bluuebunny/crossref_metadata_2025_split huggingface dataset:
miRNA-encoded regulatory peptides modulate cadmium tolerance and accumulation in rice
Authors: Lu Long , Chen Xinyu , Chen Jiaming , Zhang Zaoli , Zhang Zhen , Sun Yanyan , Wang Yuan , Xie Siwen , Ma Yinuo , Song Yuanyuan , Zeng Rensen 
Published: July 2023

AbstractMicroRNAs (miRNAs) are small non-coding RNAs that play a vital role in plant responses to abiotic and biotic stress. Recently, it has been discovered that some primary miRNAs (pri-miRNAs) encode regulatory short peptides called miPEPs. However, the presence of miPEPs in rice, and their functions in response to abiotic stress, particularly stress induced by heavy metals, remain poorly understood. Here, we identified a functional small peptide (miPEP156e) encoded by pri-miR156e that regulates the expression of miR156 and its targetSPLgenes, thereby affecting miR156-mediated cadmium (Cd) tolerance in rice. Overexpression ofmiPEP156eled to a reduction in the accumulation of reactive oxygen species (ROS) and Cd in plants under Cd stress, resulting in improved rice Cd tolerance, as observed in miR156-overexpressing lines and seedlings treated with exogenous miPEP156e. In contrast,miPEP156emutants displayed sensitivity to Cd stress due to the elevated accumulation of ROS and Cd. Transcriptome analysis further revealed that miPEP156e improved rice Cd tolerance by modulating Cd transporter and ROS scavenging genes. Moreover, we identified five novel miPEPs involved in regulating Cd resistance through exogenous treatment of seedlings with synthetic corresponding miPEPs. Our study provides insights into the regulatory mechanism of miPEP156e in rice response to Cd stress and demonstrates the potential of miPEPs as an effective tool for improving crop abiotic stress tolerance.
Molecular insight into how the position of an abasic site and its sequence environment influence DNA duplex stability and dynamics
Authors: Ashwood Brennan , Jones Michael S. , Lee Yumin , Sachleben Joseph R. , Ferguson Andrew L. , Tokmakoff Andrei 
Published: July 2023

AbstractLocal perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes. Using a combination of steady-state and time-resolved spectroscopy and molecular dynamics simulations, we unravel an interplay between AP-site position and nucleobase sequence that controls energetic and dynamic disruption to the duplex. The duplex is disrupted into two segments by an entropic barrier for base pairing on each side of the AP site. The barrier induces fraying of the short segment when an AP site is near the termini. Shifting the AP site inward promotes a transition from short-segment fraying to fully encompassing the barrier into the thermodynamics of hybridization, leading to further destabilization the duplex. Nucleobase sequence determines the length scale for this transition by tuning the barrier height and base-pair stability of the short segment, and certain sequences enable out-of-register base pairing to minimize the barrier height.
Structure and symmetries of the genetic codes for vertebrate, ascidian and yeast mitochondria
Authors: Kohli Rajeev 
Published: July 2023

AbstractGenetic codes assign sixty-four codons to twenty amino acids. These assignments are known to follow certain rules. One question long considered but still unresolved is if these rules are derived from an underlying structure in genetic codes. Knowledge of such structure could facilitate better understanding of the biochemical, physico-chemical and evolutionary causes of the observed codon assignments. Our first finding reveals a coherent and symmetric structure in the genetic codes of vertebrate, ascidian, and yeast mitochondria. This structure is derived from a “simple” code that assigns all four codons with the same second nucleotide to a single amino acid if the first nucleotide is C or G, and assigns pairs of codons with the same second nucleotide to a single amino acid if the first nucleotide is A or U, and their third nucleotides are both purines (A and G) or both pyrimidines (U and C). The translation mechanism for the three mitochondria reflects this structure, one tRNA decoding each group of two or four codons into an amino acid. Our second finding is that the mycoplasma/spiroplasma and standard genetic codes are obtained by small sequential modifications of the vertebrate mitochondrial code and retain almost all its symmetries. We use group theory to characterize the symmetries of the simple and mitochondrial codes, and speculate on the implications of the structure for detecting translation errors and the evolution of the genetic code.
Seed size control via phloem end by callose deposition/degradation of β-1,3-glucanase
Authors: Liu Xiaoyan , Nakajima Kohdai P. , Wu Xiaoyan , Zhu Shaowei , Adhikari Prakash Babu , Okada Kentaro , Kurotani Ken-ichi , Ishida Takashi , Nakamura Masayoshi , Sato Yoshikatsu , Xie Liyang , Huang Chen , He Jiale , Sawa Shinichiro , Higashiyama Tetsuya , Notaguchi Michitaka , Kasahara Ryushiro D. 
Published: July 2023

