Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response

Background Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or active temperature regulation is involved. Results Using a base analog labelling method, we directly measured the temperature coefficient, Q10, of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes, transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional process exists that controls mRNA abundance by temperature. This is partly accounted for by gene body H2A.Z which is associated with low transcription rate Q10, but is also influenced by other marks and transcription factor activities. Conclusions Our data show that less frequent chromatin states can produce temperature responses simply by virtue of their rarity and the difference between their thermal properties and those of the most common states, and underline the advantages of directly measuring transcription rate changes in dynamic systems, rather than inferring rates from changes in mRNA abundance. Background The mechanism for ambient temperature sensing in plants is unclear. Control of transcript levels is believed to be important in responses to temperature [1-4] but affects of ambient temperature on transcription and mRNA decay rates have not been measured. According to the work of Arrhenius [5] the temperature coefficient (Q10) of biochemical reactions is expected to be 2 to 3 at biological temperatures: yet less than 2% of Arabidopsis thaliana genes have a two-fold or greater difference in expression level between 17°C and 27°C [6]. The remaining genes either have rates buffered against changing temperatures, or passive increases in transcription rate must be offset by a balanced increase in decay rate, leading to higher turnover but static steady state levels. Despite this fundamental uncertainty, steady state transcriptomic responses to ambient temperature have been used to infer a role for chromatin modifications in temperature signaling [2,7]. 4-Thiouracil (4SU) is a non-toxic base analogue that has been shown to be incorporated into mammalian and yeast mRNA during transcription [8-12]. Biotinylation and column separation allow 4SU-labeled RNA to be separated from unlabeled RNA, and transcriptomic analysis using the separated samples can be used to simultaneously calculate mRNA synthesis and decay rates [8]. Here we use 4SU labeling to measure transcription rates and determine the Q10 genome-wide of mRNA synthesis and decay rates in Arabidopsis thaliana. We show that ambient temperature has large passive effects on both mRNA synthesis and decay rates, and that where temperature controls transcript abundance it does so by regulating transcription relative to decay and not vice versa. Our analysis suggests that transcription factor binding sites and epigenetic state combine to create a complex network of temperature responses in plants. Results Cells incorporate 4SU into RNA and this has been exploited in mammalian cells [8,11,12] and in yeast [13] to measure mRNA synthesis and decay rates. In order to determine whether plants can take up 4SU we floated intact seedlings in MS medium and monitored 4SU incorporation into RNA by biotinylation and dot blot (Figure S1a in Additional file 1). This clearly showed that plants incorporate 4SU from the environment into RNA and that concentrations as low as 1 mM lead to a signal detectable above background within 1 hour (Figure 1B). The resulting RNA could be separated from unlabeled RNA by biotinylation and passage through a streptavidin column as described previously. At 1.5 mM the flow-through can be depleted of detectable 4SU-labeled RNA, whilst labeled plant RNA is highly concentrated in the fraction recovered from the column [8,13] (Figure S1c in Additional file 1). To maximize recovery we chose a low concentration of 4SU at 1.5 mM [8] as high labeling frequencies are known to lead to binding of fewer more frequently labeled transcripts to the columns and reduce recovery. At this concentration Arabidopsis plants treated with 4SU showed the same growth and survival as control plants (Figure S2a in Additional file 1), suggesting 4SU has low toxicity in plants, as in other organisms. Therefore, 4SU dynamics in Arabidopsis seedlings resemble those described for other experimental systems. Preliminary experiments showed that RNA turnover was faster at 27°C compared to 12°C (Figure S2b in Additional file 1), suggesting that temperature generally affected transcription rates

