Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-cell in vivo imaging reveals light-initiated circadian oscillators in zebrafish

Circadian clock is a cell-autonomous time-keeping mechanism established gradually during embryonic development. Here we generated a transgenic zebrafish line carrying a destabilized fluorescent protein driven by the promoter of a core clock gene, nr1d1, to report in vivo circadian rhythm at the single-cell level. By time-lapse imaging of this fish line, we observed the sequential initiation of the reporter expression starting at photoreceptors in pineal gland then spreading to cells in other brain regions. Even within pineal gland, we found heterogeneous onset of nr1d1 expression in which each cell undergoes circadian oscillation superimposed over cell-type specific developmental trajectory. Furthermore, we found that single-cell expression of nr1d1 showed synchronous circadian oscillation under light-dark cycle. Remarkably, single-cell oscillations were lost in animals raised under constant darkness while developmental trend still persists. It suggests that light exposure in early clock development initializes cellular clocks rather than synchronizes existing individual oscillators as previously believed.
The complete chloroplast genome of Horsfieldia hainanensis, an Endangered species with extremely small populations

Abstract Horsfieldia hainanensis is an Endangered species with extremely small populations, inhabiting the dense forest in ravines. It has high development and utilization value in the seed oil, fatty acids, volatile oils, and liposoluble constituent. In this study, the complete chloroplast genome of Horsfieldia hainanensis was sequenced. It is 155,774 bp in size with a typical quadripartite structure: a large single-copy (LSC) region of 87,124 bp, a small single-copy (SSC) region of 20,612 bp, and 2 inverted repeat (IR) regions of 24,020 bp. The genome contains 117 genes, including 75 protein-coding genes, 34 tRNA genes, and 8 rRNA genes, 13 genes have one intron and 3 three genes have two introns. The overall GC contents of the chloroplast genome was 39.1%. The phylogenetic tree based 11 complete chloroplast genome sequences of Magnoliales shows that H. hainanensis is closely related to Horsfieldia pandurifolia.
Visualising confirmation of the endophytic relationship of Metarhizium anisopliae with maize roots using molecular tools and fluorescent labelling

ABSTRACT Metarhizium anisopliae, an entomopathogenic fungus, is found to contribute to plant nutrient uptake and condidered as a plant endophyte. However, there is very little visual evidence that demonstratrates the endophytic relationship. Since the incidence of Metarhizium within host plants may be ephemeral or of limited distribution within host tissue, visualisation is reliant on both presence and the ability to detect the fungus even when present at low levels. We inoculated maize seeds with an egfp-labelled isolate of M. anisopliae, and then detected the egfp fragment by qualitative and quantitative PCR, and examined fluorescence of mycelia in the inoculated roots by laser scanning confocal microscopy (LSCM). The optimised PCR qualitatively identified the presence of egfp-labelled M. anisopliae at a 1:3000 M. anisopliae-maize DNA ratio. Root samplings of inoculated plants at intervals over 24 days were discovered egfp-labelled fragments with 14-d roots having the highest proportion with amplification. The egfp-label concentrations ranged very low in 2.976 × 10−7.42∼−7.02 ng/μL, with a rise process in 4–11 days after M. anisopliae treatment. Under LSCM, fluorescent mycelia in roots were identified, and the clear images were captured to show hyphal development extending along a longitudinal line of root cells and even forming a hyphal mass in the intercellular space. There were many hyphae at the branch junctions of the lateral roots. The methodology used to detect the fungus will be important for exploring the multi-trophic function of M. anisopliae and co-evolution in plants.
Molecular polymorphism in dentate lavender from littoral Algerian

