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NAR Genomics and Bioinformatics Jun 2024Malat1 is a long-noncoding RNA with critical roles in gene regulation and cancer metastasis, however its functional role in stem cells is largely unexplored. We here...
Malat1 is a long-noncoding RNA with critical roles in gene regulation and cancer metastasis, however its functional role in stem cells is largely unexplored. We here perform a nuclear knockdown of Malat1 in mouse embryonic stem cells, causing the de-regulation of 320 genes and aberrant splicing of 90 transcripts, some of which potentially affecting the translated protein sequence. We find evidence that Malat1 directly interacts with gene bodies and aberrantly spliced transcripts, and that it locates upstream of down-regulated genes at their putative enhancer regions, in agreement with functional genomics data. Consistent with this, we find these genes affected at both exon and intron levels, suggesting that they are transcriptionally regulated by Malat1. Besides, the down-regulated genes are regulated by specific transcription factors and bear both activating and repressive chromatin marks, suggesting that some of them might be regulated by bivalent promoters. We propose a model in which Malat1 facilitates the transcription of genes involved in chromatid dynamics and mitosis in one pathway, and affects the splicing of transcripts that are themselves involved in RNA processing in a distinct pathway. Lastly, we compare our findings with Malat1 perturbation studies performed in other cell systems and .
PubMed: 38711862
DOI: 10.1093/nargab/lqae045 -
Nature Communications May 2024The neural basis of fear of heights remains largely unknown. In this study, we investigated the fear response to heights in male mice and observed characteristic...
The neural basis of fear of heights remains largely unknown. In this study, we investigated the fear response to heights in male mice and observed characteristic aversive behaviors resembling human height vertigo. We identified visual input as a critical factor in mouse reactions to heights, while peripheral vestibular input was found to be nonessential for fear of heights. Unexpectedly, we found that fear of heights in naïve mice does not rely on image-forming visual processing by the primary visual cortex. Instead, a subset of neurons in the ventral lateral geniculate nucleus (vLGN), which connects to the lateral/ventrolateral periaqueductal gray (l/vlPAG), drives the expression of fear associated with heights. Additionally, we observed that a subcortical visual pathway linking the superior colliculus to the lateral posterior thalamic nucleus inhibits the defensive response to height threats. These findings highlight a rapid fear response to height threats through a subcortical visual and defensive pathway from the vLGN to the l/vlPAG.
Topics: Animals; Male; Fear; Mice; Geniculate Bodies; Superior Colliculi; Mice, Inbred C57BL; Visual Pathways; Periaqueductal Gray; Neurons; Primary Visual Cortex; Visual Perception; Behavior, Animal
PubMed: 38702319
DOI: 10.1038/s41467-024-48147-x -
Environment International May 2024Environmental DNA (eDNA) technology has revolutionized biomonitoring, but challenges remain regarding water sample processing. The passive eDNA sampler (PEDS) represents...
Environmental DNA (eDNA) technology has revolutionized biomonitoring, but challenges remain regarding water sample processing. The passive eDNA sampler (PEDS) represents a viable alternative to active, water filtration-based eDNA enrichment methods, but the effectiveness of PEDS for surveying biodiverse and complex natural water bodies is unknown. Here, we collected eDNA using filtration and glass fiber filter-based PEDS (submerged in water for 1 d) from 27 sites along the final reach of the Yangtze River and the coast of the Yellow Sea, followed by eDNA metabarcoding analysis of fish biodiversity and quantitative PCR (qPCR) for a critically endangered aquatic mammal, the Yangtze finless porpoise. We ultimately detected 98 fish species via eDNA metabarcoding. Both eDNA sampling methods captured comparable local species richness and revealed largely similar spatial variation in fish assemblages and community partitions between the river and sea sites. Notably, the Yangtze finless porpoise was detected only in the metabarcoding of eDNA collected by PEDS at five sites. Also, species-specific qPCR revealed that the PEDS captured porpoise eDNA at more sites (7 vs. 2), in greater quantities, and with a higher detection probability (0.803 vs. 0.407) than did filtration. Our results demonstrate the capacity of PEDS for surveying fish biodiversity, and support that continuous eDNA collection by PEDS can be more effective than instantaneous water sampling at capturing low abundance and ephemeral species in natural waters. Thus, the PEDS approach can facilitate more efficient and convenient eDNA-based biodiversity surveillance and rare species detection.
