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Microbiology Spectrum May 2024Sweet orange () is one of the most important fruit crops worldwide. Virus infections in this crop can interfere with cellular processes, causing dramatic economic...
Sweet orange () is one of the most important fruit crops worldwide. Virus infections in this crop can interfere with cellular processes, causing dramatic economic losses. By performing RT-qPCR analyses, we demonstrated that citrus psorosis virus (CPsV)-infected orange plants exhibited higher levels of unprocessed microRNA (miRNA) precursors than healthy plants. This result correlated with the reported reduction of mature miRNAs species. The protein 24K, the CPsV suppressor of RNA silencing (VSR), interacts with miRNA precursors . Thus, this protein becomes a candidate responsible for the increased accumulation of unprocessed miRNAs. We analyzed 24K RNA-binding and protein-protein interaction domains and described patterns of its subcellular localization. We also showed that 24K colocalizes within nuclear D-bodies with the miRNA biogenesis proteins DICER-LIKE 1 (DCL1), HYPONASTIC LEAVES 1 (HYL1), and SERRATE (SE). According to the results of bimolecular fluorescence complementation and co-immunoprecipitation assays, the 24K protein interacts with HYL1 and SE. Thus, 24K may inhibit miRNA processing in CPsV-infected citrus plants by direct interaction with the miRNA processing complex. This work contributes to the understanding of how a virus can alter the regulatory mechanisms of the host, particularly miRNA biogenesis and function.IMPORTANCESweet oranges can suffer from disease symptoms induced by virus infections, thus resulting in drastic economic losses. In sweet orange plants, CPsV alters the accumulation of some precursors from the regulatory molecules called miRNAs. This alteration leads to a decreased level of mature miRNA species. This misregulation may be due to a direct association of one of the viral proteins (24K) with miRNA precursors. On the other hand, 24K may act with components of the cell miRNA processing machinery through a series of predicted RNA-binding and protein-protein interaction domains.
PubMed: 38785434
DOI: 10.1128/spectrum.03513-23 -
BioRxiv : the Preprint Server For... May 2024Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping polymerase active sites with nucleotide resolution and measuring newly...
Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping polymerase active sites with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time-intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq) which utilizes pre-adenylated single-stranded DNAs (AppDNA), a dimer blocking oligonucleotide (DBO), on-bead 5' RNA end repair, and column-based purification. These modifications enabled efficient transcriptome mapping within a single day (∼12 hours) increasing ligation efficiency, abolished adapter dimers, and reduced sample loss and RNA degradation. We demonstrate the reproducibility of rPRO-seq in measuring polymerases at promoters, gene bodies, and enhancers as compared to original PRO-seq protocols. Additionally, rPRO-seq is scalable, allowing for transcriptome mapping with as little as 25,000 cells. We apply rPRO-seq to study the role of Integrator in mouse hematopoietic stem and progenitor cell (mHSPC) homeostasis, identifying as an essential component of transcriptional regulation and RNA processing in mHSPC homeostasis. Overall, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.
PubMed: 38766081
DOI: 10.1101/2024.05.08.593182 -
International Journal of Health... May 2024In the near future, the incidence of mosquito-borne diseases may expand to new sites due to changes in temperature and rainfall patterns caused by climate change....
BACKGROUND
In the near future, the incidence of mosquito-borne diseases may expand to new sites due to changes in temperature and rainfall patterns caused by climate change. Therefore, there is a need to use recent technological advances to improve vector surveillance methodologies. Unoccupied Aerial Vehicles (UAVs), often called drones, have been used to collect high-resolution imagery to map detailed information on mosquito habitats and direct control measures to specific areas. Supervised classification approaches have been largely used to automatically detect vector habitats. However, manual data labelling for model training limits their use for rapid responses. Open-source foundation models such as the Meta AI Segment Anything Model (SAM) can facilitate the manual digitalization of high-resolution images. This pre-trained model can assist in extracting features of interest in a diverse range of images. Here, we evaluated the performance of SAM through the Samgeo package, a Python-based wrapper for geospatial data, as it has not been applied to analyse remote sensing images for epidemiological studies.
RESULTS
We tested the identification of two land cover classes of interest: water bodies and human settlements, using different UAV acquired imagery across five malaria-endemic areas in Africa, South America, and Southeast Asia. We employed manually placed point prompts and text prompts associated with specific classes of interest to guide the image segmentation and assessed the performance in the different geographic contexts. An average Dice coefficient value of 0.67 was obtained for buildings segmentation and 0.73 for water bodies using point prompts. Regarding the use of text prompts, the highest Dice coefficient value reached 0.72 for buildings and 0.70 for water bodies. Nevertheless, the performance was closely dependent on each object, landscape characteristics and selected words, resulting in varying performance.
CONCLUSIONS
Recent models such as SAM can potentially assist manual digitalization of imagery by vector control programs, quickly identifying key features when surveying an area of interest. However, accurate segmentation still requires user-provided manual prompts and corrections to obtain precise segmentation. Further evaluations are necessary, especially for applications in rural areas.