Overexploitation of plant species leads to their reduction which requires strategies for improvement and management of resources . This study aims toseek a genetic polymorphism between the different dentate lavender populations collected in the Algerian littoral. Populations of Lavandula dentata were sampled in different ecoregions. The genotypic difference between the six populations was measured by the RAPD-PCR method using 8 RAPD primers and molecular phylogeny was performed by cluster analysis. The RAPD electrophoretic diagrams of the 6 populations of Lavandula dentata showed a rate of 50.49% of polymorphic bands. The dendrogram obtained via cluster analysis allowed us to group the populations into 2 clusters with a similarity index> 68% which showed that they are genetically close despite their geographical distance.
The Effects of Molecular and Biochemical Disruptions Posed by Harm-Reduction Tobacco Products on Developing Tissues Using Human Pluripotent Stem Cells

Author(s): Walker, Lauren | Advisor(s): zur Nieden, Nicole I | Abstract: Focus on tobacco-related disease concerns has shifted from cigarettes to other forms of tobacco use over the last 20 years. Due to their perception as “safer than a cigarette” by the general public, harm-reduction tobacco products (HRTPs) offer an appealing alternative for women struggling with nicotine addiction who find themselves pregnant. Some studies, however, suggest that HRTPs may increase risk of adverse pregnancy outcomes and hinder fetal skeletal development. To date, the mechanistic etiology of HRTP embryotoxicity is unreported. This thesis aims to address this knowledge gap by answering some of the questions surrounding how HRTPs molecularly and biochemically cause changes in the developing skeleton. Early in vivo studies reported herein indicated that HRTP exposure directly targets early osteogenesis of the skull following in utero exposure of mouse embryos. To explore the molecular etiology of this outcome, the embryonic stem cell test (EST) protocol was adapted to an in vitro model of developmental osteogenesis using human pluripotent stem cells (hPSCs). Cultures were concurrently exposed to conventional sidestream cigarette smoke (CSC), harm-reduction sidestream cigarette smoke (HSC), or harm-reduction Snus smokeless tobacco extract (STE). While conventional and harm-reduction extracts both inhibited in vitro osteogenesis, only the HSC and STE harm-reduction extracts did so at sub-cytotoxic doses. Furthermore, inhibitory doses increased cellular levels of reactive oxygen species and reduced endogenous antioxidant enzyme activity. Molecular analysis found that CSC exposure incurred both DNA damage and a concurrent apoptotic response that was absent in cultures exposed to either HRTP extract. Biochemical exploration of HRTP impact on developing cultures found exclusive activation of survival kinase AKT and reduction of stress rescue kinase JNK in STE-exposed cultures. Concurrent treatment with an isoform-specific inhibitor of AKT or JNK activator rescued osteogenesis in STE cultures, implicating the specific misregulation of these kinases in poor osteogenic outcomes. Global proteomic analysis of AKT signaling targets also identified exclusive hyperphosphorylation of FOXO transcription factors—required for oxidative stress defense and adult bone homeostasis—in STE-treated cultures, marking FOXOs for nuclear exclusion. Collectively, our data suggest that HRTPs inhibit normal osteogenesis by disrupting the balance between embryonic osteogenesis, survival, and redox equilibrium mechanisms.
Optimized protocol to isolate high quality genomic DNA from different tissues of a palm species

ABSTRACT The application of molecular techniques to tackle ecological and evolutionary questions requires genomic DNA in good quality and quantity. The quality of the isolated DNA, however, can be influenced by the tissue type and the way the sample was conserved and manipulated. Therefore, customizing protocols to improve the DNA isolation and locus amplification is crucial. We optimized a cheap and manual protocol of DNA extraction and microsatellites amplification using five different tissues of a palm species of the brazilian Atlantic Forest. We successfully extracted DNA from all five tissue types. Leaf, stem, and endocarp of non-dispersed seeds presented the highest rates of successful DNA extraction and microsatellite amplification; whereas root, endocarp of dispersed seeds, and embryo showed the lowest quality and quantity. Based on these results, we discussed the implications of using different tissues for studies about seed dispersal, pollination, and population genetics.
Effects of cereals as agro-ecological service crops and no-till on organic melon, weeds and N dynamics.

