Miracle-dz/UniFAR-FTUs huggingface dataset:
Homoeologous chromosome exchange explains the creation of a QTL affecting soil‐borne pathogen resistance in tobacco

Summary Crop plant partial resistance to plant pathogens controlled by quantitative trait loci (QTL) is desirable in cultivar development programmes because of its increased durability. Mechanisms underlying such resistance are difficult to study. We performed RNA‐seq analyses for tobacco (Nicotiana tabacum) nearly isogenic lines (NILs) with and without favourable allele(s) at Phn7.1, a major QTL influencing partial resistance to the soil‐borne pathogens Phytophthora nicotianae and Ralstonia solanacearum. Based upon combined analyses of transcriptome‐based sequence variation and gene expression profiles, we concluded that allelic variability at the Phn7.1 locus was likely generated from homoeologous exchange, which led to deletion of low‐expressing members of the SAR8.2 gene family and duplication of high‐expressing SAR8.2 genes from a different subgenome of allotetraploid tobacco. The high expression of endogenous Phn7.1‐associated SAR8.2 genes was correlated with observed resistance to P. nicotianae. Our findings suggest a role for genomic rearrangements in the generation of favourable genetic variability affecting resistance to pathogens in plants.
Repeated strand invasion and extensive branch migration are hallmarks of meiotic recombination

Currently favored models for meiotic recombination posit that both noncrossover and crossover recombination are initiated by DNA double strand breaks but form by different mechanisms, noncrossovers by synthesis dependent strand annealing, and crossovers by formation and resolution of double Holliday junctions centered around the break. This dual mechanism hypothesis predicts different hybrid DNA patterns in noncrossover and crossover recombinants. We show that these predictions are not upheld, by mapping with unprecedented resolution, parental strand contributions to recombinants at a model locus. Instead, break repair in both noncrossovers and crossovers involves synthesis-dependent strand annealing, often with multiple rounds of strand invasion. Crossover-specific double Holliday junction formation occurs via processes that involve branch migration as an integral feature and that can be separated from break repair itself. These findings reveal meiotic recombination to be a highly dynamic process and prompt a new view of the relationship between crossover and noncrossover recombination.
Asymmetry in the Partitioning of Surfactants into Lipid Membranes

Asymmetry in the Partitioning of Surfactants into Lipid Membranes Helen Y. Fan Doctor of Philosophy Graduate Department of Pharmaceutical Sciences University of Toronto 2017 The emergence of modern standards of public sanitation and personal hygiene was promoted by the invention and mass production of synthetic detergents/surfactants. Detergents insert into and permeabilize cell membranes, and solubilize them completely at higher concentrations; a thorough understanding of these phenomena is particularly important for the agriculture, pharmaceutical, and cosmetics industries. The complex cell membrane is often modelled with liposomes; detergent–membrane interactions have been described by a three-stage model, which assumes equilibrated interactions in that detergents flip-flop rapidly within the membrane bilayer. However, many detergents flip-flop slowly and become asymmetrically distributed in the membrane upon insertion (e.g., sodium dodecyl sulphate at room temperature). The works presented in this thesis aim to further our understanding of asymmetric detergent–membrane interactions and to advance the methodology of characterizing them. The methods applied in these works are spectroscopic and calorimetric in nature, and extended here by developments in quantitative analysis. They were used to investigate three very different detergents: surfactin, a lipopeptide that is negatively charged near neutral pH; 12:0 lysophosphocholine (12:0 LPC), a zwitterionic product of membrane lipid metabolism; and digitonin, a nonionic surfactant often used in membrane protein studies. These detergents share the common thread of asymmetry, but interact with and solubilize membranes in different ways: Surfactin equilibrates in the membrane upon reaching a threshold content in the outer leaflet; 12:0 LPC and digitonin stay in the outer leaflet and do not solubilize the membrane even at high concentrations (digitonin being more persistent in this than 12:0 LPC). As such, all equilibrating detergent–lipid interactions are alike, in that they can be described by the three-stage model; every nonequilibrating detergent–lipid interaction is asymmetric in its own way.
An analysis of polynomial sequences and their application to discrete fractional operators

