Miracle-dz/UniFAR-FTUs huggingface dataset:
Resynthesis: Marker-Based Partial Reconstruction of Elite Genotypes in Clonally-Reproducing Plant Species

We propose a method for marker-based selection of cultivars of clonally-reproducing plant species which keeps the basic genetic architecture of a top-performing cultivar (usually a partly heterozygous genotype), with some agronomically relevant differences (such as production time, product appearance or quality), providing added value to the product or cultivation process. The method is based on selecting a) two complementary nearly-inbred lines from successive selfing generations (ideally only F2 and F3) of large size, that may generate individuals with most of their genome identical to the original cultivar but being homozygous for either of the two component haplotypes in the rest, and b) individuals with such characteristics already occurring in the F2. Option a) allows for introgressing genes from other individuals in one or both of these nearly-inbred lines. Peach, a woody-perennial, clonally-reproduced species, was chosen as a model for a proof of concept of the Resynthesis process due to its biological characteristics: self-compatibility, compact and genetically well-known genome, low recombination rates and relatively short intergeneration time (3-4 years). From 416 F2 seedlings from cultivar Sweet Dream (SD), we obtained seven individuals with 76-94% identity with SD, and selected five pairs of complementary lines with average homozygosity of the two parents ≥0.70 such that crossing would produce some individuals highly similar to SD. The application of this scheme to other species with more complex genomes or biological features, including its generalization to F1 hybrids, is discussed.
Computational analysis of ligand dose range thermal proteome profiles

Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. We present a statistical analysis method with reliable control of the false discovery rate and apply it to several datasets probing epigenetic drugs. We detect off-target drug engagement in unrelated protein families.
Identification of erythroid cell positive blood transcriptome phenotypes associated with severe respiratory syncytial virus infection

Biomarkers to assess the severity of acute respiratory syncytial virus (RSV) infection are needed. We conducted a meta-analysis of 490 unique profiles from six public RSV blood transcriptome datasets. A repertoire of 382 well-characterized transcriptional modules was used to define dominant host responses to RSV infection. The consolidated RSV cohort was stratified according to four traits: “interferon response” (IFN), “neutrophil-driven inflammation” (Infl), “cell cycle” (CC), and “erythrocytes” (Ery). Eight prevalent blood transcriptome phenotypes were thus identified. Among those three Ery+ phenotypes comprised higher proportions of patients requiring intensive care. We posit that the erythrocyte module is linked to an overabundance of immunosuppressive erythroid cells that might underlie progression to severe RSV infection. These findings outline potential priority areas for biomarker development and investigations into the immune biology of RSV infection. The approach that was employed here will also permit to delineate prevalent blood transcriptome phenotypes in other settings.
Flies improve the salience of iridescent sexual signals by orienting toward the sun

Sunlight is the ultimate source of most visual signals. Theory predicts strong selection for its effective use during communication, with functional links between signal designs and display behaviours a likely result. This is particularly true for iridescent structural colours, whose moment-to-moment appearance bears a heightened sensitivity to the position of signallers, receivers, and the sun. Here we experimentally tested this prediction using Lispe cana, a muscid fly in which males present their structurally coloured faces and wings to females during ground-based sexual displays. In field-based assays we found that males actively bias the orientation of their displays toward the solar azimuth under conditions of full sunlight and do so across the entire day. This bias breaks down, however, when the sun is naturally concealed by heavy cloud or experimentally obscured. Our modelling of the appearance of male signals revealed clear benefits for the salience of male ornaments, with a roughly four-fold increase in subjective luminance achievable through accurate display orientation. These findings offer fine-scale, causal evidence for the active control of sexual displays to enhance the appearance of iridescent signals. More broadly, they speak to predicted coevolution between dynamic signal designs and presentation behaviours, and support arguments for a richer appreciation of the fluidity of visual communication.
Impact of Thiol–Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin-Converting Enzyme 2 Receptor

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the genus Betacoronavirus, which also includes SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). The angiotensin-converting enzyme 2 (ACE2) is the functional receptor for SARS-CoV and SARS-CoV-2 to enter the host cells. In particular, the interaction of viral spike proteins with ACE2 is a critical step in the viral replication cycle. The receptor binding domain of the viral spike proteins and ACE2 have several cysteine residues. In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. The impact on the binding affinity was less severe when the disulfide bridges of only one of the binding partners were reduced to thiols. This computational finding provides a molecular basis for the severity of COVID-19 infection due to the oxidative stress.
Striped Distribution Pattern of Purkinje Cells of Different Birthdates in the Mouse Cerebellar Cortex Studied with the Neurog2-CreER Transgenic Line

