Revisiting regulatory decoherence: Accounting for temporal bias in a co-expression analysis reveals novel candidates controlling environmental response

Transcriptional Regulatory Networks (TRNs) orchestrate the timing, magnitude, and rate of organismal response to many environmental perturbations. Regulatory interactions in TRNs are dynamic but exploiting temporal variation to understand gene regulation requires a careful appreciation of both molecular biology and confounders in statistical analysis. Seeking to exploit the abundance of RNASequencing data now available, many past studies have relied upon population-level statistics from cross-sectional studies, estimating gene co-expression interactions to capture transient changes of regulatory activity. We show that population-level co-expression exhibits biases when capturing transient changes of regulatory activity in rice plants responding to elevated temperature. An apparent cause of this bias is regulatory saturation, the observation that detectable co-variance between a regulator and its target may be low as their transcript abundances are induced. This phenomenon appears to be particularly acute for rapid onset environmental stressors. However, exploiting temporal correlations appears to be a reliable means to detect transient regulatory activity following rapid onset environmental perturbations such as temperature stress. Such temporal correlation may lose information along a more gradual-onset stressor (e.g., dehydration). We here show that rice plants exposed to a dehydration stress exhibit temporal structure of coexpression in their response that can not be unveiled by temporal correlation alone. Collectively, our results point to the need to account for the nuances of molecular interactions and the possibly confounding effects that these can introduce into conventional approaches to study transcriptome datasets.

A decade of glaciological and meteorological observations in the Arctic (Werenskioldbreen, Svalbard)

The warming of the Arctic climate is well documented, but the mechanisms of Arctic amplification are still not fully understood. Thus, monitoring of glaciological and meteorological variables and the environmental response to accelerated climate warming must be continued and developed in Svalbard. Long-term meteorological observations carried out in situ on glaciers in conjunction with glaciological monitoring are rare in the Arctic and significantly expand our knowledge about processes in the polar environment. This study presents the unique glaciological and meteorological data collected in 2009–2020 in southern Spitsbergen (Werenskioldbreen). The meteorological data are comprised of air temperature, relative humidity, wind speed and direction, shortwave and longwave upwelling and downwelling radiation on 10 minutes, hourly and daily timescale (2009–2020). The snow dataset includes 49 sampling points from 2009–2019 with the snow depth, snow bulk density and SWE data. The glaciological data consist of point and surface annual winter, summer and net balance for 2009–2020. The paper also includes modelling of the daily glacier surface ablation (2009–2020) based on the presented data. The high-quality and long-term datasets are expected to serve as accurate forcing data in hydrological and glaciological models and validation of remote sensing products. The datasets are available from the and Polish Polar Database (https://ppdb.us.edu.pl/) and Zenodo (https://doi.org/10.5281/zenodo.5791748, Ignatiuk, 2021a; https://doi.org/10.5281/zenodo.5792168, Ignatiuk, 2021b).

Hydro-environmental response to the inter-basin water resource development in the middle and lower Han River, China

As one of the most important influencing factors, inter-basin water resource development has been exerting an increasingly evident impact on the hydro-environment of river basins. The Han River was selected as a case study to reveal the hydro-environmental response to China's inter-basin water resource development. The hydrological changes and water-quality variations resulted from the middle route of the South-to-North Water Transfer Project (SNWTP) and the Three Gorges Reservoir (TGR) operation were examined based on a hydro-environmental model. The results indicated that the runoff reduction is obvious after the SNWTP operation, and the low-flow duration significantly increased by 4–5 months. Consequently, the flow decrease significantly contributed to the water quality deterioration in the middle and lower Han River, while the Yangtze-Han Water Diversion Project (YHWDP) can not alleviate the situation completely. Moreover, the nutrient assimilative capacity decreased after water diversion, which agrees with the hydrological changes along the middle and lower Han River. The quantitative analysis performed in this study distinguishes the spatiotemporal variation in water quality variables using the integrated model. It provides insights into water quality management under the influences of inter-basin water resource development.

Dynamics of epigenetic modifiers and environmentally sensitive proteins in a reptile with temperature induced sex reversal

The mechanisms by which sex is determined, and how a sexual phenotype is stably maintained during adulthood, has been the focus of vigorous scientific inquiry. Resources common to the biomedical field (automated staining and imaging platforms) were leveraged to provide the first immunofluorescent data for a reptile species with temperature induced sex reversal. Two four-plex immunofluorescent panels were explored across three sex classes (sex reversed ZZf females, normal ZWf females, and normal ZZm males). One panel was stained for chromatin remodelling genes JARID2 and KDM6B, and methylation marks H3K27me3, and H3K4me3 (Jumonji Panel). The other CaRe panel stained for environmental response genes CIRBP and RelA, and H3K27me3 and H3K4me3. Our study characterised tissue specific expression and cellular localisation patterns of these proteins and histone marks, providing new insights to the molecular characteristics of adult gonads in a dragon lizard Pogona vitticeps. The confirmation that mammalian antibodies cross react in P. vitticeps paves the way for experiments that can take advantage of this new immunohistochemical resource to gain a new understanding of the role of these proteins during embryonic development, and most importantly for P. vitticeps, the molecular underpinnings of sex reversal.