We consider sequences of polynomials , where , together with both additive and multiplicative perturbations of them under rational functions. After demonstrating several algebraic and analytical properties of these sequences, we show that they can be used to prove new theorems in the qualitative analysis of discrete fractional operators, which are a class of nonlocal operators. Consequently, as an application of the algebraic results, we prove several theorems regarding conditions under which the positivity of the discrete fractional difference of f implies the monotonicity of f.
Characteristics of water solubility and color on edible film from bioselulosa nata nira siwalan with the additional of glycerol

Indonesia entered the ranks second in the world as a producer of plastic waste into the sea after China. Most of the plastic packaging is causing environmental pollution, unbiodegradable, expensive in recycling and contamination of foodstuffs packaged due to certain substances that migrate into the food. Edible film is a thin layer of transparent and made of materials that can be eaten very prospective and secure to provide selective detentions against the transfer of gas, steam, water and dissolved materials as well as protection against mechanical damage. Product development nata much utilized as raw material for paper and edible film, nata contains bioselulosa which is produced by the bacterium Acetobacter xylinum. So the researchers develop alternative modification of cellulose from nata nira siwalan. Glycerol is one of plasticizer selected researchers to be added in the manufacture of edible film. The purpose of this research is to know the concentration of glycerol that is most appropriate to get the edible film solubility characteristicsbioselulosa nata nira siwalan and to find out the optimum concentration of glycerol that is most appropriate to get the characteristics of colors edible film made from bioselulosa nata nira siwalan which is optimum. The research was carried out in December 2016-June 2017. Methods this study used a randomized complete design with four treatments and three replicates. The results of this study is the most appropriate concentration to get characteristics of water solubility on edible film bioselulosa nata nira siwalan is on treatment D with the addition of glycerol 30% of 0.42% and on the characteristics of color by value L (77.45), a (0.723) and b (9.96).
Efficacy of lettuce seed syrup on insomnia in patients with breast cancer: a pilot double blind randomized placebo controlled clinical trial

Abstract Objectives Insomnia and sleep disorders are common and can be severe amongst patients with cancer, especially during chemotherapy. The aim of this study was to evaluate the efficacy of lettuce seed syrup in breast cancer patients who suffer from insomnia or disordered sleep. Methods This pilot study was a double-blinded randomized controlled clinical trial conducted in Shoha-e-Tajrish Hospital (Tehran, Iran) from September 2018 to June 2019. 50 adult patients with breast cancer with insomnia or sleep disorders were enrolled. Participants were randomly allocated to lettuce seed syrup (5 mL twice daily), or placebo syrup at the same dose for four weeks. The Pittsburgh Sleep Quality Index (PSQI) was used to evaluate sleep quality before and after the intervention. Results Compared to placebo, the mean of the total PSQI score decreased significantly in participants who received lettuce seed syrup (p=0.014). In addition, there were statistically significant reductions in the mean scores of subject quality sleep (p=0.002), sleep duration (p=0.038), habitual sleep efficacy (p=0.029) and sleep disturbance (p=0.032) in patients who received lettuce seed syrup. Conclusions Lettuce seed syrup may improve self-reported sleep quality in participants with breast cancer. Larger trials are indicated in diverse samples of participants with caner to learn if these finds are generalizable.
Epiphyas intrepida sp. nov. (Lepidoptera: Tortricidae): an endemic, not a stowaway, on Lord Howe Island