Topics: Biodiversity; Animals; DNA, Environmental; Environmental Monitoring; Fishes; Rivers; DNA Barcoding, Taxonomic; Porpoises; China
PubMed: 38696978
DOI: 10.1016/j.envint.2024.108706 -
The Cochrane Database of Systematic... May 2024More than 767 million coronavirus 2019 (COVID-19) cases and 6.9 million deaths with COVID-19 have been recorded as of August 2023. Several public health and social... (Meta-Analysis)
Meta-Analysis
BACKGROUND
More than 767 million coronavirus 2019 (COVID-19) cases and 6.9 million deaths with COVID-19 have been recorded as of August 2023. Several public health and social measures were implemented in schools to contain the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent onward transmission. We built upon methods from a previous Cochrane review to capture current empirical evidence relating to the effectiveness of school measures to limit SARS-CoV-2 transmission.
OBJECTIVES
To provide an updated assessment of the evidence on the effectiveness of measures implemented in the school setting to keep schools open safely during the COVID-19 pandemic.
SEARCH METHODS
We searched the Cochrane COVID-19 Study Register, Educational Resources Information Center, World Health Organization (WHO) COVID-19 Global literature on coronavirus disease database, and the US Department of Veterans Affairs Evidence Synthesis Program COVID-19 Evidence Reviews on 18 February 2022.
SELECTION CRITERIA
Eligible studies focused on measures implemented in the school setting to contain the COVID-19 pandemic, among students (aged 4 to 18 years) or individuals relating to the school, or both. We categorized studies that reported quantitative measures of intervention effectiveness, and studies that assessed the performance of surveillance measures as either 'main' or 'supporting' studies based on design and approach to handling key confounders. We were interested in transmission-related outcomes and intended or unintended consequences.
DATA COLLECTION AND ANALYSIS
Two review authors screened titles, abstracts and full texts. We extracted minimal data for supporting studies. For main studies, one review author extracted comprehensive data and assessed risk of bias, which a second author checked. We narratively synthesized findings for each intervention-comparator-outcome category (body of evidence). Two review authors assessed certainty of evidence.
MAIN RESULTS
The 15 main studies consisted of measures to reduce contacts (4 studies), make contacts safer (7 studies), surveillance and response measures (6 studies; 1 assessed transmission outcomes, 5 assessed performance of surveillance measures), and multicomponent measures (1 study). These main studies assessed outcomes in the school population (12), general population (2), and adults living with a school-attending child (1). Settings included K-12 (kindergarten to grade 12; 9 studies), secondary (3 studies), and K-8 (kindergarten to grade 8; 1 study) schools. Two studies did not clearly report settings. Studies measured transmission-related outcomes (10), performance of surveillance measures (5), and intended and unintended consequences (4). The 15 main studies were based in the WHO Regions of the Americas (12), and the WHO European Region (3). Comparators were more versus less intense measures, single versus multicomponent measures, and measures versus no measures. We organized results into relevant bodies of evidence, or groups of studies relating to the same 'intervention-comparator-outcome' categories. Across all bodies of evidence, certainty of evidence ratings limit our confidence in findings. Where we describe an effect as 'beneficial', the direction of the point estimate of the effect favours the intervention; a 'harmful' effect does not favour the intervention and 'null' shows no effect either way. Measures to reduce contact (4 studies) We grouped studies into 21 bodies of evidence: moderate- (10 bodies), low- (3 bodies), or very low-certainty evidence (8 bodies). The evidence was very low to moderate certainty for beneficial effects of remote versus in-person or hybrid teaching on transmission in the general population. For students and staff, mostly harmful effects were observed when more students participated in remote teaching. Moderate-certainty evidence showed that in the general population there was probably no effect on deaths and a beneficial effect on hospitalizations for remote versus in-person teaching, but no effect for remote versus hybrid teaching. The effects of hybrid teaching, a combination of in-person and remote teaching, were mixed. Very low-certainty evidence showed that there may have been a harmful effect on risk of infection among adults living with