ABSTRACT In a two-year field experiment undertaken in Central Italy, different agro-ecological service crops (ASCs), terminated by the no-till roller crimper technology before organic melon production (Cucumis melo L.), were evaluated by assessing soil-plant N dynamics, weed management and crop performance, and by comparing with a tilled control without ASC. The ASCs (Poaceae, i.e. rye, barley, wheat, spelt and their mixture), were characterised in terms of aboveground biomass, N uptake, C : N ratio and degradation rate. During the melon growth cycle, soil mineral N (SMN), weed density and biomass were measured and the design of trial included weeded and unweeded plots. The yield and concentrations of soluble solids of the melon was measured. The ASC mulches differed in their N supply capacity and degradation rate. Rye and spelt were the best in terms of weed control, with approximately 80% lower weed density and weed biomass for either rye or spelt compared with the control. Wheat was the least effective against weeds, but it enhanced SMN. Melon yields were similar in plots with spelt and rye, weeded and unweeded treatments, but were reduced in the unweeded control (−58.5%) and barley treatment (−41.2%), compared with the respective weeded treatments. The low melon yield in the plots with rye suggested a negative allelopathic rye-melon interaction. The results highlighted that the ASCs were able to regulate, to different extents, the agro-ecosystem interactions.
Molecular game theory for a toxin-dominant food chain model

Abstract Animal toxins that are used to subdue prey and deter predators act as the key drivers in natural food chains and ecosystems. However, the predators of venomous animals may exploit feeding adaptation strategies to overcome toxins their prey produce. Much remains unknown about the genetic and molecular game process in the toxin-dominant food chain model. Here, we show an evolutionary strategy in different trophic levels of scorpion-eating amphibians, scorpions and insects, representing each predation relationship in habitats dominated by the paralytic toxins of scorpions. For scorpions preying on insects, we found that the scorpion α-toxins irreversibly activate the skeletal muscle sodium channel of their prey (insect, BgNaV1) through a membrane delivery mechanism and an efficient binding with the Asp/Lys-Tyr motif of BgNaV1. However, in the predatory game between frogs and scorpions, with a single point mutation (Lys to Glu) in this motif of the frog's skeletal muscle sodium channel (fNaV1.4), fNaV1.4 breaks this interaction and diminishes muscular toxicity to the frog; thus, frogs can regularly prey on scorpions without showing paralysis. Interestingly, this molecular strategy also has been employed by some other scorpion-eating amphibians, especially anurans. In contrast to these amphibians, the Asp/Lys-Tyr motifs are structurally and functionally conserved in other animals that do not prey on scorpions. Together, our findings elucidate the protein-protein interacting mechanism of a toxin-dominant predator-prey system, implying the evolutionary game theory at a molecular level.
Large-scale ciliary reversal mediates capture of individual algal prey by Müller’s larva

We documented capture of microalgal prey by several species of wild-caught Müller’s larvae of polyclad flatworm. To our knowledge, this is the first direct observation of feeding mechanism in this classical larval type. High-speed video recordings show that virtually all captures are mediated by large-scale transient ciliary reversal over one or more portions of the main ciliary band corresponding to individual lobes or tentacles. Local ciliary beat reversals alter near-field flow to suck parcels of food-containing water mouthward. Many capture episodes entail sufficient coordinated flow disruption that these compact-bodied larvae tumble dramatically. Similar behaviors were recorded in at least four distinct species, one of which corresponds to the ascidian-eating polyclad Pseudoceros.
Characterization of some Egyptian Sheep Populations Using Microsatellite and Protein Markers

