ultraviolet (UV), blue and long- wavelength sensitive photoreceptors (opsins). Additionally, Heliconius possess a duplicated UV opsin, and its expression varies widely within the genus. In Heliconius erato, opsin expression is sexually dimorphic; only females express both UV-sensitive opsins, enabling UV wavelength discrimination. However, the selective pressures responsible for sex-specific differences in opsin expression and visual perception remain unresolved. Female Heliconius invest heavily in finding suitable hostplants for oviposition, a behaviour heavily dependent on visual cues. Here, we tested the hypothesis that UV vision is important for oviposition in H. erato and Heliconius himera females by manipulating the availability of UV in behavioural experiments under natural conditions. Our results indicate that UV does not influence the number of oviposition attempts or eggs laid, and the hostplant, Passiflora punctata, does not reflect UV wavelengths. Models of H. erato female vision suggest only minimal stimulation of the UV opsins. Overall, these findings suggest that UV wavelengths do not directly affect the ability of Heliconius females to find suitable oviposition sites. Alternatively, UV discrimination could be used in the context of foraging or mate choice, but this remains to be tested.

opencc-by-4.0Jun 2023View details →

Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells

The datasets analysed in the manuscript "Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells".

opencc-zeroJun 2023View details →

RNA-seq data showing PLS role in gene expression control in Arabidopsis

The vital plant ethylene receptor (ETR1) contains an essential Cu(I) ion, and as for other vesicular cupro-proteins, the final step of Cu(I) maturation at the endoplasmic reticulum (ER) is undefined. We previously discovered that mutants in the Arabidopsisgene POLARIS (PLS), encoding a 36 amino acid peptide, exhibit constitutive ethylene signalling responses. Here we report a 1:2 thiol-dependent Cu(I):PLS2 complex, with an affinity of 3.79 (±1.5) x1019 M-2. We demonstrate interactions with the transmembrane domain of ETR1, the Cu(I) chaperones ATX1 and CCH, and Cu(I)-transporting P1B-type ATPase RAN1 at the ER. Formation of Cu(I)-dependent PLS-cuproprotein adducts at the ER provides a mechanism to modulate the metalation of ETR1, thereby regulating its activity and representing a distinct mechanism for plant hormone receptor regulation.

opencc-by-4.0Jun 2023View details →

Massive Chinese domestic pigs provide missing sequences in reference genome and reveal non-coding sequence variations regulating gene expression across Eurasian boars

This dataset contains novel sequences in Chinese domestic pigs but is absent in Sscrofa 11.1 reference genome. The detailed information for each file is recorded in the README file.

opencc-zeroJul 2023View details →

Context‐dependent expression of variation in defensive behaviour in the lower termite Zootermopsis nevadensis

Eusocial animals exhibit a sophisticated division of labour. The self-organized colony requires coordination of local interactions at the individual level. Termites are a well-known group exhibiting social organization among castes within a colony, and helper castes have facilitated their ecological and evolutionary success. Termites have soldier castes specialized in defence, but other castes are also known to exhibit defensive behaviour depending on the context. However, it is unclear how the variation in the frequencies of defensive behaviour emerged. Here, we investigate the effects of presence of nestmates on individual defensive behaviour in the dampwood termite Zootermopsis nevadensis. We experimentally prepared three conditions and observed biting behaviour against the ant Camponotus obscuripes. First, the frequency of biting was significantly higher in soldiers than that in pseudergates (i.e., workers) under isolated conditions. Second, the results showed that the frequencies of biting exhibited by soldiers were much higher than those of pseudergates in the pseudergate–soldier pairs. Finally, we investigated the social conditions in the presence of the same castes, that is, pseudergate–pseudergate and soldier–soldier pairs. The frequencies of biting exhibited by first-biting individuals were significantly higher than those exhibited by second-biting individuals in both paired conditions. Our findings demonstrate that defensive behaviour can be frequently observed in first-biting individuals despite the presence of two individuals of the same caste, suggesting that the variation of defensive behaviour may be increased in the presence of nestmates.