a school student for closing playgrounds and cafeterias, a null effect for keeping the same teacher, and a beneficial effect for cancelling extracurricular activities, keeping the same students together and restricting entry for parents and caregivers. Measures to make contact safer (7 studies) We grouped studies into eight bodies of evidence: moderate- (5 bodies), and low-certainty evidence (3 bodies). Low-certainty evidence showed that there may have been a beneficial effect of mask mandates on transmission-related outcomes. Moderate-certainty evidence showed full mandates were probably more beneficial than partial or no mandates. Evidence of a beneficial effect of physical distancing on risk of infection among staff and students was mixed. Moderate-certainty evidence showed that ventilation measures probably reduce cases among staff and students. One study (very low-certainty evidence) found that there may be a beneficial effect of not sharing supplies and increasing desk space on risk of infection for adults living with a school student, but showed there may be a harmful effect of desk shields. Surveillance and response measures (6 studies) We grouped studies into seven bodies of evidence: moderate- (3 bodies), low- (1 body), and very low-certainty evidence (3 bodies). Daily testing strategies to replace or reduce quarantine probably helped to reduce missed school days and decrease the proportion of asymptomatic school contacts testing positive (moderate-certainty evidence). For studies that assessed the performance of surveillance measures, the proportion of cases detected by rapid antigen detection testing ranged from 28.6% to 95.8%, positive predictive value ranged from 24.0% to 100.0% (very low-certainty evidence). There was probably no onward transmission from contacts of a positive case (moderate-certainty evidence) and replacing or shortening quarantine with testing may have reduced missed school days (low-certainty evidence). Multicomponent measures (1 study) Combining multiple measures may have led to a reduction in risk of infection among adults living with a student (very low-certainty evidence).
AUTHORS' CONCLUSIONS
A range of measures can have a beneficial effect on transmission-related outcomes, healthcare utilization and school attendance. We rated the current findings at a higher level of certainty than the original review. Further high-quality research into school measures to control SARS-CoV-2 in a wider variety of contexts is needed to develop a more evidence-based understanding of how to keep schools open safely during COVID-19 or a similar public health emergency.
Topics: Adolescent; Child; Child, Preschool; Humans; COVID-19; Pandemics; SARS-CoV-2; Schools
PubMed: 38695826
DOI: 10.1002/14651858.CD015029.pub2 -
Annals of Neurosciences Apr 2024Multiple sclerosis (MS) is a global health concern affecting around 2.6 million people. It is characterised by neural inflammation, myelin breakdown and cognitive...
Multiple sclerosis (MS) is a global health concern affecting around 2.6 million people. It is characterised by neural inflammation, myelin breakdown and cognitive decline. Cognitive impairment, especially reduced cognitive processing speed (CPS), which affects up to 67% of MS patients and frequently manifests before mobility concerns, is one of the disease's most serious side effects. Effective adaptation and the application of cognitive rehabilitation treatments depend on the early diagnosis of cognitive impairment. Although pharmaceutical therapies have some drawbacks, endurance training has become a promising alternative. Intensity-controlled endurance exercise has the ability to delay the onset of MS symptoms and enhance cognitive function. Exercise has also been shown to have neuroprotective effects in a number of neurological disorders, including MS, Parkinson's disease and stroke. This includes both aerobic and resistance training. A mix of aerobic exercise and weight training has shown promise, especially for people with mild cognitive impairment, but according to recent studies any amount of physical activity is beneficial to cognitive performance. In conclusion, this in-depth analysis highlights the crucial part endurance exercise plays in treating MS-related cognitive impairment. It improves not only neurological health in general but also cognitive performance. Exercise can help control MS in a way that dramatically improves quality of life and well-being.
PubMed: 38694717
DOI: 10.1177/09727531241227674 -
Scientific Reports Apr 2024Parkinson's disease (PD) is a progressive neurodegenerative disorder affecting over 3% of those over 65. It's caused by reduced dopaminergic neurons and Lewy bodies,...