Heterogeneity of Purkinje cells (PCs) that are arranged into discrete longitudinal stripes in the cerebellar cortex is related to the timing of PC generation. To understand the cerebellar compartmental organization, we mapped the PC birthdate (or differentiation timing) in the entire cerebellar cortex. We used the birthdate-tagging system of neurog2-CreER (G2A) mice hybridized with the AldocV strain which clarifies the zebrin (aldolase C) longitudinal striped pattern. The pattern of the birthdate-dependent PC distribution was arranged consistently into longitudinally-oriented stripes throughout almost all lobules except for the nodulus, paraflocculus and flocculus, in which distinct stripes were observed.Boundaries of the PC birthdate stripes were found either in the middle or coincided with that of the zebrin stripes. PCs in each birthdate stripe were born in various periods between embryonic day (E) 10.0 and E 13.5. In the vermis, PCs were chronologically distributed from lateral to medial stripes. In the paravermis, PCs of early birthdates were distributed in the long lateral zebrin-positive stripe (stripe 4+//5+) and the medially neighboring narrow zebrin-negative substripe (3d-//e2-), while PCs of late birthdates were distributed in the rest of all paravermal areas. In the hemisphere, PCs of early and late birthdates were intermingled in the majority of areas. The results indicate that the birthdate of a PC is a partial determinant for the zebrin compartment in which it is located. However, the correlation between the PC birthdate and the zebrin compartmentalization is not simple, and distinct among the vermis, paravermis, hemisphere, nodulus, and flocculus. Highlights Birthdates of Purkinje cells (PCs) were mapped on the cerebellar zebrin striped pattern by using Neurog2-CreER (G2A) mice. The vermis, paravermis, hemisphere, nodulus, and flocculus had distinct longitudinally-striped patterns of PC birthdate distribution. PCs in each birthdate stripe were born in various periods between embryonic day (E) 10.0 and E 13.5. Boundaries of PC birthdate distributions were located at the boundaries of zebrin stripes or in the middle of a zebrin stripe. The results indicate that the PC birthdate is a partial determinant for the zebrin compartment in which a PC is located.
The winning methods for predicting cellular position in the DREAM single cell transcriptomics challenge

Motivation Predicting cell locations is important since with the understanding of cell locations, we may estimate the function of cells and their integration with the spatial environment. Thus, the DREAM Challenge on Single Cell Transcriptomics required participants to predict the locations of single cells in the Drosophila embryo using single cell transcriptomic data. Results We have developed over 50 pipelines by combining different ways of pre-processing the RNA-seq data, selecting the genes, predicting the cell locations, and validating predicted cell locations, resulting in the winning methods for two out of three sub-challenges in the competition. In this paper, we present an R package, SCTCwhatateam, which includes all the methods we developed and the Shiny web-application to facilitate the research on single cell spatial reconstruction. All the data and the example use cases are available in the Supplementary material. Availability The scripts of the package are available at https://github.com/thanhbuu04/SCTCwhatateam and the Shiny application is available at https://github.com/pvvhoang/SCTCwhatateam-ShinyApp Contact Thuc.Le@unisa.edu. au Supplementary information Supplementary data are available at Briefings in Bioinformatics online.
Neuropathic Pain Linked to Defective Dopaminergic Inhibition in Anterior Cingulate Cortex

Pyramidal neurons in the anterior cingulate cortex (ACC), a prefrontal region involved in processing the affective components of pain, display hyperexcitability in chronic neuropathic conditions and their silencing abolishes hyperalgesia in rodents. We show here that dopamine, through D1-like receptor signaling, inhibits layer 2/3 pyramidal neurons of mouse ACC. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels control the firing activity of these pyramidal neurons. Through Gs-coupled D1-like receptors, dopamine induces the opening of HCN channels at physiological membrane potentials, driving a significant decrease in input resistance and excitability. Systemic L-DOPA rescues HCN channel activity, pyramidal excitability in ACC as well as sensory phenotype in neuropathic mice while microinjection of a selective D1-like agonist in ACC induces relief of ongoing pain in neuropathic animals. We conclude that decreased dopaminergic inhibition in ACC plays a critical role in an abnormal top-down modulation leading to neuropathic pain.
Fatigue Indices and Perceived Exertion Highlight Ergometer Specificity for Repeated Sprint Ability Testing