opencc-by-4.0Jul 2023View details →

TCGA Bladder Urothelial Carcinoma (BLCA) Gene Expression

Abstract: The Cancer Genome Atlas (TCGA) was a large-scale collaborative project initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). It aimed to comprehensively characterize the genomic and molecular landscape of various cancer types. This dataset's gene expression profile was measured experimentally using the Illumina HiSeq 2000 RNA Sequencing platform by the University of North Carolina TCGA genome characterization center. The Sample IDs serve as unique identifiers for each sample. The dataset contains information about 426 samples and 20530 genes.  Inspiration: This dataset was uploaded to UBRITE for GTKB project.  Instruction: The log2(x+1) normalization was removed, and z-normalization was performed on the dataset using a Python script. Acknowledgments: Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8 The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764 U-BRITE last update: 07/13/2023

opencc-zeroJul 2023View details →

Data for: The effect of seminal fluid gene expression on paternity

When females mate with more than one male, competition between rival ejaculates is expected to favour adaptations that promote fertilization success. There is now compelling evidence that sperm competition selects for increased production and allocation of sperm. However, sperm come packaged in ejaculates that also contain protein rich seminal fluids. Predicting how males should allocate individual seminal fluid proteins in response to sperm competition is hampered by our limited knowledge of their precise function. We use gene expression studies and interference RNA to ask how seminal fluid proteins in the ejaculate of a cricket, Teleogryllus oceanicus, affect a male's paternity share when in competition for fertilizations. We find that the relative expression of one seminal fluid gene, gagein, positively effects the paternity share of competing males, and that knockdown of this and two other seminal fluid protein genes renders males mating in the offensive role of sperm competition incapable of fathering living offspring. Despite having a negative effect on offspring viability these seminal fluid genes have been found to be up regulated in response to rival males, consistent with a role in promoting competitive fertilization success. Our data contribute to a growing body of evidence that, like sperm, seminal fluid gene expression is subject to post-mating sexual selection via sperm competition.

opencc-by-4.0Jul 2023View details →

Deep model predictive control of gene expression in thousands of single cells

Experimental data, training datasets, and trained models for our study on deep model predictive control of gene expression in bacteria. This data can be used to reproduce our results and figures. See our preprint here: <a href="https://www.biorxiv.org/content/10.1101/2022.10.28.514305">biorxiv.org/content/10.1101/2022.10.28.514305</a> And our code repository here: <a href="https://gitlab.com/dunloplab/deepcellcontrol">gitlab.com/dunloplab/deepcellcontrol</a> Contents: <ul> <li>datasets.zip: Formatted experimental data used to train and validate fluorescence forecasting models.</li> <li>experiments.zip: Processed data for all control experiments.</li> <li>misc.zip: Files necessary to reproduce some figures or to exactly reproduce some of our results.</li> <li>models.zip: Trained neural network models and associated files.</li> </ul>

opencc-zeroJul 2023View details →

Data from: Sorghum bicolor TX08001 nodal root tissue development gene expression profiling

<div class="page"> <div class="section"> <div class="layoutArea"> <div class="column"> Bioenergy sorghum's large nodal root system enables deposition of soil organic carbon deep in soil profiles aiding production of low carbon intensity biofuels from this crop. During bioenergy sorghum's long growing season, plants produce ~175 nodal roots In review bearing lateral roots that take up water and nutrients from >2 m deep in soil profiles, and aerial roots that support a complex phyllosphere. In the current study, nodal root bud development, a slow process spanning ~40 days, was characterized using microscopy and transcriptome analysis. A first ring of 10-15 nodal root buds was initiated in the stem pulvinus of phytomer 7 near sub-epidermal vascular bundles. A second ring of buds formed above the first ring much later in phytomer development. Nascent nodal root buds from phytomer 7 exhibited relatively high expression of pericycle marker genes (PFA) and genes involved in auxin transport (ABCB19, PIN4, LAX2), cytokinin signaling (TSO, MYB3R1), and cell proliferation (CYCB2;4, CDKB2;1, REM1). Following initiation, expression of genes involved in cell proliferation and cytokinin-signaling decreased while expression of genes involved in proliferative arrest, ABA-signaling, dormancy and stress tolerance increased. Further bud development was correlated with increased expression of WOX11 and PLT5 followed by PLT2, PLT4 and genes encoding RGF peptides that regulate PLT-expression and bud development. Expression of the ARF7-regulated LBD29, a gene required for nodal root formation, increased in parallel with increasing bud size to a maximum late in NRB development. Appearance of the nodal root bud cap late in development coincided with expression of SMB and FEZ, whereas genes such as WOX5 and two MYB36 family members were expressed at higher levels in outgrowing aerial roots. Genes involved in gibberellin, brassinosteroid, strigolactone, ethylene, jasmonate, salicyclic acid, and eATP signaling showed complex patterns of expression during nodal root bud formation. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for molecular analysis of networks that regulate nodal root development. </div> </div> </div> </div>

