bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-quality pseudo-phased genome forMelaleuca quinquenerviashows allelic diversity of NLR-type resistance genes
Authors: Chen Stephanie H , Martino Alyssa M , Luo Zhenyan , Schwessinger Benjamin , Jones Ashley , Tolessa Tamene , Bragg Jason G , Tobias Peri A , Edwards Richard J 
Published: April 2023

AbstractBackgroundThe coastal wetland tree speciesMelaleuca quinquenervia(Cav.) S.T.Blake (Myrtaceae), commonly named the broad-leaved paperbark, is a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. The species has been widely grown as an ornamental, becoming invasive in areas such as Florida in the United States. Long-lived trees must respond to a wide range pests and pathogens throughout their lifespan, and immune receptors encoded by the nucleotide- binding domain and leucine-rich repeat containing (NLR) gene family play a key role in plant stress responses. Expansion of this gene family is driven largely by tandem duplication, resulting in a clustering arrangement on chromosomes. Due to this clustering and their highly repetitive domain structure, comprehensive annotation of NLR encoding genes within genomes has been difficult. Additionally, as many genomes are still presented in their haploid, collapsed state, the full allelic diversity of the NLR gene family has not been widely published for outcrossing tree species.ResultsWe assembled a chromosome-level pseudo-phased genome forM.quinquenerviaand describe the full allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, differences in clusters and in the types and numbers of novel integrated domains.ConclusionsWe anticipate that the high quality of the genome forM. quinquenerviawill provide a new framework for functional and evolutionary studies into this important tree species. Our results indicate a likely role for maintenance of NLR allelic diversity to enable response to environmental stress, and we suggest that this allelic diversity may be even more important for long-lived plants.
High-fat diet in early life triggers both reversible and persistent epigenetic changes in the medaka fish (Oryzias latipes)
Authors: Inoue Yusuke , Suzuki Yuta , Kunishima Yoshimi , Washio Terumi , Morishita Shinichi , Takeda Hiroyuki 
Published: April 2023

AbstractThe nutritional status during early life can have enduring effects on an animal’s metabolism, although the mechanisms underlying these long-term effects are still unclear. Epigenetic modifications are considered a prime candidate mechanism for encoding early-life nutritional memories during this critical developmental period. However, the extent to which these epigenetic changes occur and persist over time remains uncertain, in part due to challenges associated with directly stimulating the fetus with specific nutrients in viviparous mammalian systems. In this study, we used medaka as an oviparous vertebrate model to establish an early-life high-fat diet (HFD) model. Larvae were fed with HFD from the hatching stages (one week after fertilization) for six weeks, followed by normal chow (NC) for eight weeks until the adult stage. We examined the changes in the transcriptomic and epigenetic state of the liver over this period. We found that HFD induces fatty liver phenotypes, accompanied by drastic changes in the hepatic transcriptome, chromatin accessibility, and histone modifications, especially in metabolic genes. These changes were largely reversed after the long-term NC, demonstrating the high plasticity of the epigenetic state in hepatocytes. However, we found a certain number of genomic loci showing non-reversible epigenetic changes, especially around genes related to cell signaling, liver fibrosis, and hepatocellular carcinoma, implying persistent changes in the cellular state of the liver triggered by early-life HFD feeding. Our data provide novel insights into the epigenetic mechanism of nutritional programming and a comprehensive atlas of the long-term epigenetic state in an early-life HFD model of non-mammalian vertebrates.
Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution
Authors: Zabaikina Iryna , Bokes Pavol , Singh Abhyudai 
Published: April 2023

AbstractWe consider a protein that negatively regulates the rate with which a cell grows. Since less growth means less protein dilution, this mechanism forms a positive feedback loop on the protein concentration. We couple the feedback model with a simple description of the cell cycle, in which a division event is triggered when the cell volume reaches a critical threshold. Following the division we either track only one of the daughter cells (single cell framework) or both cells (population frame-work). For both frameworks, we find an exact time-independent distribution of protein concentration and cell volume. We explore the consequences of dilution feedback on ergodicity, population growth rate, and the bias of the population distribution towards faster growing cells with less protein.
Essential roles of the ANKRD31-REC114 interaction in meiotic recombination and mouse spermatogenesis
Authors: Xu Jiaqi , Li Tao , Kim Soonjoung , Boekhout Michiel , Keeney Scott 
Published: April 2023