The tortricid moth genus Epiphyas Turner, 1927, comprises 39 described species and is largely confined to the Australian mainland and Tasmania. Lord Howe Island is the only other place where more than one Epiphyas species is found, these being Epiphyas postvittana (Walker, 1863), a widely polyphagous and widespread horticultural pest commonly known as the ‘light brown apple moth’, and a second species identified by J. D. Bradley as Epiphyas aulacana (Meyrick, 1881). Because Lord Howe Island is on the UNESCO's world heritage register, it is important to distinguish native from exotic insects as a means for uncovering and managing biosecurity threats to the island. To test whether E. aulacana sensu Bradley is indeed conspecific with E. aulacana‐like moths from the Australian mainland and Tasmania, specimens from all three islands were examined, and nucleotide sequence data obtained and compared from the mitochondrial gene region cytochrome c oxidase subunit I (COI) and three nuclear gene regions: isocitrate dehydrogenase (IDH), malate dehydrogenase (MDH), and the carbomoylphosphate synthetase (CPS) domain of the gene known as CAD. The results suggest that the second species is not E. aulacana but a new species, Epiphyas intrepida sp. nov., which like its larval host plant Cassinia tenuifolia Bentham, 1867, is endemic to the island.
TCAB1 prevents nucleolar accumulation of the telomerase RNA to promote telomerase assembly

Localization of a wide variety of RNAs to non-membrane bound cellular compartments such as nucleoli, Cajal bodies, and stress-granules is critical for their function and stability. The molecular mechanisms that underly the recruitment and exclusion of specific RNAs from these phase-separated organelles is incompletely understood. Telomerase is a ribonucleoprotein (RNP) that is composed of the reverse transcriptase protein TERT, the telomerase RNA (TR), and several auxiliary proteins that associate with TR, including TCAB1. Here we show that in the absence of TCAB1, TR is tightly bound to the nucleolus, while TERT localizes to the nucleoplasm and is largely excluded from the nucleolus, significantly reducing telomerase assembly. Thus, nuclear compartmentalization by the non-membrane bound nucleolus counteracts telomerase assembly and TCAB1 is required to exclude the telomerase RNA from the nucleolus. Our work provides insight into the mechanism and functional consequences of RNA recruitment to organelles formed by phase separation proposes a new model explaining the critical role of TCAB1 in telomerase function.
Reconsider phase reconstruction in signals with dynamic periodicity from the modern signal processing perspective

Phase is the most fundamental physical quantity when we study an oscillatory time series. There are many tools aiming to estimate phase, most of them are developed based on the analytic function model. Unfortunately, this approach might not be suitable for modern signals with intrinsic nonstartionary structure, including multiple oscillatory components, each with time-varying frequency, amplitude, and non-sinusoidal oscillation, e.g., biomedical signals. Specifically, due to the lack of consensus of model and algorithm, phases estimated from signals simultaneously recorded from different sensors for the same physiological system from the same subject might be different. This fact might challenge reproducibility, communication, and scientific interpretation and thus we need a standardized approach with theoretical support over a unified model. In this paper, after summarizing existing models for phase and discussing the main challenge caused by the above-mentioned intrinsic nonstartionary structure, we introduce the adaptive non-harmonic model (ANHM), provide a definition of phase called fundamental phase, which is a vector-valued function describing the dynamics of all oscillatory components in the signal, and suggest a time-varying bandpass filter (tvBPF) scheme based on time-frequency analysis tools to estimate the fundamental phase. The proposed approach is validated with a simulated database and a real-world database with experts’ labels, and it is applied to two real-world databases, each of which has biomedical signals recorded from different sensors, to show how to standardize the definition of phase in the real-world experimental environment. Specifically, we report that the phase describing a physiological system, if properly modeled and extracted, is immune to the selected sensor for that system, while other approaches might fail. In conclusion, the proposed approach resolves the above-mentioned scientific challenge. We expect its scientific impact on a broad range of applications.
Prediction-error neurons in circuits with multiple neuron types: Formation, refinement, and functional implications