Three Egyptian sheep populations, collected from three geographically isolated regions namely Siwa, El-Dakhla and El-Farafra oases of the Egyptian western desert, were investigated using six polymorphic microsatellite markers and electrophoretic protein by SDS-PAGE. Six polymorphic microsatellite markers and electrophoretic protein were used to reveal that the genetic diversity, conduct genetic structure and assignment of microsatellite. The results indicated that; one hundred and five alleles were detected; 34 are common alleles and 71 specific alleles across six loci (67.62%). Thirteen specific alleles for Siwa sheep population ranged from 1 to 5. Also, for Dakhla sheep population 21 alleles ranged from 1 to 8. While 37 ones were obtained in the case of Farafra sheep population ranging from 1 to 14. When the heterozygotsity is high we will have the highest effective number of alleles (ENA) and the expected heterozygosity (gene diversity). The highest ENA was 10.29 for BM1314 when HE was 0.94, while the lowest ENA was 2.22 for BM8125 when HE was 0.58 with El-Dakhla sheep population. The protein profile for 33 sheep population samples collected from three different regions, Siwa had 20 protein bands that MW ranged from 17 to 269KDa. At the same concentration of protein and molecular weight, the band's volume or intensity values changed from sample to other. The homogeneity of individual Siwa samples was 30%. ElDakhla population had 23 protein bands that ranged from17 to 283KDa. The heterogeneity’s El -Dakhla population was 74%. While, Elfarfra populations varied in electrophoretic protein pattern, it had 21 bands that ranged from 17 to 252 KDa. The homogeneity percentage was 24%. Finally, protein profile can be used as a marker depending on the presence or absence bands, band intensity, molecular weight and relative front values.
Chloride dynamics alter the input-output properties of neurons

Fast synaptic inhibition is a critical determinant of neuronal output, with subcellular targeting of synaptic inhibition able to exert different transformations of the neuronal input-output function. At the receptor level, synaptic inhibition is primarily mediated by chloride-permeable Type A GABA receptors. Consequently, dynamics in the neuronal chloride concentration can alter the functional properties of inhibitory synapses. How differences in the spatial targeting of inhibitory synapses interact with intracellular chloride dynamics to modulate the input-output function of neurons is not well understood. To address this, we developed computational models of multi-compartment neurons that incorporate experimentally parametrised mechanisms to account for neuronal chloride influx, diffusion, and extrusion. We found that synaptic input (either excitatory, inhibitory, or both) can lead to subcellular variations in chloride concentration, despite a uniform distribution of chloride extrusion mechanisms. Accounting for chloride changes resulted in substantial alterations in the neuronal input-output function. This was particularly the case for peripherally targeted dendritic inhibition where dynamic chloride compromised the ability of inhibition to offset neuronal input-output curves. Our simulations revealed that progressive changes in chloride concentration mean that the neuronal input-output function is not static but varies significantly as a function of the duration of synaptic drive. Finally, we found that the observed effects of dynamic chloride on neuronal output were entirely mediated by changes in the dendritic reversal potential for GABA. Our findings provide a framework for understanding the computational effects of chloride dynamics on dendritically targeted synaptic inhibition. Author Summary The fundamental unit of computation in the brain is the neuron, whose output reflects information within the brain. A determining factor in the transfer and processing of information in the brain is the modulation of activity by inhibitory synaptic inputs. Fast synaptic inhibition is mediated by the neurotransmitter GABA binding to GABAA receptors, which are permeable to chloride ions. How changes in chloride ion concentration affect neuronal output is an important consideration for information flow in the brain that is currently not being thoroughly investigated. In this research, we used multi-compartmental models of neurons to link the deleterious effects that accumulation of chloride ions can have on inhibitory signalling with changes in neuronal ouput. Together, our results highlight the importance of accounting for changes in chloride concentration in theoretical and computer-based models that seek to explore the computational properties of inhibition.
Root and shoot competition lead to contrasting competitive outcomes under water stress: A Meta-analysis

Background Competition is a critical process that shapes plant communities and interacts with environmental constraints. Though important to natural communities and agricultural systems, there are surprising knowledge gaps related to mechanisms that belie those processes: the contribution of different plant parts on competitive outcomes and the effect of environmental constraints on these contributions. Objective Studies that partition competition into root-only and shoot-only interactions assess whether plant parts impose different competitive intensities using physical partitions and serve as an important way to fill knowledge gaps. Given predicted drought escalation due to climate change, we focused meta-analytic techniques on the effects of water supply and competitive outcomes. Methods We searched Web of Science for peer-reviewed studies and found 2042 results. From which six suitable studies with 92 effect sizes on 10 species were identified to test these effects. Results Water availability and competition treatment (root-only, shoot-only, and full plant competition) significantly interact to affect plant growth responses (p < 0.0001). Root-only and full plant competition are more intense in low water availability conditions than shoot-only competition. Shoot-only competition in high-water availability was the most intense showing the opposite pattern. These results also show that the intensity of full competition is similar to root-only competition and that low-water availability intensifies root competition while weakening shoot competition. Conclusions These results emphasize the importance of root competition and these patterns of competition may shift in a changing climate, creating further urgency for further filling knowledge gaps to address issues of drought on plant interactions and communities.
Speech recognition system for Turkish language with hybrid method