Meiotic DNA double-strand breaks (DSBs) initiate homologous recombination and are crucial for ensuring proper chromosome segregation. In mice, ANKRD31 recently emerged as a regulator of DSB timing, number, and location, with a particularly important role in targeting DSBs to the pseudoautosomal regions (PARs) of sex chromosomes. ANKRD31 interacts with multiple proteins, including the conserved and essential DSB-promoting factor REC114, so it was hypothesized to be a modular scaffold that “anchors” other proteins together and to meiotic chromosomes. To determine if and why the REC114 interaction is important for ANKRD31 function, we generated mice withAnkrd31mutations that either reduced (missense mutation) or eliminated (C-terminal truncation) the ANKRD31– REC114 interaction without diminishing contacts with other known partners. A complete lack of the ANKRD31–REC114 interaction mimicked anAnkrd31null, with delayed DSB formation and recombination, defects in DSB repair, and altered DSB locations including failure to target DSBs to the PARs. In contrast, when the ANKRD31– REC114 interaction was substantially but not completely disrupted, spermatocytes again showed delayed DSB formation globally, but recombination and repair were hardly affected and DSB locations were similar to control mice. The missenseAnkrd31allele showed a dosage effect, wherein combining it with the null or C-terminal truncation allele resulted in intermediate phenotypes for DSB formation, recombination, and DSB locations. Our results show that ANKRD31 function is critically dependent on its interaction with REC114, and that defects in ANKRD31 activity correlate with the severity of the disruption of the interaction.SignificanceHomologous recombination initiated by double-strand breaks (DSBs) during meiosis is a nearly universal feature of eukaryotic lifecycles, but is also dangerous because DSBs are potentially toxic or mutagenic. The vertebrate-specific protein ANKRD31 is an important regulator of DSB formation, proposed to be a scaffold protein that coordinates the activities of multiple DSB-promoting factors, including the widely conserved REC114. We test this hypothesis here through generation of targetedAnkrd31mutations that specifically attenuate or eliminate the ANKRD31-REC114 interaction. Analysis of this allelic series demonstrates that the ANKRD31-REC114 interaction is essential for all ANKRD31 activities in vivo, providing insight into how ANKRD31 controls DSB locations, timing, and number.
The missing fraction problem as an episodes of selection problem
Authors: Mittell Elizabeth A. , Morrissey Michael B. 
Published: April 2023

AbstractIn evolutionary quantitative genetics, the missing fraction problem refers to the case where phenotypes seen later in life are biased because a non-random subset of those phenotypes are missing from the population due to prior viability selection on correlated traits. As any such missing fraction will bias our estimates of selection, and therefore, responses to selection, it is one potential explanation for the paradox of stasis seen in wild populations. The two components required for the missing fraction problem to arise are: (1) viability selection; and (2) correlation between later-life traits and those important for early-life survival. Although it is plausible that these conditions are widespread in wild populations, this problem has received very little attention since it was first discussed (Grafen 1988; Hadfield 2008). It is impossible to know what phenotypes would have been expressed later in life by individuals who died during an earlier episode of viability selection, which has probably put researchers off. Here we show that we can break the problem down into episodes of selection and recover either (a) true estimates of phenotypic selection for later-life traits, or (b) adjusted estimates of the response to selection, depending on the data available. Implementation of complex statistics should uncover how prevalent the problem may be across many existing datasets (the latter approach). Whereas overall, we hope that viewing the missing fraction problem as an episodes of selection problem increases motivation, and provides justification, for a shift in focus to directly studying early-life viability selection.“…what a correlation with [lifetime reproductive success] or its components tells you depends on the causes of the natural variation in the character. It will not always be easy to discover those causes.”— Grafen (1988)“It is surprising that the problem of missing data has received so little attention given that viability selection is central to evolutionary biology.”— Hadfield (2008)
Characterization of the smallArabidopsis thalianaGTPase and ADP-ribosylation factor-like 2 protein TITAN 5
Authors: Mohr Inga , Mirzaiebadizi Amin , Sanyal Sibaji K. , Chuenban Pichaporn , Ahmadian Mohammad R. , Ivanov Rumen , Bauer Petra 
Published: April 2023