SummarySeed formation is crucial for lives of plants as well as humans; however, the mechanisms governing seed size require further investigation. Here, we present a new mechanism to modify the seed size by the newly identified phloem end that support nutrient transport, at the chalazal end of the ovule, however, blocked by callose deposition. Callose is removed after central cell fertilization (open state), allowing nutrients to be transported to the seed. However, if fertilization fails, callose deposition persists (closed state), preventing the phloem end from transporting nutrients. β-1,3-glucanase genes, including putative plasmodesmata-associated proteins (AtBG_ppap), were identified as regulators of callose removal. TheAtbg_ppapmutant had the phloem end in the closed state and produced smaller seeds due to incomplete callose degradation. In contrast, theAtBG_ppapoverexpression line produced larger seeds than the wild type due to continuous callose degradation, indicating that the phloem end regulates substance flow via callose deposition/degradation.
Prevalence, determinants, and trends in the experience and perpetration of intimate partner violence among a cohort of gay, bisexual, and other men who have sex with men in Montréal, Toronto, and Vancouver, Canada (2017-2022)
Authors: Juwono Stephen , Anato Jorge Luis Flores , Kirschbaum Allison L. , Metheny Nicholas , Dvorakova Milada , Skakoon-Sparling Shayna , Moore David M. , Grace Daniel , Hart Trevor A. , Lambert Gilles , Lachowsky Nathan J. , Jollimore Jody , Cox Joseph , Maheu-Giroux Mathieu 
Published: July 2023

AbstractPurposeLongitudinal data on the experience and perpetration of intimate partner violence (IPV) among gay, bisexual, and other men who have sex with men (GBM) is limited. We estimated the prevalence of past six-month (P6M) physical and/or sexual IPV (hereafter IPV) experience and perpetration, identified their determinants, and assessed temporal trends, including the impact of the COVID-19 pandemic.MethodsWe used data from the Engage Cohort Study (2017-2022) of GBM recruited using respondent-driven sampling in Montréal, Toronto, and Vancouver. Adjusted prevalence ratios (aPR) for determinants and self-reported P6M IPV were estimated using generalized estimating equations, accounting for attrition (inverse probability of censoring weights) and relevant covariates. Longitudinal trends of IPV were also assessed.ResultsBetween 2017-2022, 1,455 partnered GBM (median age 32 years, 82% gay, and 71% white) had at least one follow-up visit. Baseline proportions were 31% for lifetime IPV experience and 17% for lifetime perpetration. During follow-up, P6M IPV experience was more common (6%, 95%CI: 5-7%) than perpetration (4%, 95%CI: 3-5%). Factors associated with P6M IPV experience include prior IPV experience (aPR=2.79, 95%CI: 1.83-4.27), less education (aPR=2.08, 95%CI: 1.14-3.79), and substance use (injection aPR=5.68, 95%CI: 2.92-11.54, non-injection aPR=1.70, 95%CI: 1.05-2.76). Similar factors were associated with IPV perpetration. IPV was stable over time; periods of COVID-19 restrictions were not associated with IPV changes in this cohort.ConclusionPrevalence of IPV was high among GBM. Determinants related to marginalization are associated with an increased risk of IPV. Interventions should address these determinants to reduce IPV and improve health.
Unconventional stabilization of the human T-cell leukemia virus type 1 immature Gag lattice
Authors: Obr Martin , Percipalle Mathias , Chernikova Darya , Yang Huixin , Thader Andreas , Pinke Gergely , Porley Dario , Mansky Louis M , Dick Robert A , Schur Florian KM 
Published: July 2023