This study aimed to compare the time course of measures of performance, fatigue, and perceived exertion during repeated-sprint ability (RSA) testing performed on a non-motorized treadmill (NMT) and cycling ergometer (CE). Fourteen physically active participants performed two 10 ×6 s−1 RSA tests with a 1:4 work-to-rest ratio (24 s recovery) on NMT and CE. Measures of performance [peak and mean power output (PPO and MPO), cadence, and the time to reach PPO (TTP)] and of fatigue (fatigue index and decrement score) and ratings of perceived exertion (RPE) were collected during each session. The level of significance was set at p < 0.05. Participants completed the RSA test at a MPO of 1,041 ± 141 W on CE and 431 ± 48 W on NMT, achieving PPO of 2,310 ± 339 W on CE and 1,763 ± 289 W on NMT. Participants' weight was significantly correlated with PPO and MPO on CE (p < 0.001) and with MPO on NMT (p < 0.001). PPO on CE and NMT was significantly correlated only for absolute measures of power (p < 0.01). Cadence was higher and decreased throughout the RSA on NMT compared to CE, where it decreased only at the seventh bout. TTP was significantly shorter and more affected by fatigue on NMT than on CE. Fatigue indices were significantly greater on NMT compared to CE, with significant correlations between the decrement score and absolute and relative PPO on CE and NMT, between the fatigue index and absolute and relative PPO only on NMT, and no significant correlations with MPO. During RSA, RPE increased more on NMT compared to CE from bouts 3 to 7. During recovery, RPE was consistently higher on NMT at 1, 3, and 5 min post exercise compared to CE. These findings indicate that RSA performed on NMT induces greater fatigue and physiological load than CE, which originated in the lower resistive torque typically used on NMT compared to CE, resulting in a front loaded power output profile from the greater acceleration and cadence. From these results, we discuss that despite providing highly correlated measures of power output, NMT and CE should not be used interchangeably to assess RSA as they elicit markedly different responses. We also discuss these results from the fundamental differences in active muscle mass and power application patterns between running and cycling, which could form the basis of future studies.
An evolutionarily conserved metallophosphodiesterase is a determinant of lifespan in Drosophila

Evolutionarily conserved genes usually have a critical role to play during organismal aging and longevity. Here, we show that a previously uncharacterized Class III metallophosphoesterase in Drosophila, an ortholog of the MPPED1 and MPPED2 proteins in mammals, is necessary for optimal lifespan. dMPPED is the product of the gene CG16717 and hydrolyzed a variety of phosphodiester substrates in a metal-dependent manner. dMPPED was expressed widely during development and in the adult fly. Deletion of the gene in flies dramatically reduced lifespan, without affecting development or fecundity. Longevity was restored on ubiquitous expression of the protein, and neuronal expression of both wild type and the catalytically inactive form of dMPPED was also able to restore normal lifespan. Overexpression of the protein, both ubiquitously and neuronally in wild type flies extended lifespan by ~ 20%. RNA-seq analysis of dMPPEDKO flies revealed mis-regulation of innate immune pathways, a number of transcription factors and genes earlier reported to affect aging and lifespan. Importantly, neuronal expression of mammalian MPPED2 was able to rescue lifespan in dMPPEDKO flies, but not extend lifespan in wild type flies. This reports the first description of the biological role of an evolutionarily conserved metallophosphoesterase that may serve as a scaffolding protein in diverse signaling pathways to modulate longevity in the fly.
Loss of Arid1a Promotes Neuronal Survival Following Optic Nerve Injury

Trauma or neurodegenerative diseases trigger the retrograde death of retinal ganglion cells (RGCs), causing an irreversible functional loss. AT-rich interaction domain 1A (ARID1A), a subunit of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex, has been shown to play crucial roles in cell homeostasis and tissue regeneration. However, its function in adult RGC regeneration remains elusive. Here, we show that optic nerve injury induces dynamic changes of Arid1a expression. Importantly, deleting Arid1a in mice dramatically promotes RGC survival, but insignificantly impacts axon regeneration after optic nerve injury. Next, joint profiling of transcripts and accessible chromatin in mature RGCs reveals that Arid1a regulates several genes involved in apoptosis and JAK/STAT signaling pathway. Thus, our findings suggest modulation of Arid1a as a potential therapeutic strategy to promote RGC neuroprotection after damage.
Polishing copy number variant calls on exome sequencing data via deep learning

