Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Rose rosette virus and development of reverse genetic system for studying virus accumulation and movement in whole plants

Rose rosette virus (RRV) is an Emaravirus, a negative-sense RNA virus with a 7-segmented genome that is enclosed by a double membrane. While the genome sequences of many emaraviruses are reported, there is negligible information concerning virus replication and movement in host plants. Computational methods determined that RNA1 encoded the RNA dependent RNA polymerase (RdRp), RNA2 encoded glycoprotein precursor, and the RNA3 encoded the nucleocapsid (N), all share significant homologies with similar proteins of the Orthobunyavirus family. The RRV terminal UTR sequences are complementary and share significant identity with the UTR sequences of Bunyamwera virus. We report a minireplicon system and a full length infectious clone of RRV, which are the first for any emaravirus species. The photoreversible fluorescent iLOV protein was used to replace the RNA5 open reading frame (R5-iLOV). We demonstrate that agro-infiltration of Nicotiana benthamiana leaves to deliver RNA1, RNA3, and R5-iLOV cDNAs led to iLOV expression. A mutation was introduced into the RdRp active site and iLOV expression was eliminated. Delivery of four segments or seven segments of the RRV infectious clone produced systemic infection in N. benthamiana and rose plants. iLOV was also fused to the glycoprotein precursor (R2-iLOV). Using confocal microscopy, the R2-iLOV was seen in spherical bodies along membrane strands inside N. benthamiana epidermal cells. This new technology will enable future research to functionally characterize the RRV proteins, to study the virus-host interactions governing local and systemic infection, and examine the subcellular functions of the Gc.RRV has emerged as a severe threat to cultivated roses, causing millions of dollars in losses to commercial producers. The majority of the viral gene products have not been researched or characterized until now. We constructed a minireplicon system and an infectious clone of the seven-segmented RRV genome that is contained in a binary vector and delivered by Agrobacterium. This technology has been slow to develop for viruses with negative-strand RNA genomes. It has been especially tricky for plant viruses with multicomponent negative-strand RNA genomes. We report the first reverse genetic system for a member of the genus Emaravirus, Rose rosette virus (RRV). We introduced the iLOV fluorescent protein as a fusion to the Gc protein and as a replacement for the open reading frame in genome segment 5. This game-changing reverse genetic system creates new opportunities for studying negative-strand RNA viruses in plants.
Clonal Heterogeneity Supports Mitochondrial Metabolism in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDA) is characterized by a heterogenous and densely fibrotic microenvironment. This limits functional vasculature and diffusion of nutrients through the tumor1,2. Accordingly, pancreatic cancer cells develop numerous metabolic adaptations to survive and proliferate in nutrient austere conditions3-7. Subtypes of PDA have been characterized by transcriptional and functional differences8-12, which have been reported to exist within the same tumor13-15. However, it remains unclear if this diversity extends to metabolic programming. Here, using a combination of metabolomic profiling and functional interrogation of metabolic dependencies, we identify two distinct metabolic subclasses within neoplastic populations isolated from a single pancreatic tumor. Furthermore, these populations are poised for metabolic crosstalk, and in examining this, we find an unexpected role for asparagine in maintaining cell proliferation following mitochondrial inhibition. Functionally, when challenged by mitochondrial inhibition, asparagine supplementation increases intracellular levels of asparagine and aspartate, a rate limiting biosynthetic precursor16-18. Conversely, depletion of extracellular asparagine with PEG-asparaginase sensitizes pancreatic tumors to mitochondrial targeting with phenformin. Together, these data extend the concept of metabolic diversity to neoplastic populations within individual tumors, while illustrating a new method of intratumoral communication that supports tumor fitness19,20. Finally, the combination of asparaginase with mitochondrial inhibition could provide a powerful new strategy for this difficult to treat disease.
A Spatially Explicit Model of Stabilizing Selection for Improving Phylogenetic Inference