Nidoviruses in Reptiles: A Review

Since their discovery in 2014, reptile nidoviruses (also known as serpentoviruses) have emerged as significant pathogens worldwide. They are known for causing severe and often fatal respiratory disease in various captive snake species, especially pythons. Related viruses have been detected in other reptiles with and without respiratory disease, including captive and wild populations of lizards, and wild populations of freshwater turtles. There are many opportunities to better understand the viral diversity, species susceptibility, and clinical presentation in different species in this relatively new field of research. In captive snake collections, reptile nidoviruses can spread quickly and be associated with high morbidity and mortality, yet the potential disease risk to wild reptile populations remains largely unknown, despite reptile species declining on a global scale. Experimental studies or investigations of disease outbreaks in wild reptile populations are scarce, leaving the available literature limited mostly to exploring findings of naturally infected animals in captivity. Further studies into the pathogenesis of different reptile nidoviruses in a variety of reptile species is required to explore the complexity of disease and routes of transmission. This review focuses on the biology of these viruses, hosts and geographic distribution, clinical signs and pathology, laboratory diagnosis and management of reptile nidovirus infections to better understand nidovirus infections in reptiles

Fabrication of high quality optical coherence tomography (OCT) calibration artefacts using femtosecond inscription

Optical coherence tomography (OCT) is a non-invasive three-dimensional imaging system that is capable of producing high resolution in-vivo images. OCT is approved for use in clinical trials in Japan, USA and Europe. For OCT to be used effectively in a clinical diagnosis, a method of standardisation is required to assess the performance across different systems. This standardisation can be implemented using highly accurate and reproducible artefacts for calibration at both installation and throughout the lifetime of a system. Femtosecond lasers can write highly reproducible and highly localised micro-structured calibration artefacts within a transparent media. We report on the fabrication of high quality OCT calibration artefacts in fused silica using a femtosecond laser. The calibration artefacts were written in fused silica due to its high purity and ability to withstand high energy femtosecond pulses. An Amplitude Systemes s-Pulse Yb:YAG femtosecond laser with an operating wavelength of 1026 nm was used to inscribe three dimensional patterns within the highly optically transmissive substrate. Four unique artefacts have been designed to measure a wide variety of parameters, including the points spread function (PSF), modulation transfer function (MTF), sensitivity, distortion and resolution - key parameters which define the performance of the OCT. The calibration artefacts have been characterised using an optical microscope and tested on a swept source OCT. The results demonstrate that the femtosecond laser inscribed artefacts have the potential of quantitatively and qualitatively validating the performance of any OCT system

Polar positioning of a conjugation protein from the integrative and conjugative element ICEBs1 of Bacillus subtilis

ICEBs1 is an integrative and conjugative element found in the chromosome of Bacillus subtilis. ICEBs1 encodes functions needed for its excision and transfer to recipient cells. We found that the ICEBs1 gene conE (formerly yddE) is required for conjugation and that conjugative transfer of ICEBs1 requires a conserved ATPase motif of ConE. ConE belongs to the HerA/FtsK superfamily of ATPases, which includes the well-characterized proteins FtsK, SpoIIIE, VirB4, and VirD4. We found that a ConE-GFP (green fluorescent protein) fusion associated with the membrane predominantly at the cell poles in ICEBs1 donor cells. At least one ICEBs1 product likely interacts with ConE to target it to the membrane and cell poles, as ConE-GFP was dispersed throughout the cytoplasm in a strain lacking ICEBs1. We also visualized the subcellular location of ICEBs1. When integrated in the chromosome, ICEBs1 was located near midcell along the length of the cell, a position characteristic of that chromosomal region. Following excision, ICEBs1 was more frequently found near a cell pole. Excision of ICEBs1 also caused altered positioning of at least one component of the replisome. Taken together, our findings indicate that ConE is a critical component of the ICEBs1 conjugation machinery, that conjugative transfer of ICEBs1 from B. subtilis likely initiates at a donor cell pole, and that ICEBs1 affects the subcellular position of the replisome.Public Health Service (grant GM50895 (A.D.G.))Suffolk University. Department of Chemistry and Biochemistr

Parametric study of femtosecond inscription of microstructures for OCT artefact fabrication

As optical coherence tomography (OCT) becomes widespread, validation and characterization of systems becomes important. Reference standards are required to qualitatively and quantitatively measure the performance between difference systems. This would allow the performance degradation of the system over time to be monitored. In this report, the properties of the femtosecond inscribed structures from three different systems for making suitable OCT characterization artefacts (phantoms) are analyzed. The parameter test samples are directly inscribed inside transparent materials. The structures are characterized using an optical microscope and a swept-source OCT. The high reproducibility of the inscribed structures shows high potential for producing multi-modality OCT calibration and characterization phantoms. Such that a single artefact can be used to characterize multiple performance parameters such the resolution, linearity, distortion, and imaging depths