AbstractHuman T-cell leukemia virus type 1 (HTLV-1) has an atypical immature particle morphology compared to other retroviruses. This indicates that these particles are formed in a way that is unique. Here we report the results of cryo-electron tomography (cryo-ET) studies of HTLV-1 virus-like particles (VLPs) assembledin vitro, as well as derived from cells. This work shows that HTLV-1 employs an unconventional mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature CA tubular arrays reveals that the primary stabilizing component in HTLV-1 is CA-NTD. Mutagenesis and biophysical analysis support this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the CA-CTD. These results are the first to provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus, and this helps explain why HTLV-1 particles are morphologically distinct.
The penetration of sunflower root tissues by the parasitic plantOrobanche cumanaWallr. is intracellular
Authors: Auriac MC , Griffiths C , Robin-Soriano A , Legendre A , Boniface MC , Muños S , Fournier J , Chabaud M 
Published: July 2023

AbstractParasitic plants cause yield losses for important crops. Among these,Orobanche cumanaWallr, sunflower broomrape, is one of the major pests for sunflower. Previous studies stated that in most cases, the haustorium, a specific parasitic plant organ, penetrates host roots intercellularly. However, host cellular mechanisms involved during the parasitic cells penetration remained poorly described.We investigated sunflower root cellular behavior during haustorium penetration using various microscopy approaches including live cell imaging of inoculated transgenic fluorescent sunflower roots.We showed that the haustorium ofO. cumanapenetrated living sunflower root tissues, as a result of the degradation of the host cell wall and the formation of a new host trans-cellular apoplastic compartment for haustorium accommodation. Moreover, broomrape induced cell divisions in outer root tissues at very early stages of the interaction, leading to localized hypertrophy at the site of broomrape attachments.These findings are a change of paradigm in the research field of parasitic plants. They extend host root intracellular accommodation mechanisms initially shown for symbiotic and pathogenic biotrophic fungi to parasitic plants. It paves the way for future understanding and development of resistance to parasitic plants.Key messageCombination ofin vivoconfocal, large field and transmission electron microscopy approaches revealed how intimate the relationship between the parasitic plant broomrape (Orobanche cumanaWallr.) and its sunflower host (Helianthus annusL.) is at very early stages of their interaction.
The microbial metabolite Urolithin A reducesC. difficiletoxin expression and repairs toxin-induced epithelial damage
Authors: Ghosh Sweta , Erickson Daniel , Chua Michelle J , Collins James , Jala Venkatakrishna Rao 
Published: July 2023

