High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes.

Concentrations of RNAs and proteins provide important determinants of cell fate. Robust gene circuit design requires an understanding of how the combined actions of individual genetic components influence both mRNA and protein levels. Here, we simultaneously measure mRNA and protein levels in single cells using HCR Flow-FISH for a set of commonly used synthetic promoters.

Spatial and Temporal Dynamics of Chemical and Microbial Contamination in Nonurban Floodwaters.

During major flood events, waterborne contaminants are relatively poorly characterized. This is due to logistical difficulties associated with obtaining water samples in potentially dangerous flood conditions. Herein, we report analyses of water samples from a large, flooded landscape in Victoria, Australia, during a major flood event.

Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells.

To realize the potential of engineered cells in therapeutic applications, transgenes must be expressed within the window of therapeutic efficacy. Differences in copy number and other sources of extrinsic noise generate variance in transgene expression and limit the performance of synthetic gene circuits. In a therapeutic context, supraphysiological expression of transgenes can compromise engineered phenotypes and lead to toxicity.

A matrigel-free method for culture of pancreatic endocrine-like cells in defined protein-based hydrogels.

The transplantation of pancreatic endocrine islet cells from cadaveric donors is a promising treatment for type 1 diabetes (T1D), which is a chronic autoimmune disease that affects approximately nine million people worldwide. However, the demand for donor islets outstrips supply. This problem could be solved by differentiating stem and progenitor cells to islet cells.

Supercoiling-mediated feedback rapidly couples and tunes transcription.

Transcription induces a wave of DNA supercoiling, altering the binding affinity of RNA polymerases and reshaping the biochemical landscape of gene regulation. As supercoiling rapidly diffuses, transcription dynamically reshapes the regulation of proximal genes, forming a complex feedback loop. However, a theoretical framework is needed to integrate biophysical regulation with biochemical transcriptional regulation.

Evaluation of physiological stress in free-ranging bears: current knowledge and future directions.

Stress responses, which are mediated by the neurogenic system (NS) and hypothalamic-pituitary-adrenal (HPA) axis help vertebrates maintain physiological homeostasis. Fight-or-flight responses are activated by the NS, which releases norepinephrine/noradrenaline and epinephrine/adrenaline in response to immediate stressors, whilst the HPA axis releases glucocorticoid hormones (e.g.

Genetically Programmable Microbial Assembly.

Engineered microbial communities show promise in a wide range of applications, including environmental remediation, microbiome engineering, and synthesis of fine chemicals. Here we present methods by which bacterial aggregates can be directed into several distinct architectures by inducible surface expression of heteroassociative protein domains (SpyTag/SpyCatcher and SynZip17/18). Programmed aggregation can be used to activate a quorum-sensing circuit, and aggregate size can be tuned control of the amount of the associative protein displayed on the cell surface.

Transcriptome-wide changes associated with the reproductive behaviour of male guppies exposed to 17α-ethinyl estradiol.

Although many pharmaceutical compounds (and their metabolites) can induce harmful impacts at the molecular, physiological and behavioural levels, their underlying mechanistic associations have remained largely unexplored. Here, we utilized RNA-Seq to build a whole brain transcriptome profile to examine the impact of a common endocrine disrupting pharmaceutical (17α-ethinyl estradiol, EE2) on reproductive behaviour in wild guppies (Poecilia reticulata). Specifically, we annotated 16,791 coding transcripts in whole brain tissue in relation to the courtship behaviour (i.

Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales.

Connecting the molecular structure and function of chromatin across length and timescales remains a grand challenge to understanding and engineering cellular behaviors. Across five orders of magnitude, dynamic processes constantly reshape chromatin structures, driving spaciotemporal patterns of gene expression and cell fate. Through the interplay of structure and function, the genome operates as a highly dynamic feedback control system.

The endocrine disruptor, 17α-ethinyl estradiol, alters male mate choice in a freshwater fish.

Among the handful of studies on the behavioural effects of endocrine disrupting chemicals (EDCs), only a few have set out to disentangle the mechanisms underpinning behavioural changes. In fish, previous studies have shown that both visual and chemical cues play an important role in mate choice. As such, contaminant-induced changes in either transmission or perception of mate choice cues could have direct implications for individual's fitness.

Behavioural effects of psychoactive pharmaceutical exposure on European perch (Perca fluviatilis) in a multi-stressor environment.

With the ability to resist biodegradation and exert therapeutic effects at low concentrations, pharmaceutical contaminants have become environmental stressors for wildlife. One such contaminant is the anxiolytic oxazepam, a psychoactive pharmaceutical that is frequently detected in surface waters globally. Despite growing interest in understanding how wildlife respond to anxiolytics, synergistic effects of pharmaceuticals and other abiotic (e.

Field-realistic exposure to the androgenic endocrine disruptor 17β-trenbolone alters ecologically important behaviours in female fish across multiple contexts.