AbstractSmall GTPases function by conformational switching ability between GDP- and GTP-bound states in rapid cell signaling events. The ADP-ribosylation factor (ARF) family is involved in vesicle trafficking. Though evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. Here, we characterized biochemical properties and cellular localization of the essential small ARF-like GTPase TITAN 5/HALLIMASCH/ARL2/ARLC1 (hereafter termed TTN5) fromArabidopsis thaliana. Two TTN5 variants were included in the study with point mutations at conserved residues, suspected to be functional for nucleotide exchange and GTP hydrolysis, TTN5T30Nand TTN5Q70L. We found that TTN5 had a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanism. TTN5 acted as a non-classical small GTPase with a remarkably low GTP hydrolysis activity, suggesting it is likely present in GTP-loaded active form in the cell. We analyzed signals from yellow fluorescent protein (YFP)-tagged TTN5 and fromin situimmunolocalization of hemagglutine-tagged HA3-TTN5 in Arabidopsis seedlings and in a transient expression system. Together with colocalization using endomembrane markers and pharmacological treatments the microscopic analysis suggests that TTN5 can be present at the plasma membrane and dynamically associated with membranes of vesicles, Golgi stacks and multivesicular bodies. While the TTN5Q70Lvariant showed similar GTPase activities and localization behavior as wild-type TTN5, the TTN5T30Nmutant differed in some aspects.Hence, the unusual capacity of rapid nucleotide exchange activity of TTN5 is linked with cell membrane dynamics, likely associated with vesicle transport pathways in the endomembrane system.HighlightsThe small ARF-like GTPase TTN5 has a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanismBiochemical data classified TTN5 as a non-classical small GTPase, likely present in GTP-loaded active form in the cellYFP-TTN5 is dynamically associated with vesicle transport and different processes of the endomembrane system, requiring the active form of TTN5
Small ARF-like 2 GTPase TITAN 5 is linked with the dynamic regulation of IRON-REGULATED TRANSPORTER 1
Authors: Mohr Inga , Eutebach Monique , Knopf Marie C. , Schommen Naima , Gratz Regina , Angrand Kalina , Genders Lara , Brumbarova Tzvetina , Bauer Petra , Ivanov Rumen 
Published: April 2023

AbstractIron acquisition is crucial for plants. The abundance of IRON-REGULATED TRANSPORTER 1 (IRT1) at the plasma membrane is controlled through endomembrane trafficking. Vesicular trafficking requires small ARF-like GTPases, one of them is TITAN 5 (TTN5). Its physiological functions during the life cycle and cellular targets remain unknown. Little is known how the vesicular trafficking mechanism affects IRT1 localization.We show that TTN5 interacts with the large cytoplasmic variable region and protein-regulatory platform of IRT1.ttn5-1+/-plants have a reduced activity of root iron reductase, needed for iron uptake via IRT1. Fluorescent fusion proteins of TTN5 and IRT1 colocalize at the plasma membrane and in endosomes/multivesicular bodies, where IRT1 sorting and cycling between the plasma membrane and the vacuole are coordinated. Colocalization at the plasma membrane depends partly on the interaction ability of TTN5. TTN5 can also interact with peripheral membrane proteins that are components of the IRT1 regulation machinery, like the trafficking factor SNX1, the C2 domain protein EHB1 and the SEC14-GOLD protein PATL2. Hence, this work links iron acquisition and vesicular trafficking involving a small GTPase of the ARF family. This opens up the possibility to study the involvement of TTN5 in nutritional cell biology in the endomembrane system.HighlightsTTN5 interacts with the large intracellular loop and variable region of IRON-REGULATED TRANSPORTER 1 (IRT1)TTN5 has a positive effect on root iron (Fe) reductase activity.TTN5 and IRT1 colocalize at the plasma membrane and in the endomembrane system related to vesicle transportTTN5 can interact with peripheral membrane proteins of the IRT1 interactome, EHB1, PATL2 and SNX1 suggesting a coordinating role in IRT1 regulationOne-sentence summaryTTN5, a small ARF-like GTPase, is connected to the dynamic regulation of IRON-REGULATED TRANSPORTER 1 (IRT1) in the vesicular trafficking system through direct protein interaction and colocalization, linking with various peripheral membrane proteins of the IRT1 interactome and iron reductase activity.
Yield and agronomic performance of sweet corn in response to inoculation withAzospirillumsp. in arid land conditions
Authors: Contreras-Liza Sergio , Villadeza Christofer , Grados Pedro Rodriguez , Palomares Edison Goethe , Arbizu Carlos Irwin 
Published: April 2023