Predictable sensory stimuli do not evoke significant responses in a subset of cortical excitatory neurons. Some of those neurons, however, change their activity upon mismatches between actual and predicted stimuli. Different variants of these prediction-error neurons exist and they differ in their responses to unexpected sensory stimuli. However, it is unclear how these variants can develop and co-exist in the same recurrent network, and how they are simultaneously shaped by the astonishing diversity of inhibitory interneurons. Here, we study these questions in a computational network model with three types of inhibitory interneurons. We find that balancing excitation and inhibition in multiple pathways gives rise to heterogeneous prediction-error circuits. Dependent on the network’s initial connectivity and distribution of actual and predicted sensory inputs, these circuits can form different variants of prediction-error neurons that are robust to network perturbations and generalize to stimuli not seen during learning. These variants can be learned simultaneously via homeostatic inhibitory plasticity with low baseline firing rates. Finally, we demonstrate that prediction-error neurons can support biased perception, we illustrate a number of functional implications, and we discuss testable predictions.
Systemic regulation of nitrogen acquisition and use in Oryza longistaminata ramets under nitrogen heterogeneity

Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We studied the response of ramet pairs to heterogeneous nitrogen availability by using a split hydroponic system that allowed each ramet root to be exposed to different conditions. Ammonium uptake was compensatively enhanced in the sufficient-side root when roots of the ramet pairs were exposed to ammonium-sufficient and deficient conditions. Comparative transcriptome analysis revealed that a gene regulatory network for effective ammonium assimilation and amino acid biosynthesis was activated in the sufficient-side roots. Allocation of absorbed nitrogen from the nitrogen-sufficient to the deficient ramets was rather limited. Nitrogen was preferentially used for newly growing axillary buds on the sufficient-side ramets. Biosynthesis of trans-zeatin, a cytokinin, was up-regulated in response to the nitrogen supply, but trans-zeatin appears not to target the compensatory regulation. Our results also implied that the O. longistaminata ortholog of OsCEP1 plays a role as a nitrogen-deficient signal in inter-ramet communication, providing compensatory up-regulation of nitrogen assimilatory genes. These results provide insights into the molecular basis for efficient growth strategies of asexually proliferating plants growing in areas where nitrogen distribution is spatially heterogeneous. One sentence summary Oryza longistaminata, a rhizomatous wild rice, systemically regulates nitrogen acquisition and use in response to spatially heterogeneous nitrogen availability via inter-ramet communication.
DNA Replication-Transcription Conflicts Do Not Significantly Contribute to Spontaneous Mutations Due to Replication Errors in Escherichia coli

Because DNA replication and transcription occur on the same DNA template, encounters between the two machines occur frequently. When these encounters are head-to-head, genomic disruption can occur. ABSTRACT Encounters between DNA replication and transcription can cause genomic disruption, particularly when the two meet head-on. Whether these conflicts produce point mutations is debated. This paper presents detailed analyses of a large collection of mutations generated during mutation accumulation experiments with mismatch repair (MMR)-defective Escherichia coli. With MMR absent, mutations are primarily due to DNA replication errors. Overall, there were no differences in the frequencies of base pair substitutions or small indels (i.e., insertion and deletions of ≤4 bp) in the coding sequences or promoters of genes oriented codirectionally versus head-on to replication. Among a subset of highly expressed genes, there was a 2- to 3-fold bias for indels in genes oriented head-on to replication, but this difference was almost entirely due to the asymmetrical genomic locations of tRNA genes containing mononucleotide runs, which are hot spots for indels. No additional orientation bias in mutation frequencies occurred when MMR− strains were also defective for transcription-coupled repair (TCR). However, in contrast to other reports, loss of TCR slightly increased the overall mutation rate, meaning that TCR is antimutagenic. There was no orientation bias in mutation frequencies among the stress response genes that are regulated by RpoS or induced by DNA damage. Thus, biases in the locations of mutational targets can account for most, if not all, apparent biases in mutation frequencies between genes oriented head-on versus codirectional to replication. In addition, the data revealed a strong correlation of the frequency of base pair substitutions with gene length but no correlation with gene expression levels. IMPORTANCE Because DNA replication and transcription occur on the same DNA template, encounters between the two machines occur frequently. When these encounters are head-to-head, genomic disruption can occur. However, whether replication-transcription conflicts contribute to spontaneous mutations is debated. Analyzing in detail a large collection of mutations generated with mismatch repair-defective Escherichia coli strains, we found that across the genome there are no significant differences in mutation frequencies between genes oriented codirectionally and those oriented head-on to replication. Among a subset of highly expressed genes, there was a 2- to 3-fold bias for small insertions and deletions in head-on-oriented genes, but this difference was almost entirely due to the asymmetrical locations of tRNA genes containing mononucleotide runs, which are hot spots for these mutations. Thus, biases in the positions of mutational target sequences can account for most, if not all, apparent biases in mutation frequencies between genes oriented head-on and codirectionally to replication.
A Combinatorial PCR Method for Efficient, Selective Oligo Retrieval from Complex Oligo Pools