AbstractClostridioides difficileis a gram-positive, anaerobic, spore-forming bacterium that is responsible for antibiotic-associated pseudomembranous colitis.Clostridioides difficileinfection (CDI) symptoms can range from diarrhea to life-threatening colon damage. Toxins produced byC. difficile(TcdA and TcdB) cause intestinal epithelial injury and lead to severe gut barrier dysfunction, stem cell damage, and impaired regeneration of the gut epithelium. Current treatment options for intestinal repair are limited. In this study, we demonstrate that treatment with the microbial metabolite urolithin A (UroA) attenuates CDI-induced adverse effects on the colon epithelium in a preclinical model of CDI-induced colitis. Moreover, our analysis suggests that UroA treatment protects againstC. difficile-induced inflammation, disruption of gut barrier integrity, and intestinal tight junction proteins in the colon of CDI mice. Importantly, UroA treatment significantly reduced the expression and release of toxins fromC. difficile, without inducing bacterial cell death. These results indicate the direct regulatory effects of UroA on bacterial gene regulation. Overall, our findings reveal a novel aspect of UroA activities, as it appears to act at both the bacterial and host levels to protect against CDI-induced colitis pathogenesis. This research sheds light on a promising avenue for the development of novel treatments forC. difficileinfection.ImportanceTherapy forC. difficileinfections includes the use of antibiotics, immunosuppressors, and fecal microbiota transplantation (FMT). However, these treatments have several drawbacks, including the loss of colonization resistance, promotion of autoimmune disorders, and the potential for unknown pathogens in donor samples. To date, the potential benefits of microbial metabolites in CDI-induced colitis have not been fully investigated. Here, we report for the first time that the microbial metabolite Urolithin A has the potential to block toxin production fromC. difficileand enhance gut barrier function to mitigate CDI-induced colitis.
LucFlow: A method to measure Luciferase reporter expression in single cells
Authors: Nooti Sunil , Naylor Madison , Long Trevor , Groll Braydon , Manu  
Published: July 2023

AbstractReporter assays, in which the expression of an inert protein is driven by gene regulatory elements such as promoters and enhancers, are a workhorse for investigating gene regulation. Techniques for measuring reporter gene expression vary from single-cell or single-molecule approaches having low throughput to bulk Luciferase assays that have high throughput. We developed a Luciferase Reporter Assay using Flow-Cytometry (LucFlow), which measures reporter expression in single cells immunostained for Luciferase. We optimized and tested LucFlow with a murine cell line that can be differentiated into neutrophils, into which promoter-reporter and enhancer-promoter-reporter constructs have been integrated in a site-specific manner. The single-cell measurements are comparable to bulk ones but we found that dead cells have no detectable Luciferase protein, so that bulk assays underestimate reporter expression. LucFlow is able to achieve a higher accuracy than bulk methods by excluding dead cells during flow cytometry. Prior to fixation and staining, the samples are spiked with stained cells that can be discriminated during flow cytometry and control for tube-to-tube variation in experimental conditions. Computing fold change relative to control cells allows LucFlow to achieve a high level of precision. LucFlow, therefore, enables the accurate and precise measurement of reporter expression in a high throughput manner.
Resolution enhancement with deblurring by pixel reassignment (DPR)
Authors: Zhao Bingying , Mertz Jerome 
Published: July 2023

AbstractImproving the spatial resolution of a fluorescence microscope has been an ongoing challenge in the imaging community. To address this challenge, a variety of approaches have been taken, ranging from instrumentation development to image post-processing. An example of the latter is deconvolution, where images are numerically deblurred based on a knowledge of the microscope point spread function. However, deconvolution can easily lead to noise-amplification artifacts. Deblurring by post-processing can also lead to negativities or fail to conserve local linearity between sample and image. We describe here a simple image deblurring algorithm based on pixel reassignment that inherently avoids such artifacts and can be applied to general microscope modalities and fluorophore types. Our algorithm helps distinguish nearby fluorophores even when these are separated by distances smaller than the conventional resolution limit, helping facilitate, for example, the application of single-molecule localization microscopy in dense samples. We demonstrate the versatility and performance of our algorithm under a variety of imaging conditions.
Enterobacter Sp. SM3Exhibits Run-and-Tumble Motility
Authors: Johnson Silverio , Freedman Brian , Tang Jay X. 
Published: July 2023