Depression, Loneliness, and Life Satisfaction in Emerging Adults

Abstract: Existing research indicates that loneliness can lead to negative outcomes such as depression and anxiety (United States Department of Health and Human Services, 2023). When examining the role sleep plays in this relationship, research has shown that an increase in sleep quality is related to a decrease in levels of loneliness (Hladek, 2021). In addition, we examined the relationship between depression and life satisfaction, with the variable gratitude serving as a mediator to that relationship. Previous research has indicated that higher levels of gratitude negatively effects levels of depression (Wood et al., 2008). In previous research, as levels of depression began to decrease, life satisfaction levels increased with hope and gratitude both serving as mediators (Kwok, 2016). However, within our study we are focusing our research on emerging adults and focusing solely on gratitude to evaluate a mediated relationship. Within our study, emerging adult college students (N= 46) took a Qualtrics survey that measured: demographics and levels of life satisfaction, gratitude, loneliness, and sleep quality. Results indicated that higher levels of loneliness did not significantly predict lower levels of life satisfaction, considering sleep quality as a mediator. However, there was a significant indirect effect of depression on life satisfaction via gratitude as a mediator, b = -0.237, boot SE = 0.094, 95% bootstrap CI [-0.432, -0.071]. These results indicate that lower levels of gratitude can be attributed as a reason why high depression leads to lower life satisfaction, and further suggests that improving gratitude may be necessary to combat the negative effects of depression on life satisfaction in the emerging adult population

Linear/Nonlinear Relations of Activity and Fitness with Children’s Academic Achievement

This is an an accepted manuscript and not the final published version.ABSTRACT: A growing research base suggests the benefits of physical activity (PA) and aerobic fitness for children extend beyond overall health/well-being to include academic achievement (AA). The majority of research studies on relations of PA and fitness with AA have utilized linear-only analytic approaches, thereby precluding the possibility that PA and fitness could have a differing impact on AA for those more/less active or fit. OBJECTIVE: Evaluate both linear and non-linear associations of PA and aerobic fitness with children’s AA among a sample of 687 2nd and 3rd grade students from 17 Midwest schools. STUDY DESIGN: Using baseline data (fall 2011) from a larger 3-year intervention trial, multi-level regression analyses examined the linear and non-linear associations of AA with PA and with PACER laps (i.e., aerobic fitness), controlling for relevant covariates. RESULTS: Fitness, but not PA, had a significant quadratic association with both spelling and math achievement. Results indicate that 22–28 laps on the PACER was the point at which the associated increase in achievement per lap plateaued for spelling and math. CONCLUSIONS: Increasing fitness could potentially have the greatest impact on children’s AA for those below the 50th fitness percentile on the PACER

High Risk Hustling: Payment Processors Sexual Proxies and Discrimination by Design

Sex workers are increasingly documenting financial discrimination when accessing banks, payment processors and financial providers. As hustle economy workers, barriers to digital financial infrastructure impact sex workers’ abilities to maintain their livelihoods, resulting in structural marginalization and vulnerability to violence. Internationally, peer-led sex worker organizations have documented payment processors that discriminate, collating public policies and user experiences. They report refusals of merchant services, being unable to open accounts, being denied loans, finance or insurance, higher premiums, and having money frozen, withheld or forfeited. In this article, we examine the policies of banks and payment providers who refuse service to sex workers, sex industry businesses and other sexual purposes. Drawing from sex worker media from two different regulatory environments, the United States and Australia, we show how sex workers are identified via multiple means, including through algorithmic detection, malicious flagging, unique business names, service descriptions, external links, use of pseudonyms, linking of personal and professional identities, and sex work activism. We argue that the ‘sexual proxies’ that identify sex workers are founded on problematic assumptions of sex as high risk and operate to capture a wide variety of uses, including access to sex education, abortion services and mutual aid funds. We position financial discrimination against sex workers as a multi-layered problem, stemming from classist, racist, transphobic, and whorephobic laws and policies, accelerated by automated risk assessments and privatization of financial infrastructure. Financial discrimination is enabled by the criminalization of sex work, and, due to the exportation of U.S. policy, continues even in jurisdictions where sex work is decriminalized, buoyed by anti-trafficking policies that conflate sex work with exploitation and identity verification policies driven by anti-terrorism and anti-fraud legislation. As a result, financial discrimination disproportionately impacts sex workers who are undocumented, marginalized or most at risk of violence. The current challenge facing sex workers is how to survive in this system, including by holding payment processors accountable. We outline a series of potential accountability measures, including an overhaul of law and policy frameworks