Intrinsic and induced quantum quenches for enhancing qubit-based quantum noise spectroscopy

Quantum sensing protocols that exploit the dephasing of a probe qubit are powerful and ubiquitous methods for interrogating an unknown environment. They have a variety of applications, ranging from noise mitigation in quantum processors, to the study of correlated electron states. Here, we discuss a simple strategy for enhancing these methods, based on the fact that they often give rise to an inadvertent quench of the probed system: there is an effective sudden change in the environmental Hamiltonian at the start of the sensing protocol. These quenches are extremely sensitive to the initial environmental state, and lead to observable changes in the sensor qubit evolution. We show how these new features give access to environmental response properties. This enables methods for direct measurement of bath temperature, and for detecting non-thermal equilibrium states. We also discuss how to deliberately control and modulate this quench physics, which enables reconstruction of the bath spectral function. Extensions to non-Gaussian quantum baths are also discussed, as is the application of our ideas to a range of sensing platforms (e.g., nitrogen-vacancy (NV) centers in diamond, semiconductor quantum dots, and superconducting circuits).

The Relationship between the Community Structure and Function of Bacterioplankton and the Environmental Response in Qingcaosha Reservoir

Phytoplankton and bacterioplankton play a vital role in the structure and function of aquatic ecosystems, and their activity is closely linked to water eutrophication. However, few researchers have considered the temporal and spatial succession of phytoplankton and bacterioplankton, and their responses to environmental factors. The temporal and spatial succession of bacterioplankton and their ecological interaction with phytoplankton and water quality were analyzed using 16S rDNA high-throughput sequencing for their identification, and the functions of bacterioplankton were predicted. The results showed that the dominant classes of bacterioplankton in the Qingcaosha Reservoir were Gammaproteobacteria, Alphaproteobacteria, Actinomycetes, Acidimicrobiia, and Cyanobacteria. In addition, the Shannon diversity indexes were compared, and the results showed significant temporal differences based on monthly averaged value, although no significant spatial difference. The community structure was found to be mainly influenced by phytoplankton density and biomass, dissolved oxygen, and electrical conductivity. The presence of Pseudomonas and Legionella was positively correlated with that of Pseudanabaena sp., and Sphingomonas and Paragonimus with Melosira granulata. On the contrary, the presence of Planctomycetes was negatively correlated with Melosira granulata, as was Deinococcus-Thermus with Cyclotella sp. The relative abundance of denitrifying bacteria decreased from April to December, while the abundance of nitrogen-fixing bacteria increased. This study provides a scientific basis for understanding the ecological interactions between bacteria, algae, and water quality in reservoir ecosystems.

The relative effects of cognitive, emotional and physiological factors on human response to urban and park environments

Studies on the effect of urban and green environments on human risk to health and well-being tend to focus on either physiological or cognitive and emotional effects. For each of these effects, several indicators have been proposed. They are determined either by a physiological-emotional theory or by a cognitive theory of direct attention. However, the interrelationships between these indices have not been thoroughly investigated. Recently, a neurovisceral model that incorporates all three aspects has been proposed. Furthermore, it appears that the autonomic system, as measured by Heart Rate Variability (HRV), influences emotional and cognitive performance. The present article focuses on the interrelations among nine commonly used indices that represent the physiological, emotional and cognitive aspects of environmental response to urban and green environments. Path analysis and principal component analysis are used in order to identify the interrelations among the physiological, cognitive and emotional indices and the directions of these interrelations. According to the findings, the autonomic nervous system (ANS), as measured by HRV and primarily the parasympathetic tone (High frequency -HF) is the pivotal mechanism that modulates emotions and cognition in response to environmental nuisances. The ANS response precedes and may trigger the emotional and cognitive responses, which are only partially interrelated. It appears that the autonomic balance measured by SDNN and HF, the cognitive index of restoration and the emotional indices of discomfort and relaxation are closely interrelated. These seemingly disparate operands work together to form a comprehensive underlying network that causes stress and risk to health in urban environments while restoring health in green environments. The relative effects of cognitive, emotional and physiological factors on human response to urban and park environments