With the rapidly decreasing cost of array-based oligo synthesis, large-scale oligo pools offer significant benefits for advanced applications, including gene synthesis, CRISPR-based gene editing, and DNA data storage. Selectively retrieving specific oligos from these complex pools traditionally uses Polymerase Chain Reaction (PCR), in which any selected oligos are exponentially amplified to quickly outnumber non-selected ones. In this case, the number of orthogonal PCR primers is limited due to interactions between them. This lack of specificity presents a serious challenge, particularly for DNA data storage, where the size of an oligo pool (i.e., a DNA database) is orders of magnitude larger than it is for other applications. Although a nested file address system was recently developed to increase the number of accessible files for DNA storage, it requires a more complicated lab protocol and more expensive reagents to achieve high specificity. Instead, we developed a new combinatorial PCR method that outperforms prior work without compromising the fidelity of retrieved material or complicating wet lab processes. Our method quadratically increases the number of accessible oligos while maintaining high specificity. In experiments, we accessed three arbitrarily chosen files from a DNA prototype database that contained 81 different files. Initially comprising only 1% of the original database, the selected files were enriched to over 99.9% using our combinatorial primer method. Our method thus provides a viable path for scaling up DNA data storage systems and has broader utility whenever scientists need access to a specific target oligo and can design their own primer regions.
Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation

Many metabolic enzymes self-assemble into micron-scale filaments to organize and regulate metabolism. The appearance of these assemblies often coincides with large metabolic changes as in development, cancer, and stress. Yeast undergo cytoplasmic acidification upon starvation, triggering the assembly of many metabolic enzymes into filaments. However, it is unclear how these filaments assemble at the molecular level and what their role is in the yeast starvation response. CTP Synthase (CTPS) assembles into metabolic filaments across many species. Here, we characterize in vitro polymerization and investigate in vivo consequences of CTPS assembly in yeast. Cryo-EM structures reveal a pH-sensitive assembly mechanism and highly ordered filament bundles that stabilize an inactive state of the enzyme, features unique to yeast CTPS. Disruption of filaments in cells with non-assembly or hyper-assembly mutations decreases growth rate, reflecting the importance of regulated CTPS filament assembly in homeotstasis.
An efficient and robust HPLC method to determine the sialylation levels of human epithelial cells

Sialyltransferase, an enzyme responsible for attaching sialic acid to the cell surface, is reported to play a key role in cancer, making sialyltransferase a potent therapeutic target in drug development for cancer. Hence, this paper aimed to develop a simple method to detect and quantify sialic acids in cancer cells. An efficient method was developed using a reverse-phase ion-pairing HPLC-UV using triisopropanolamine as the ion-pairing agent with a C18 column. Neu5Ac was successfully eluted with the retention time 6.344 min with a flow rate of 0.4 mL/min. The proposed method was validated appropriately according to the AOAC guidelines (2013). This work demonstrates that the proposed method is not only relatively simple but also cost and time effective compared to pre-existing methods to successfully determine both free and protein-bound Neu5Ac in a complex cancer cell matrix. Furthermore, by applying the proposed method, a statistically significant decrease was observed for both HeLa and HuCCT1 cell lines with the application of deoxycholic acid – a known sialyltransferase inhibitor. Hence, the proposed method may be applicable to evaluate the effectiveness of sialyltransferase inhibitors.