Accurate and efficient detection of copy number variants (CNVs) is of critical importance due to their significant association with complex genetic diseases. Although algorithms that use whole genome sequencing (WGS) data provide stable results with mostly-valid statistical assumptions, copy number detection on whole exome sequencing (WES) data shows comparatively lower accuracy. This is unfortunate as WES data is cost efficient, compact and is relatively ubiquitous. The bottleneck is primarily due to non-contiguous nature of the targeted capture: biases in targeted genomic hybridization, GC content, targeting probes, and sample batching during sequencing. Here, we present a novel deep learning model, DECoNT, which uses the matched WES and WGS data and learns to correct the copy number variations reported by any off-the-shelf WES-based germline CNV caller. We train DECoNT on the 1000 Genomes Project data, and we show that we can efficiently triple the duplication call precision and double the deletion call precision of the state-of-the-art algorithms. We also show that our model consistently improves the performance independent from (i) sequencing technology, (ii) exome capture kit and (iii) CNV caller. Using DECoNT as a universal exome CNV call polisher has the potential to improve the reliability of germline CNV detection on WES data sets.
Converting endogenous genes of the malaria mosquito into simple non-autonomous gene drives for population replacement

Gene drives for mosquito population replacement are promising tools for malaria control. However, there is currently no clear pathway for safely testing such tools in endemic countries. The lack of well-characterized promoters for infection-relevant tissues and regulatory hurdles are further obstacles for their design and use. Here we explore how minimal genetic modifications of endogenous mosquito genes can convert them directly into non-autonomous gene drives without disrupting their expression. We co-opted the native regulatory sequences of three midgut-specific loci of the malaria vector Anopheles gambiae to host a prototypical antimalarial molecule and guide-RNAs encoded within artificial introns, that support efficient gene drive. We assess the propensity of these modifications to interfere with the development of Plasmodium falciparum and their effect on fitness. Because of their inherent simplicity and passive mode of drive such traits could form part of an accepted testing pathway of gene drives for malaria eradication.
Whole Genome Sequences of Aedes aegypti (Linn.) Field Isolates from Southern India

Aedes spp. mosquitoes are a major health concern as they transmit several viral pathogens resulting in millions of deaths annually around the world. This is compounded by the emergence of insecticide-resistant strains and global warming, which could expose more than half of the world's population to Aedes-borne diseases in the future. Therefore, a comprehensive understanding of vector biology and the genomic basis of phenotypes such as insecticide resistance in natural populations are of paramount importance. Here, we sequenced the genome of Aedes aegypti mosquitos sampled from dengue-endemic areas and investigated the genetic variations between the previously reported laboratory-reared strain and our field isolates. The mosquito genomic DNA was used for paired-end sequencing using the Illumina platform. The reads were used for template-based assembly and mapped to the Aedes aegypti reference genome. Stringent parameters and multiple variant calling methods were used to identify unique single nucleotide variants (SNVs) and insertions-deletions (indels) and mapped to the Aedes chromosomes to create a draft consensus genome. Gene Ontology analyses was performed on the variant-enriched genes while two gene families involved in insecticide resistance were used for comparative sequence and phylogenetic analyses. Comparative sequence variant analyses showed that the majority of the high-quality variants in our samples mapped to non-coding regions of the genome, while gene ontology analyses of genic variants revealed enrichment of terms relevant to drug binding and insecticide resistance. Importantly, one mutation implicated in pyrethroid resistance was found in one Aedes sample. This is the first report of genome sequences of A. aegypti field isolates from India which reveals variants specific to the wild population. This is a useful resource which will facilitate development of robust integrated vector control strategies for management of Aedes-borne diseases through genetic manipulation of local mosquito populations.
Isolation, culture and characterization of primary cell lines of human buccal mucosal fibroblasts: A combination of explant enzamytic technique

Background: The cell culture technique has become a routine and a popular method for its wide applications in the field of cell biology and biotechnology and in medical research. Isolation of primary cells over the cancer cells is an essential component of cell culture technology as they are the reliable source to understand normal physiological, morphological and molecular process of human cells. As fibroblasts are the prominent cells of the connective tissue of oral mucosa, many disease entities and histogenesis are linked to fibroblasts. Culture of oral fibroblast cells helps the oral biologists and researchers to study the morphological and molecular process in the oral diseases. Aim: The aim of our experiment is to isolate and culture the human buccal mucosal fibroblast cells from healthy individuals using a combination of explant–enzymatic method and characterization of the cells by short tandem repeat (STR) profiling. Materials and Methods: The tissue samples were collected from healthy individuals undergoing routine impacted third molar extraction. A combination of explant–enzymatic technique was used for the isolation from the tissue samples. The cells were further subcultured, maintained and stored as per the standard protocols. Thus, to confirm the oral fibroblasts of human origin and its uniqueness, they were characterized using STR profiling. Results and Conclusion: Using the combination technique, we were successful in isolating the cells at a faster rate by detachment of cells on day 3 and confluency on day 10. The morphological assessment and STR profiling further confirmed that the isolated cell lines resemble human fibroblast cells.