Ultraconserved elements (UCEs) are stretches of hundreds of nucleotides with highly conserved cores flanked by variable regions. Although the selective forces responsible for the preservation of UCEs are unknown, they are nonetheless believed to contain phylogenetically meaningful information from deep to shallow divergence events. Phylogenetic applications of UCEs assume the same degree of rate heterogeneity applies across the entire locus, including variable flanking regions. We present a Wright-Fisher model of selection on nucleotides (SelON) which includes the effects of mutation, drift, and spatially varying, stabilizing selection for an optimal nucleotide sequence. The SelON model assumes the strength of stabilizing selection follows a position dependent Gaussian function whose exact shape can vary between UCEs. We evaluate SelON by comparing its performance to a simpler and spatially invariant GTR+Γ model using an empirical dataset of 400 vertebrate UCEs used to determine the phylogenetic position of turtles. We observe much improvement in model fit of SelON over the GTR+Γ model, and support for turtles as sister to lepidosaurs. Overall, the UCE specific parameters SelON estimates provide a compact way of quantifying the strength and variation in selection within and across UCEs. SelON can also be extended to include more realistic mapping functions between sequence and stabilizing selection as well as allow for greater levels of rate heterogeneity. By more explicitly modeling the nature of selection on UCEs, SelON and similar approaches can be used to better understand the biological mechanisms responsible for their preservation across highly divergent taxa and long evolutionary time scales.
Aberrant PARP1 Activity Couples DNA Breaks to Deregulated Presynaptic Calcium Signalling and Lethal Seizures

Defects in DNA single-strand break repair result in cerebellar ataxia which in Xrcc1Nes-Cre mice is promoted by hyperactivity of the DNA strand break sensor protein, Parp1. Here, we show that Parp1 hyperactivity extends beyond the cerebellum in Xrcc1-defective brain, resulting in lethal seizures and shortened lifespan. We demonstrate that aberrant Parp1 activation triggers seizure-like activity in Xrcc1-defective hippocampus ex vivo and aberrant presynaptic calcium signalling in isolated hippocampal neurons in vitro. Moreover, we show that these defects are prevented by Parp1 inhibition and/or deletion. Collectively, these data identify aberrant Parp1 activity at unrepaired DNA breaks as a cell-autonomous source of deregulated presynaptic calcium signalling, and highlight PARP inhibition as a possible therapeutic approach in XRCC1-mutated neurodegenerative disease.PARP1 activity and presynaptic Ca2+ signalling
Using singleton densities to detect recent selection in Bos taurus

Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the ‘Singleton Density Score’, to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural-cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans – milk protein content, milk fat content, and stature – have been subject to directional selection. Simulations demonstrate that since B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods are reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies. Impact statement Many traits of ecological or economic importance (including height, disease propensity, climatic adaptation) are ‘polygenic’. That is, they are affected by a large number of genetic variants, with each one only making a small contribution to a trait, but collectively influence variation. As selection acts on all of these variants simultaneously, it only changes the frequency of each one by a small amount, making it hard to detect such selection from genome data. This situation has changed in recent years, with the proliferation of whole–genome data from many individuals, along with the development of methods to detect the subtle effects of polygenic selection. Here, we use data from 102 genomes from domesticated cattle (Bos taurus) that has experienced intense artificial selection since domestication, and test if we can detect signatures of recent selection (arising up to 740 years ago). Domesticated species are appealing for this kind of study, as they are subject to extensive genome sequencing studies, and genetic variants can be related to traits under selection. We carried out our analysis in two parts. We first performed a genome–wide scan to find individual genetic regions that show signatures of recent selection. We identify some relating to cell regulation, catabolic processes, neural-cell adhesion and immunity. In the second part, we then analysed genetic regions associated with three key traits: milk protein content, milk fat content, and stature. We tested if these regions collectively showed a signature of selection, but did not find a significant result in either case. Simulations suggest that the domestication history of cattle affected the power of these methods. We end with a discussion on how to best detect polygenic selection in future studies.
The plate-to-rod transition in trabecular bone loss is elusive

Changes in trabecular micro-architecture are key to our understanding of osteoporosis. Previous work focusing on structure model index (SMI) measurements have concluded that disease progression entails a shift from plates to rods in trabecular bone, but SMI is heavily biased by bone volume fraction. As an alternative to SMI, we proposed the Ellipsoid Factor (EF) as a continuous measure of local trabecular shape between plate-like and rod-like extremes. We investigated the relationship between EF distributions, SMI and bone volume fraction of the trabecular geometry in a murine model of disuse osteoporosis as well as from human vertebrae of differing bone volume fraction. We observed a moderate shift in EF median (at later disease stages in mouse tibia) and EF mode (in the vertebral samples with low bone volume fraction) towards a more rod-like geometry, but not in EF maximum and minimum. These results support the notion that the plate to rod transition does not coincide with the onset of bone loss and is considerably more moderate, when it does occur, than SMI suggests. A variety of local shapes not straightforward to categorise as rod or plate exist in all our trabecular bone samples.
LiBis: An ultrasensitive alignment method for low-input bisulfite sequencing