Topics: Humans; Animals; Climate Change; Malaria; Mosquito Vectors; Remote Sensing Technology; Geographic Information Systems; Image Processing, Computer-Assisted
PubMed: 38764024
DOI: 10.1186/s12942-024-00371-w -
Biology Letters May 2024Neural circuits govern the interface between the external environment, internal cues and outwardly directed behaviours. To process multiple environmental stimuli and... (Review)
Review
Neural circuits govern the interface between the external environment, internal cues and outwardly directed behaviours. To process multiple environmental stimuli and integrate these with internal state requires considerable neural computation. Expansion in neural network size, most readily represented by whole brain size, has historically been linked to behavioural complexity, or the predominance of cognitive behaviours. Yet, it is largely unclear which aspects of circuit variation impact variation in performance. A key question in the field of evolutionary neurobiology is therefore how neural circuits evolve to allow improved behavioural performance or innovation. We discuss this question by first exploring how volumetric changes in brain areas reflect actual neural circuit change. We explore three major axes of neural circuit evolution-replication, restructuring and reconditioning of cells and circuits-and discuss how these could relate to broader phenotypes and behavioural variation. This discussion touches on the relevant uses and limitations of volumetrics, while advocating a more circuit-based view of cognition. We then use this framework to showcase an example from the insect brain, the multi-sensory integration and internal processing that is shared between the mushroom bodies and central complex. We end by identifying future trends in this research area, which promise to advance the field of evolutionary neurobiology.
Topics: Cognition; Animals; Biological Evolution; Brain; Nerve Net; Insecta; Mushroom Bodies
PubMed: 38747685
DOI: 10.1098/rsbl.2023.0576 -
Frontiers in Plant Science 2024Rice blast disease caused by has long been the main cause of rice ( L.) yield reduction worldwide. The quinone external inhibitor pyraclostrobin is widely used as a...
INTRODUCTION
Rice blast disease caused by has long been the main cause of rice ( L.) yield reduction worldwide. The quinone external inhibitor pyraclostrobin is widely used as a fungicide to effectively control the spread of pathogenic fungi, including . However, can develop resistance through multiple levels of mutation, such as target protein cytb mutation G143A/S, leading to a decrease in the effectiveness of the biocide after a period of application. Therefore, uncovering the possible mutational mechanisms from multiple perspectives will further provide feasible targets for drug development.
METHODS
In this work, we determined the gene expression changes in in response to pyraclostrobin stress and their relationship with DNA methylation by transcriptome and methylome.
RESULTS
The results showed that under pyraclostrobin treatment, endoplasmic reticulum (ER)-associated and ubiquitin-mediated proteolysis were enhanced, suggesting that more aberrant proteins may be generated that need to be cleared. DNA replication and repair processes were inhibited. Glutathione metabolism was enhanced, while lipid metabolism was impaired. The number of alternative splicing events increased. These changes may be related to the elevated methylation levels of cytosine and adenine in gene bodies. Both hypermethylation and hypomethylation of differentially methylated genes (DMGs) mainly occurred in exons and promoters. Some DMGs and differentially expressed genes (DEGs) were annotated to the same pathways by GO and KEGG, including protein processing in the ER, ubiquitin-mediated proteolysis, RNA transport and glutathione metabolism, suggesting that pyraclostrobin may affect gene expression by altering the methylation patterns of cytosine and adenine.
DISCUSSION
Our results revealed that 5mC and 6mA in the gene body are associated with gene expression and contribute to adversity adaptation in . This enriched the understanding for potential mechanism of quinone inhibitor resistance, which will facilitate the development of feasible strategies for maintaining the high efficacy of this kind of fungicide.
PubMed: 38745924
DOI: 10.3389/fpls.2024.1391900 -
PLoS Biology May 2024The processing of sensory information, even at early stages, is influenced by the internal state of the animal. Internal states, such as arousal, are often characterized...
The processing of sensory information, even at early stages, is influenced by the internal state of the animal. Internal states, such as arousal, are often characterized by relating neural activity to a single "level" of arousal, defined by a behavioral indicator such as pupil size. In this study, we expand the understanding of arousal-related modulations in sensory systems by uncovering multiple timescales of pupil dynamics and their relationship to neural activity. Specifically, we observed a robust coupling between spiking activity in the mouse dorsolateral geniculate nucleus (dLGN) of the thalamus and pupil dynamics across timescales spanning a few seconds to several minutes. Throughout all these timescales, 2 distinct spiking modes-individual tonic spikes and tightly clustered bursts of spikes-preferred opposite phases of pupil dynamics. This multi-scale coupling reveals modulations distinct from those captured by pupil size per se, locomotion, and eye movements. Furthermore, coupling persisted even during viewing of a naturalistic movie, where it contributed to differences in the encoding of visual information. We conclude that dLGN spiking activity is under the simultaneous influence of multiple arousal-related processes associated with pupil dynamics occurring over a broad range of timescales.