AbstractNitrogen is the most common limiting factor for crop productivity and most maize cultivars require fertilizing. Here we report the possibility of partially replacing the nitrogenous fertilizer in sweet corn inoculated with a native strain of Azospirillum in arid land on the coast of Peru. We examined an agronomic experiment in a crop field of arid soils under drip irrigation in Huacho (Peru) using a commercial variety of sweet corn. The treatments were two levels of nitrogen (90 and 180 kg N ha-1), one or two applications to the foliage of a native strain ofAzospirillumsp. (1 × 108CFU/mL) and a control treatment only with nitrogen fertilizer. Eleven agronomic variables related to productive aspects were evaluated, performing statistical analysis and the comparison of treatment means. The inoculation withAzospirillumsp. did not significantly (p> 0.05) affect the total weight of ears, the number of ears per plant and the number of male flowers, but it significantly (p< 0.05) influenced the grain yield per hectare, survival of plants, the weight of grain per plant, diameter and length of the cob. In some productive characteristics of sweet corn cv“Pardo”, a significant effect was found by inoculation withAzospirillumsp., surpassing in grain yield the control only with nitrogen fertilization, suggesting that it is possible to complement the application of nitrogen to the soil through the inoculation of this strain, replacing up to 50% of the levels of fertilizer application since the B/C ratio increased.
Workflows for detecting fungicide resistance in net form and spot form net blotch pathogens
Authors: Knight N. L. , Adhikari K. C. , Dodhia K. , Mair W. J. , Lopez-Ruiz F. J. 
Published: April 2023

AbstractFungicide resistance inPyrenophora teresf.maculataandP. teresf.tereshas become an important disease management issue. Control of the associated barley foliar diseases, spot form and net form net blotch, respectively, relies on three major groups of fungicides, demethylation inhibitors (DMI), succinate dehydrogenase inhibitors (SDHI) and quinone outside inhibitors (QoI). However, resistance has been reported for the DMI and SDHI fungicides in Australia. To enhance detection of different resistance levels, phenotyping and genotyping workflows were designed. The phenotyping workflow generated cultures directly from lesions and compared growth on discriminatory doses of tebuconazole (DMI) and fluxapyroxad (SDHI). Genotyping real-time PCR assays were based on alleles associated with sensitivity or resistance to the DMI and SDHI fungicides. These workflows were applied to a net blotch collection from 2019 consisting predominantly ofP. teresf.teresfrom South Australia andP. teresf.maculatafrom Western Australia. For South Australia theCyp51AL489-3 andSdhC-R134 alleles, associated with resistance to tebuconazole and fluxapyroxad, respectively, were the most prevalent. These alleles were frequently found in single isolates with dual resistance. This study also reports the first detection of a 134 base pair insertion located at position −66 (PtTi-6) in theCyp51Apromoter ofP. teresf.maculatafrom South Australia. For Western Australia, the PtTi-1 insertion was the most common allele associated with resistance to tebuconazole. These workflows will be valuable for screeningP. terespopulations for fungicide resistance, and informing appropriate management strategies.
Listening with generative models
Authors: Cusimano Maddie , Hewitt Luke B. , McDermott Josh H. 
Published: April 2023