The capacity of pharmaceutical pollution to alter behaviour in wildlife is of increasing environmental concern. A major pathway of these pollutants into the environment is the treatment of livestock with hormonal growth promotants (HGPs), which are highly potent veterinary pharmaceuticals that enter aquatic ecosystems via effluent runoff. Hormonal growth promotants are designed to exert biological effects at low doses, can act on physiological pathways that are evolutionarily conserved across taxa, and have been detected in ecosystems worldwide.

A 20-year investigation of declining leatherback hatching success: implications of climate variation.

Unprecedented increases in air temperature and erratic precipitation patterns are predicted throughout the twenty-first century as a result of climate change. A recent global analysis of leatherback turtle hatchling output predicts that the nesting site at Sandy Point National Wildlife Refuge (SPNWR) will experience the most significant regional climate alterations. We aimed to identify how local air temperatures and precipitation patterns influenced within-nest mortality and overall hatchling output at this site between 1990 and 2010.

Characterisation of the transcriptome of male and female wild-type guppy brains with RNA-Seq and consequences of exposure to the pharmaceutical pollutant, 17α-ethinyl estradiol.

Waterways are increasingly being contaminated by chemical compounds that can disrupt the endocrinology of organisms. One such compound is 17α-ethinyl estradiol (EE2), a synthetic estrogen used in the contraceptive pill. Despite considerable research interest in the effects of EE2 on reproduction and gene expression, surprisingly, only a few studies have capitalised on technologies, such as next-generation sequencing (NGS), to uncover the molecular pathways related to EE2 exposure.

Use of erythrocyte indicators of health and condition in vertebrate ecophysiology: a review and appraisal.

We review evidence for and against the use of erythrocyte indicators of health status and condition, parasite infection level and physiological stress in free-living vertebrates. The use of indicators that are measured directly from the blood, such as haemoglobin concentration, haematocrit and erythrocyte sedimentation rate, and parameters that are calculated from multiple measured metrics, such as mean cell volume, mean cell haemoglobin content or mean cell haemoglobin concentration is evaluated. The evidence for or against the use of any given metric is equivocal when the relevant research is considered in total, although there is sometimes strong support for using a particular metric in a particular taxon.

Impacts of the antidepressant fluoxetine on the anti-predator behaviours of wild guppies (Poecilia reticulata).

Chemical pollution from pharmaceuticals is increasingly recognised as a major threat to aquatic communities. One compound of great concern is fluoxetine, which is one of the most widely prescribed psychoactive drugs in the world and frequently detected in the environment. The aim of this study was to investigate the effects of 28-d fluoxetine exposure at two environmentally relevant levels (measured concentrations: 4ng/L and 16ng/L) on anti-predator behaviour in wild guppies (Poecilia reticulata).

Sex in troubled waters: Widespread agricultural contaminant disrupts reproductive behaviour in fish.

Chemical pollution is a pervasive and insidious agent of environmental change. One class of chemical pollutant threatening ecosystems globally is the endocrine disrupting chemicals (EDCs). The capacity of EDCs to disrupt development and reproduction is well established, but their effects on behaviour have received far less attention.

Reproductive investment compromises maternal health in three species of freshwater turtle.

Life-history theory predicts that a trade-off in the allocation of resources between different physiological systems exists because resources are finite. As a result, females investing heavily in reproduction may compromise their future health. We used hematology, serum biochemistry, mass, and morphometric measurements as indicators of physiological health state to investigate whether reproductive investment altered subsequent maternal health in three Australian freshwater turtles: the oblong turtle (Chelodina oblonga; n = 12), the Macquarie turtle (Emydura macquarii; n = 9), and the eastern long-necked turtle (Chelodina longicollis; n = 8).

Interpreting indices of physiological stress in free-living vertebrates.

When vertebrate physiological ecologists use the terms 'stress' or 'physiological stress', they typically mean the level of hypothalamus-pituitary-adrenal (HPA-) axis activation. Measurements of stress hormone concentrations (e.g.

Response of the agile antechinus to habitat edge, configuration and condition in fragmented forest.

Habitat fragmentation and degradation seriously threaten native animal communities. We studied the response of a small marsupial, the agile antechinus Antechinus agilis, to several environmental variables in anthropogenically fragmented Eucalyptus forest in south-east Australia. Agile antechinus were captured more in microhabitats dominated by woody debris than in other microhabitats.

Does habitat fragmentation cause stress in the agile antechinus? A haematological approach.

Although the vertebrate stress response is essential for survival, frequent or prolonged stress responses can result in chronic physiological stress, which is associated with a suite of conditions that can impair survivorship and reproductive output. Anthropogenic habitat fragmentation and degradation are potential stressors of free-living vertebrates, and in theory could result in chronic stress. To address this issue, we compared haematological indicators of stress and condition in agile antechinus (Antechinus agilis) populations in 30 forest fragments and 30 undisturbed, continuous forest sites (pseudofragments) in south-eastern Australia over 2 years.