Reef-fidelity and migration of tiger sharks, Galeocerdo cuvier, across the Coral Sea

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e83249, doi:10.1371/journal.pone.0083249.Knowledge of the habitat use and migration patterns of large sharks is important for assessing the effectiveness of large predator Marine Protected Areas (MPAs), vulnerability to fisheries and environmental influences, and management of shark–human interactions. Here we compare movement, reef-fidelity, and ocean migration for tiger sharks, Galeocerdo cuvier, across the Coral Sea, with an emphasis on New Caledonia. Thirty-three tiger sharks (1.54 to 3.9 m total length) were tagged with passive acoustic transmitters and their localised movements monitored on receiver arrays in New Caledonia, the Chesterfield and Lord Howe Islands in the Coral Sea, and the east coast of Queensland, Australia. Satellite tags were also used to determine habitat use and movements among habitats across the Coral Sea. Sub-adults and one male adult tiger shark displayed year-round residency in the Chesterfields with two females tagged in the Chesterfields and detected on the Great Barrier Reef, Australia, after 591 and 842 days respectively. In coastal barrier reefs, tiger sharks were transient at acoustic arrays and each individual demonstrated a unique pattern of occurrence. From 2009 to 2013, fourteen sharks with satellite and acoustic tags undertook wide-ranging movements up to 1114 km across the Coral Sea with eight detected back on acoustic arrays up to 405 days after being tagged. Tiger sharks dove 1136 m and utilised three-dimensional activity spaces averaged at 2360 km3. The Chesterfield Islands appear to be important habitat for sub-adults and adult male tiger sharks. Management strategies need to consider the wide-ranging movements of large (sub-adult and adult) male and female tiger sharks at the individual level, whereas fidelity to specific coastal reefs may be consistent across groups of individuals. Coastal barrier reef MPAs, however, only afford brief protection for large tiger sharks, therefore determining the importance of other oceanic Coral Sea reefs should be a priority for future research.Funding was provided by the the Agence Francaise de Développement (http://www.afd.fr), French Pacific Fund, the CRISP program (www.crisponline.info) and QLD Fisheries

Indirect and direct relations between aerobic fitness, physical activity, and academic achievement in elementary school students

BACKGROUND: There is evidence to suggest that increasing physical activity (PA) improves academic achievement (AA) in children and that aerobic fitness is associated with both cognitive function and AA. However, it is not known how these variables are interrelated and analyses with adequate control for socioeconomic variables are needed. It was hypothesized that PA would not directly affect AA but would have an indirect effect on AA through its effect on aerobic fitness. The purpose of this study was to test this hypothesized mediation using path analysis. METHODS: Cross-sectional data including AA, aerobic fitness, and daily PA assessed through accelerometry were collected from a large sample (N = 687) of 2nd and 3rd grade students. Demographic data were assessed via parent self-report. RESULTS: A total of 401 students wore the accelerometer for at least 10 hours on 3 days or more and were included in the final path analysis to evaluate potential relations among PA (predictor), aerobic fitness (mediator), and WIAT-III subtest standard scores (outcomes; i.e., reading, spelling, and mathematics). Findings showed a direct effect of PA on aerobic fitness (b = 0.009, p < 0.001) and an indirect effect (mediation) of PA via fitness on math achievement (b = 0.003, p < 0.01) after controlling for student’s grade, gender, body mass index, mother’s education level, and household income, as well as intraclass correlations among classes and schools. Neither PA nor aerobic fitness were correlated with WIAT-III reading or spelling scores. CONCLUSIONS: Mediation analysis indicated that PA exerted an influence on math achievement through its effects on aerobic fitness but was not associated with reading or spelling achievement scores