Topics: Animals; Pupil; Geniculate Bodies; Mice; Action Potentials; Arousal; Male; Mice, Inbred C57BL; Photic Stimulation; Neurons; Thalamus; Eye Movements; Time Factors; Visual Pathways
PubMed: 38743775
DOI: 10.1371/journal.pbio.3002614 -
Foods (Basel, Switzerland) Apr 2024Oil bodies (OBs) are naturally occurring pre-emulsified oil droplets that have broad application prospects in emulsions and gels. The main purpose of this research was...
Oil bodies (OBs) are naturally occurring pre-emulsified oil droplets that have broad application prospects in emulsions and gels. The main purpose of this research was to examine the impact of the OB content on the structure and functional aspects of acid-mediated soy protein isolate (SPI) gel filled with OBs. The results indicated that the peanut oil body (POBs) content significantly affected the water holding capacity of the gel. The rheological and textural analyses showed that POBs reduced the gel strength and hardness. The scanning electron and confocal laser scanning microscopy analyses revealed that POBs aggregated during gel formation and reduced the gel network density. The Fourier transform infrared spectrum (FTIR) analysis demonstrated that POBs participated in protein gels through hydrogen bonds, steric hindrance and hydrophobic interactions. Therefore, OBs served as inactive filler in the acid-mediated protein gel, replaced traditional oils and provided alternative ingredients for the development of new emulsion-filled gels.
PubMed: 38731660
DOI: 10.3390/foods13091289 -
Materials (Basel, Switzerland) Apr 2024The sintering of high-performance ceramics with complex shapes at low temperatures has a significant impact on the future application of ceramics. A joint process of...
The sintering of high-performance ceramics with complex shapes at low temperatures has a significant impact on the future application of ceramics. A joint process of digital light processing (DLP) 3D printing technology and a nitrogen-gas pressure-assisted sintering method were proposed to fabricate AlN ceramics in the present work. Printing parameters, including exposure energy and time, were optimized for the shaping of green bodies. The effects of sintering temperature, as well as nitrogen pressure, on the microstructure, density, and thermal conductivity of AlN ceramics were systematically discussed. A high thermal conductivity of 168 W·m·K was achieved by sintering and holding at a significantly reduced temperature of 1720 °C with the assistance of a 0.6 MPa nitrogen-gas pressure. Further, a large-sized AlN ceramic plate and a heat sink with an internal mini-channel structure were designed and successfully fabricated by using the optimized printing and sintering parameters proposed in this study. The heat transfer performance of the ceramic heat sink was evaluated by infrared thermal imaging, showing excellent cooling abilities, which provides new opportunities for the development of ceramic heat dissipation modules with complex geometries and superior thermal management properties.
PubMed: 38730816
DOI: 10.3390/ma17092010 -
Alzheimer's & Dementia (Amsterdam,... 2024Dementia with Lewy bodies (DLB) and Alzheimer's disease (AD), the two most common neurodegenerative dementias, both exhibit altered emotional processing. However, how...
UNLABELLED
Dementia with Lewy bodies (DLB) and Alzheimer's disease (AD), the two most common neurodegenerative dementias, both exhibit altered emotional processing. However, how vocal emotional expressions alter in and differ between DLB and AD remains uninvestigated. We collected voice data during story reading from 152 older adults comprising DLB, AD, and cognitively unimpaired (CU) groups and compared their emotional prosody in terms of valence and arousal dimensions. Compared with matched AD and CU participants, DLB patients showed reduced overall emotional expressiveness, as well as lower valence (more negative) and lower arousal (calmer), the extent of which was associated with cognitive impairment and insular atrophy. Classification models using vocal features discriminated DLB from AD and CU with an AUC of 0.83 and 0.78, respectively. Our findings may aid in discriminating DLB patients from AD and CU individuals, serving as a surrogate marker for clinical and neuropathological changes in DLB.
HIGHLIGHTS
DLB showed distinctive reduction in vocal expression of emotions.Cognitive impairment was associated with reduced vocal emotional expression in DLB.Insular atrophy was associated with reduced vocal emotional expression in DLB.Emotional expression measures successfully differentiated DLB from AD or controls.
PubMed: 38721025
DOI: 10.1002/dad2.12594 -
IScience Apr 2024Music has profoundly shaped the human experience across cultures and generations, yet its impact on our minds and bodies remains elusive. This study examined how the...
Music has profoundly shaped the human experience across cultures and generations, yet its impact on our minds and bodies remains elusive. This study examined how the perception of musical chord elicits bodily sensations and emotions through the brain's predictive processing. By deploying body-mapping tests and emotional evaluations on 527 participants exposed to chord progressions, we unveiled the intricate interplay between musical uncertainty, prediction error in eliciting specific bodily sensations and emotions. Our results demonstrated that certain chord progressions elicit cardiac and abdominal sensations, linked to interoception, and associated with aesthetic appreciation and positive valence. These findings highlight the crucial role of musical uncertainty and prediction error in emotional response and sound embodiment. This study offers insight into the potential connection between music-induced interoception and mental well-being, underscoring the musical effects on our minds and bodies.
PubMed: 38715936
DOI: 10.1016/j.isci.2024.109498