Parkinson's disease (PD) is a progressive neurodegenerative disorder affecting over 3% of those over 65. It's caused by reduced dopaminergic neurons and Lewy bodies, leading to motor and non-motor symptoms. The relationship between COMT gene polymorphisms and PD is complex and not fully elucidated. Some studies have reported associations between certain COMT gene variants and PD risk, while others have not found significant associations. This study investigates how COMT gene variations impact cortical thickness changes in PD patients over time, aiming to link genetic factors, especially COMT gene variations, with PD progression. This study analyzed data from 44 PD patients with complete 4-year imaging follow-up from the Parkinson Progression Marker Initiative (PPMI) database. Magnetic resonance imaging (MRI) scans were acquired using consistent methods across 9 different MRI scanners. COMT single-nucleotide polymorphisms (SNPs) were assessed based on whole genome sequencing data. Longitudinal image analysis was conducted using FreeSurfer's processing pipeline. Linear mixed-effect models were employed to examine the interaction effect of genetic variations and time on cortical thickness, while controlling for covariates and subject-specific variations. The rs165599 SNP stands out as a potential contributor to alterations in cortical thickness, showing a significant reduction in overall mean cortical thickness in both hemispheres in homozygotes (Left: P = 0.023, Right: P = 0.028). The supramarginal, precentral, and superior frontal regions demonstrated significant bilateral alterations linked to rs165599. Our findings suggest that the rs165599 variant leads to earlier manifestation of cortical thinning during the course of the disease. However, it does not result in more severe cortical thinning outcomes over time. There is a need for larger cohorts and control groups to validate these findings and consider genetic variant interactions and clinical features to elucidate the specific mechanisms underlying COMT-related neurodegenerative processes in PD.
Topics: Humans; Catechol O-Methyltransferase; Parkinson Disease; Male; Female; Polymorphism, Single Nucleotide; Aged; Longitudinal Studies; Middle Aged; Magnetic Resonance Imaging; Cerebral Cortex; Disease Progression; Brain Cortical Thickness; Genetic Predisposition to Disease
PubMed: 38689006
DOI: 10.1038/s41598-024-60828-7 -
Psychological Science Jun 2024As a powerful social signal, a body, face, or gaze facing toward oneself holds an individual's attention. We asked whether, going beyond an egocentric stance, facingness...
As a powerful social signal, a body, face, or gaze facing toward oneself holds an individual's attention. We asked whether, going beyond an egocentric stance, facingness between others has a similar effect and why. In a preferential-looking time paradigm, human adults showed spontaneous preference to look at two bodies facing toward (vs. away from) each other (Experiment 1a, = 24). Moreover, facing dyads were rated higher on social semantic dimensions, showing that facingness adds social value to stimuli (Experiment 1b, = 138). The same visual preference was found in juvenile macaque monkeys (Experiment 2, = 21). Finally, on the human development timescale, this preference emerged by 5 years, although young infants by 7 months of age already discriminate visual scenes on the basis of body positioning (Experiment 3, = 120). We discuss how the preference for facing dyads-shared by human adults, young children, and macaques-can signal a new milestone in social cognition development, supporting processing and learning from third-party social interactions.
Topics: Humans; Animals; Male; Female; Adult; Infant; Visual Perception; Young Adult; Social Perception; Attention; Child, Preschool; Social Cognition; Space Perception; Social Interaction
PubMed: 38683657
DOI: 10.1177/09567976241242995 -
Frontiers in Bioengineering and... 2024Magnetic Resonance Imaging (MRI) is essential in diagnosing cervical spondylosis, providing detailed visualization of osseous and soft tissue structures in the cervical...
Magnetic Resonance Imaging (MRI) is essential in diagnosing cervical spondylosis, providing detailed visualization of osseous and soft tissue structures in the cervical spine. However, manual measurements hinder the assessment of cervical spine sagittal balance, leading to time-consuming and error-prone processes. This study presents the Pyramid DBSCAN Simple Linear Iterative Cluster (PDB-SLIC), an automated segmentation algorithm for vertebral bodies in T2-weighted MR images, aiming to streamline sagittal balance assessment for spinal surgeons. PDB-SLIC combines the SLIC superpixel segmentation algorithm with DBSCAN clustering and underwent rigorous testing using an extensive dataset of T2-weighted mid-sagittal MR images from 4,258 patients across ten hospitals in China. The efficacy of PDB-SLIC was compared against other algorithms and networks in terms of superpixel segmentation quality and vertebral body segmentation accuracy. Validation included a comparative analysis of manual and automated measurements of cervical sagittal parameters and scrutiny of PDB-SLIC's measurement stability across diverse hospital settings and MR scanning machines. PDB-SLIC outperforms other algorithms in vertebral body segmentation quality, with high accuracy, recall, and Jaccard index. Minimal error deviation was observed compared to manual measurements, with correlation coefficients exceeding 95%. PDB-SLIC demonstrated commendable performance in processing cervical spine T2-weighted MR images from various hospital settings, MRI machines, and patient demographics. The PDB-SLIC algorithm emerges as an accurate, objective, and efficient tool for evaluating cervical spine sagittal balance, providing valuable assistance to spinal surgeons in preoperative assessment, surgical strategy formulation, and prognostic inference. Additionally, it facilitates comprehensive measurement of sagittal balance parameters across diverse patient cohorts, contributing to the establishment of normative standards for cervical spine MR imaging.