The cell-free DNA (cfDNA) methylation profile in liquid biopsies has been utilized to diagnose early-stage disease and estimate therapy response. However, in typical clinical settings, only very small amounts of cfDNA can be purified. Whole-genome bisulfite sequencing (WGBS) is the gold standard to measure DNA methylation; however, WGBS using small amounts of fragmented DNA introduces a critical challenge for data analysis, namely a low mapping ratio. This, in turn, generates low sequencing depth and low coverage for CpG sites genome wide. The lack of informative CpGs has become a bottleneck for the clinical application of cfDNA-based WGBS assays. Hence, we developed LiBis (Low-input Bisulfite Sequencing), a novel method for low-input WGBS data alignment. By dynamically clipping initially unmapped reads and remapping clipped fragments, we judiciously rescued those reads and uniquely aligned them to the genome. By substantially increasing the mapping ratio by up to 88%, LiBis dramatically improved the number of informative CpGs and the precision in quantifying the methylation status of individual CpG sites. The high sensitivity and cost effectiveness afforded by LiBis for low-input samples will allow the discovery of genetic and epigenetic features suitable for downstream analysis and biomarker identification using liquid biopsy.
Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen‐enrichment sequencing (PenSeq)

Potato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence, or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. To identify the P. infestans effector recognized by Rpi-amr1, we screened available effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. By using SMRT and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569 which triggers a highly specific cell death response when transiently co-expressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RxLR effector families, and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RxLR effector family that is associated with the recognition by Rpi-amr1.
A Deletion in GDF7 is Associated with a Heritable Forebrain Commissural Malformation Concurrent with Ventriculomegaly and Interhemispheric Cysts in Cats

An inherited neurologic syndrome in a family of mixed-breed Oriental cats has been characterized as forebrain commissural malformation concurrent with ventriculomegaly and interhemispheric cysts. However, the genetic basis for this autosomal recessive syndrome in cats is unknown. Forty-three cats were genotyped on the Illumina Infinium Feline 63K iSelect DNA Array and used for analyses. Genome-wide association studies, including a sib-transmission disequilibrium test, a case-control association analysis, and homozygosity mapping, identified a critical region on cat chromosome A3. Short-read whole genome sequencing was completed for a cat trio segregating with the syndrome. A homozygous 7 bp deletion in growth differentiation factor 7 (GDF7) (c.221_227delGCCGCGC [p.Arg74Profs]) was identified in affected cats by comparison to the 99 Lives Cat variant dataset, validated using Sanger sequencing, and genotyped by fragment analyses. This variant was not identified in 192 unaffected cats in the 99 Lives dataset. The variant segregated concordantly in an extended pedigree. Obligate carrier cats were heterozygous. In mice, GDF7 mRNA is expressed within the roof plate when commissural axons initiate ventrally-directed growth. This finding emphasizes the importance of GDF7 in the neurodevelopmental process in the mammalian brain. A genetic test can be developed for use by cat breeders to eradicate this variant.
Insecticidal Activities and Repellent Effects of Plant Extracts against the Brown Planthopper (Nilaparvata lugens Stal)

Methanol extracts of 35 plant species in 20 families were tested for their insecticidal activities and repellent effects against Nilaparvata lugens female adult by topical application and spray methods. The insecticidal activities and repellent effects of variousplant species and parts were different. The methanol extracts from stem of Garcinia xanthochymus, Senecio scandens and Phytolacca americana, seedcoat of Ginkgo biloba, and leaf+stem of Ailanthus altissima and Catalpa ovata showed potent insecticidal activities against N. lugens. Specially, the G. biloba extract exhibited higher than 90% mortality against N. lugens at a concentration of 4,000 ppm. Repellent effects of plant extracts obtained from whole plant of Daucus carota, fruit of Semecarpus anacardium, leaf+stem of C. ovata and Wisteria sinensis were active, and potent. Also, the plant extracts that are potent in insecticidal activity not necessarily have high repellent activity showing no significant corelation between the two activities.
Are mice born normally with an egg-only diet?