Currently, technological developments are accompanied by a number of associated problems. Security takes the first place amongst such problems. In particular, biometric systems such as authentication constitute a significant fraction of the security problem. This is because sound recordings having connection with various crimes are required to be analysed for forensic purposes. Authentication systems necessitate transmission, design and classification of biometric data in a secure manner. The aim of this study is to actualise an automatic voice and speech recognition system using wavelet transform, taking Turkish sound forms and properties into consideration. Approximately 3740 Turkish voice samples of words and clauses of differing lengths were collected from 25 males and 25 females. The features of these voice samples were obtained using Mel-frequency cepstral coefficients (MFCCs), Mel-frequency discrete wavelet coefficients (MFDWCs) and linear prediction cepstral coefficient (LPCC). Feature vectors of the voice samples obtained were trained with k-means, artificial neural network (ANN) and hybrid model. The hybrid model was formed by combining with k-means clustering and ANN. In the first phase of this model, k-means performed subsets obtained with voice feature vectors. In the second phase, a set of training and tests were formed from these sub-clusters. Thus, for being trained more suitable data by clustering increased the accuracy. In the test phase, the owner of a given voice sample was identified by taking the trained voice samples into consideration. The results and performance of the algorithms used for classification are also demonstrated in a comparative manner.
Natural LXRβ agonist stigmasterol confers protection against excitotoxicity after hypoxia- reoxygenation (H/R) injury via regulation of mitophagy in primary hippocampal neurons

Ischemic brain injury represents insufficient oxygen supply to the brain and further damage occurs upon reoxygenation due to elevated intracellular levels excitatory neurotransmitter glutamate and subsequent production of reactive oxygen species (ROS) which has long been related to neuronal cell death of hippocampus brain region. Previously, using cell biological assay and transcriptomics analysis we reported that naturally occurring phytosterol Stigmasterol (ST) promotes brain development and function through the enhancement of neuronal cytoarchitectural complexity and functional maturation in rat hippocampal neurons by induction of immediate early genes (IEGs). In the present study we investigated the STs role in neuroprotection and found that ST also dose-dependently increased the neuronal viability in hypoxia reoxygenation (H/R) induced injury at hippocampal culture. ST, at an optimal concentration of 20 μM, significantly reduced the transport of vesicular glutamate (VGULT1), synaptic vesicle pool size, expression of GluN2B, rate of ROS formation (DCFDA) but restore mitochondrial membrane potential (JC1) and DNA fragmentation (H2AX) against H/R induced injury. More interestingly, ST also significantly induces the expression of autophagy marker protein LC3BII and the adaptor protein P62 but not HSC70 which indicates STs capability of induction of chaperon independent autophagy at H/R treated cultures. Furthermore densitometric analysis reveals ST also significantly increases PINK1 (PTEN induced protein kinase 1) expression therefore, indicates its role in mitophagy. In addition, molecular dynamic simulations study indicates that ST bind to LXRβ and forms hydrogen bonds with ASN239, GLU281, ARG319, THR316, SER278, ASN239 and SER278 residues at high occupancy with GLU281(20.21%) and ARG319 (21.04%,) residues, which is necessary for sterol binding to the LXRβ. Taken together these findings suggest that neuroprotective effect of ST might be associated with anti-excitatory and anti-oxidative actions on CNS neurons and could be a promising drug candidate for the treatment or prevention of ischemic stroke related neurological disorders.