PubMed: 38681963
DOI: 10.3389/fbioe.2024.1337808 -
Scientific Reports Apr 2024Monitoring burned areas in Thailand and other tropical countries during the post-harvest season is becoming increasingly important. High-resolution remote sensing data...
Monitoring burned areas in Thailand and other tropical countries during the post-harvest season is becoming increasingly important. High-resolution remote sensing data from Sentinel-2 satellites, which have a short revisit time, is ideal for accurately and efficiently mapping burned regions. However, automating the mapping of agriculture residual on a national scale is challenging due to the volume of information and level of detail involved. In this study, a Sentinel-2A Level-1C Multispectral Instrument image (MSI) from February 27, 2018 was combined with object-based image analysis (OBIA) algorithms to identify burned areas in Mae Chaem, Chom Thong, Hod, Mae Sariang, and Mae La Noi Districts in Chiang Mai, Thailand. OBIA techniques were used to classify forest, agricultural, water bodies, newly burned, and old burned regions. The segmentation scale parameter value of 50 was obtained using only the original Sentinel-2A band in red, green, blue, near infrared (NIR), and Normalized Difference Vegetation Index (NDVI). The accuracy of the produced maps was assessed using an existing burned area dataset, and the burned area identified through OBIA was found to be 85.2% accurate compared to 500 random burned points from the dataset. These results suggest that the combination of OBIA and Sentinel-2A with a 10 m spatial resolution is very effective and promising for the process of burned area mapping.
Topics: Thailand; Satellite Imagery; Algorithms; Image Processing, Computer-Assisted; Agriculture; Trees; Environmental Monitoring; Remote Sensing Technology
PubMed: 38671156
DOI: 10.1038/s41598-024-60512-w -
Current Topics in Developmental Biology 2024Satellite cells, named for their satellite position around the sarcolemma of the myofibre, are responsible for skeletal muscle regeneration. Satellite cells normally... (Review)
Review
Satellite cells, named for their satellite position around the sarcolemma of the myofibre, are responsible for skeletal muscle regeneration. Satellite cells normally reside in a quiescent state, but rapidly activate the myogenic program and the cell cycle in response to injury. Translational control of gene expression has emerged as an important regulator of satellite cell activity. Quiescent satellite cells maintain low levels of protein synthesis and selectively translate specific mRNAs to conserve limited energy. Activated satellite cells rapidly restore global protein synthesis to meet the demands of proliferating myogenic progenitors that participate in muscle repair. We propose a model by which translational control enables rapid protein level changes in response to injury-induced environmental shifts, serving as both a brake mechanism during quiescence and an accelerator for injury response. In this Chapter, we navigate the processing, translation and metabolism of newly transcribed mRNAs. We review the modifications of mRNA that occur during mRNA processing in the nucleus of satellite cells, and illustrate how these modifications impact the translation and stability of mRNAs. In the cytoplasm, we review how pathways work in concert to regulate protein synthesis globally, while trans acting microRNAs and RNA binding proteins modify specific mRNA translation within a context of tightly regulated protein synthesis. While navigating translational control of gene expression in satellite cells, this chapter reveals that despite significant progress, the field remains nascent in the broader scope of translational control in cell biology. We propose that future investigations will benefit from incorporating emerging global analyses to study translational control of gene expression in rare satellite cells, and we pose unanswered questions that warrant future exploration.
Topics: Satellite Cells, Skeletal Muscle; Animals; Protein Biosynthesis; Humans; Gene Expression Regulation; RNA, Messenger
PubMed: 38670709
DOI: 10.1016/bs.ctdb.2024.02.013