AbstractPerception has long been envisioned to use an internal model of the world to explain the causes of sensory signals. However, such accounts have historically not been testable, typically requiring intractable search through the space of possible explanations. Using auditory scenes as a case study, we leveraged contemporary computational tools to infer explanations of sounds in a candidate internal model of the auditory world (ecologically inspired audio synthesizers). Model inferences accounted for many classic illusions. Unlike traditional accounts of auditory illusions, the model is applicable to any sound, and exhibited human-like perceptual organization for real world sound mixtures. The combination of stimulus-computability and interpretable model structure enabled ‘rich falsification’, revealing additional assumptions about sound generation needed to account for perception. The results show how generative models can account for the perception of both classic illusions and everyday sensory signals, and provide the basis on which to build theories of perception.
Attraction of female house mice to male ultrasonic courtship vocalizations depends on their social experience and estrous stage
Authors: Beck Jakob , Wernisch Bettina , Klaus Teresa , Penn Dustin J. , Zala Sarah M. 
Published: April 2023

AbstractMale house mice (Mus musculus) produce complex ultrasonic vocalizations (USVs), especially during courtship and mating. Playback experiments suggest that female attraction towards recordings of male USVs depends on their social experience, paternal exposure, and estrous stage. We conducted a playback experiment with wild-derived female house mice(M. musculus musculus)and compared their attraction to male USVs versus the same recording without USVs (background noise). We tested whether female attraction to USVs is influenced by the following factors: (1) social housing (two versus one female per cage); (2) neonatal paternal exposure (rearing females with versus without father); and (3) sexual receptivity (pro-estrous and estrous stages versus non-receptive metestrous and diestrous stages). We found that females showed a significant attraction to male USVs but only if females were housed with another female. Individually housed females showed the opposite response. We found no evidence that pre-weaning exposure to a father influenced females’ preferences, whereas sexual receptivity influenced females’ attraction to male USVs: non-receptive females showed preferences towards male USVs but receptive females did not. Finally, we found that individually housed females were more likely to be in sexually receptive estrous stages than those housed socially, and that attraction to male USVs was most pronounced amongst non-receptive females that were socially housed. Our findings indicate that the attraction of female mice to male USVs depends upon their social experience and estrous stage, though not paternal exposure. They contribute to the growing number of studies showing that social housing and estrous stage influence the behavior of house mice and we show how such unreported variables can contribute to the replication crisis.
Computer Vision Estimation of Stress and Anxiety Using a Gamified Mobile-based Ecological Momentary Assessment and Deep Learning: Research Protocol
Authors: Kargarandehkordi Ali , Washington Peter 
Published: April 2023

AbstractStress and anxiety can contribute to the development of major health problems such as heart disease, depression, and obesity. Due to its subjective nature, it is challenging to precisely measure human affect by relying on automated approaches. We therefore propose a personalized prediction framework fine-tuned for each participant in lieu of the traditional “one-size-fits-all” machine learning approach. We aim to collect such individualized data via two distinct procedures: 1) a smartphone-based ecological momentary assessment of stress, and 2) Zoom calls. The data collected from these periodic self-reports will include selfie photographs and ecological momentary assessments of affect. To enhance user engagement during the data collection process, we propose the use of gamification, an emerging trend which involves influencing user behavior and lifestyle by incorporating fun and engaging game elements into non-game contexts (e.g., health-related tasks). In addition to developing a standardized platform to achieve more accurate recognition of stress and anxiety, we plan to conduct a concurrent study in which we will capture videos of our subjects undertaking the Stroop Color Word and Amygdala Test and analyze the footage to identify additional significant characteristics that relate to anxiety. This could include features such as head and mouth movements, lip and cheek deformations, eye gaze, and blinking rates. The final results will provide a comparative evaluation of both objective measures of stress. This research project was approved by the University of Hawaii Institutional Review Board.