Chicken eggs (egg) contain high amounts of important proteins and fat with a very low amount of carbohydrates, and also contain all vitamins and minerals needed for the chick to develop. We mated 8-week-old mice consuming an egg-only diet, and examined whether mice got pregnant and mice gave birth. Then we continued to raise newborn mice only consuming an egg-only diet compared to normal chew diet. We found that the rate of pregnancy of the mice consuming an egg-only diet was not different from that of the mice consuming normal chew diet. Further, we found that the number of pupus born from the mother consuming only eggs was not different from that of the mother consuming normal chew diet. However, the newborn mice from the mother fed only eggs did not grow healthy when they consume egg-only diet. Only few mice were alive at one month after birth. Then we change the diet just before or just after birth from egg only diet to normal chew diet and we found that both group grew healthy more than one month. These results indicate that mice are born healthy only with egg only diet.
Once delayed non-invasive remote ischemic preconditioning protects against early stroke by modulating neuroinflammatory responses in rats

Once delayed non-invasive remote ischemic preconditioning (RIPC) has been proven to provide endogenous protection against injury induced by ischemia–reperfusion in the central nervous system. However, for thus ischemic preconditioning method, it is still unclear how long this protection can maintain and what the underlying mechanism is. In this study, we tested the hypothesis that once delayed non-invasive RIPC protects brain injury at short reperfusion time. The rat was stimulated by transient middle cerebral artery occlusion (MCAo) for 90 min, and subsequent reperfusion was performed at 6 h, 72 h and 7 days after MCAo. RIPC was conducted in both hind limbs 24 h before MCAo for 3 cycles (10 min ischemia/ 10 min reperfusion). The infarct size was measured by 2, 3, 5-triphenyl-2H-tetrazolium chloride (TTC) staining and Cresyl violet (CV) staining. The mRNA and protein levels of inflammatory cytokines in the brain were measured by real-time RT-PCR and ELISA. The results showed that once delayed non-invasive RIPC reduced the infarct size, improved neurological functions and behavioral performance at 6 and 72 h post-stroke. There was no change by reperfusion at 7 d after MCAo. RIPC reduced the levels of TNFα, IL-1β and IL-6 in the brain at 72 h post stroke. It also reduced the levels of TNFα and IL-1β when reperfusion at 6 h after MCAo. Our results strongly supported that once delayed non-invasive RIPC protects against stroke as a non-invasive neuroprotective strategy, which maintained for both short and middle term ischemic reperfusion time. The protective effect is mediated by the modulation of inflammatory response in the ischemic brain.
Predator complex of the horse chestnut leafminer Cameraria ohridella: identification and impact assessment

Abstract: The control of Cameraria ohridella Deschka and Dimic (Lepidoptera, Gracillariidae) by natural enemies in Europe is poor. Thus, in the past 15 years epidemic population densities of the moth regularly caused a continuous pre‐mature defoliation of horse chestnut trees, Aesculus hippocastanum L. Whereas several studies investigated the parasitoid complex of the leafminer and revealed its inefficiency, only little is known about the predators of C. ohridella. The aim of this study was to identify the predator complex in European horse chestnut stands by visual observations and exposure experiments and to assess the impact of different predator guilds on C. ohridella populations by an exclusion experiment. Of all potential predators observed, only blue tits, Parus caeruleus L. , great tits, Parus major L. , marsh tits, Parus palustris L. and the southern oak bushcricket Meconema meridionale (Costa) were found to prey on the pre‐imaginal leafminer stages. Bushcrickets have to our knowledge never before been recorded preying on leafminers; moreover M. meridionale showed a measurable negative impact on the C. ohridella population. However, birds seem to be of greater importance as predators of C. ohridella than arthropods. Predation rates of birds ranged from 2 to 4% of leafminer populations, which is of the same order of magnitude as published parasitism rates. We conclude that the augmentation of tit densities, for example via nesting boxes in chestnut trees, should be considered as a component of an integrated control strategy against the horse chestnut leafminer.
r- and K-Selection in Typha

A comparison of environmental and population parameters between sites differing in length of frost-free period indicated that populations from short growing season locations should be more subject to r-selection, while populations from locations with a long growing season should be more subject to K-selection. Properties of population samples of three species of Typha conformed to the theory. Specifically, the following hypotheses were confirmed: (i) r-selected genotypes have a greater developmental speed; (ii) r-selected genotypes have higher fecundity; (iii) r-selected genotypes produce more offspring, but invest less energy in each offspring; (iv) r-selected genotypes show less evidence of selection for traits increasing competitive ability in high density situations; (v) there is a selective trade-off between mechanisms contributing to colonization potential and those contributing to competitive potential. Superimposed on the selection pattern along the climatic gradient was an r-K dichotomy between the species occurring throughout the gradient, T. latifolia, and the two species, T. angustifolia and T. domingensis, restricted to different ends of the gradient.