opencc-by-4.0Jan 2023View details →

Development of a pipeline for analyzing the gene expression profile of transcripts

<pre>Data corresponding to the scientific initiation project in bioinformatics. </pre> <pre>The data in the parcial_report_input folder are equivalent to raw counts, metadata and data of FPKM values of genes from the analysis performed during the first six months of the project. They correspond the counts and metadata from a previous study from renal cell carcinoma. As for the Final_report_input, it also contains counts and metadata, but from a previous study of ostesarcoma. The metadata and raw data files can be found under the accesion number hs000699.v1.p1 in dbGAP. The scripts wrote to perform pre-processing of samples, differential expression analysis, network analysis and functional annotation can be found in <a href="https://github.com/meidanis-lab/trans-pipeline">GitHub repository</a>. </pre>

opencc-zeroAug 2023View details →

Variable expression of cyanide detoxification and tolerance genes in cyanogenic and acyanogenic white clover (Trifolium repens L.)

Premise of the study: β-cyanoalanine synthase (β-CAS) and alternative oxidase (AOX) play important roles in the ability of plants to detoxify and tolerate hydrogen cyanide (HCN) stress. These functions are critical for all plants, as HCN is produced at low levels during basic metabolic processes, but are likely to be especially important in cyanogenic species, which release high levels of HCN following tissue damage. However, their expression has not been examined in cyanogenic species, nor has it been compared between cyanogenic and acyanogenic genotypes within a species. Methods: We used a natural polymorphism for cyanogenesis in white clover to examine β-CAS and Aox gene expression in relation to cyanogenesis-associated HCN exposure. We identified all β-CAS and Aox gene copies present in the genome, including members of the Aox1, Aox2a and Aox2d subfamilies previously reported in legumes. Expression levels were compared between cyanogenic and acyanogenic genotypes, and under conditions of leaf tissue damage compared to undamaged tissue. Key results: Results indicate that β-CAS and Aox2a expression are differentially elevated in cyanogenic genotypes, and that tissue damage is not required to induce this increased expression. Aox2d, in contrast, appears to be upregulated as a generalized wounding response. Conclusions: These findings suggest a heightened constitutive role for both HCN detoxification (via elevated β-CAS expression) and HCN-toxicity mitigation (via elevated Aox2a expression) in plants that are capable of cyanogenesis. As such, freezing-induced cyanide autotoxicity is unlikely to be the primary selective factor in the evolution of climate-associated cyanogenesis clines.

opencc-zeroAug 2023View details →

Takeout gene expression is associated with temporal kin recognition

A key component of parental care is avoiding killing and eating your own offspring. Many organisms commit infanticide of young but switch to parental care at the time when their own offspring would be expected, known as temporal kin recognition. It is unclear why such indirect kin recognition is so common across taxa. One possibility is that conserved mechanisms that regulate timing and feeding in other contexts are co-opted to enable the evolution of temporal kin recognition. Here we determine whether takeout, a gene implicated in coordinating feeding, influences temporal kin recognition in the subsocial beetle the roundneck sexton beetle, Nicrophorus orbicollis. We find that takeout expression is not associated with non-parental feeding changes resulting from hunger, or in the general switch to the full parental care repertoire. However, beetles that accepted and provided care to their offspring had a higher takeout expression than beetles that committed infanticide. Together, these data support the idea that the evolution of temporal kin recognition may be enabled by co-option of mechanisms that integrate feeding behaviour in other contexts.