ABSTRACTThe recent discovery of the peritrichous, swarm-competent bacteriumEnterobacter sp. SM3has offered a new opportunity to elucidate the role of swarming motility in the gut microbiome. Here we present first findings of the run-and-tumble behavior ofSM3in both a control solution of motility buffer and upon bulk exposure to the chemoattractants serine and aspartate, drawing a comparison with the well-studied behavior ofE. coli. It was found thatSM3runs with an average speed of approximately 30 µm/s for an average duration of 0.77 s. Tumble events occur for an average duration of 0.11 s with a 69◦average tumble angle. Both values are similar to that ofE. coli. When exposed to serine,SM3suppresses the frequency of tumble events, which in turn increases the average run duration. In addition, the average tumble angle was found to decrease in response to serine. However, when exposed to up to a millimolar concentration of aspartate,SM3does not demonstrate a notable change in run-and-tumble parameters. These results suggest that run-and-tumble is the characteristic swimming behavior ofSM3in its planktonic state. These findings serve as a benchmark in a quest to determine the connection among swimming, swarming, and the complex dynamics of the gut microbiome.IMPORTANCEBacteria form the largest domain of living creatures on this planet. Our interactions with bacteria influence us in many ways, not the least of which being in regards to human health. A recently identified species of gut bacteria,Enterobacter sp. SM3, has been shown to reduce intestinal inflammation, suggesting that swarming could play a physiologically beneficial role. In this report, we study the motility of individualSM3bacteria This study is an essential step towards an overarching goal to understand the influence of bacterial motility on human health.
In silico designing of a multitope vaccine against Rhizopus microspores
Authors: Venkateswarulu T.C. , Shaik Asra Tasneem , Meduri Druthi Sri , Vajiha Vajiha , Dhusia Kalyani , Peele Abraham 
Published: July 2023

PurposeMucorales has been described to be widely distributed during the most recent COVID-19 pandemic, with a greater frequency of disease in India, particularly among those with immune deficiencies. This study aims to use computational tools to develop a vaccine.Design/methodology/approachThe authors investigated at Mucorales proteins that had previously been associated to virulence factors. Recent research suggests that a vaccine based on high-level cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B-cell lymphocyte (BCL) epitopes from diverse proteins might be developed. Furthermore, the vaccine assembly contains the targeted epitopes as well as PADRE peptides to induce an immune response. Computational approaches were used to analyze the immunological parameters used to build the suggested vaccine and validate its TLR-3 binding.FindingsThese studies show that the vaccination is capable of triggering a particular immune response. The authors offer a technique for developing and evaluating candidate vaccines using computational tools. To the best of their knowledge, this is the first immunoinformatic research of a prospective mucormycosis vaccine.Originality/valueDuring this audit, a successful attempt was made to create a subunit MEV against black fungus. In the current study, MEV has been proposed as a suitable neutralizer candidate since it is immunogenic, secure, stable and interacts with human receptors. A stream study, on the other hand, is produced via a mixed vaccinosis approach. Following that, vaccinologists may perform more exploratory testing to evaluate whether the vaccine is effective.
COVID stress and depressive symptoms among high school students: a moderated mediation model of sleep quality and optimism
Authors: Nguyen Hung Thanh , Ho Thi Truc Quynh , Dau Minh Long 
Published: July 2023

PurposeThis study aimed to investigate whether optimism buffers an indirect relationship between COVID stress and depressive symptoms via poor sleep quality among Vietnamese high school students.Design/methodology/approachSix hundred and eighty-five participants completed the Coronavirus Stress Measure, the Life Orientation Test-Revised, the Pittsburgh Sleep Quality Index and the Depression, Anxiety and Stress Scales. Process Macro 3.5 for SPSS (Model 4 and Model 14) was used to analyze the mediating effect and moderated mediation effect.FindingsThe results indicated that COVID stress was associated with an increase in depressive symptoms via the indirect pathway of poor sleep quality. Furthermore, optimism moderated the indirect relationship between COVID stress and depressive symptoms through poor sleep quality among Vietnamese students.Originality/valueThe study's findings may serve as a basis for the development of depression prevention interventions for students with high COVID stress in the COVID-19 pandemic.