Analysis of Clock-Regulated Genes in Neurospora Reveals Widespread Posttranscriptional Control of Metabolic Potential

Neurospora crassa has been for decades a principal model for filamentous fungal genetics and physiology as well as for understanding the mechanism of circadian clocks. Eukaryotic fungal and animal clocks comprise transcription-translation-based feedback loops that control rhythmic transcription of a substantial fraction of these transcriptomes, yielding the changes in protein abundance that mediate circadian regulation of physiology and metabolism: Understanding circadian control of gene expression is key to understanding eukaryotic, including fungal, physiology. Indeed, the isolation of clock-controlled genes (ccgs) was pioneered in Neurospora where circadian output begins with binding of the core circadian transcription factor WCC to a subset of ccg promoters, including those of many transcription factors. High temporal resolution (2-h) sampling over 48 h using RNA sequencing (RNA-Seq) identified circadianly expressed genes in Neurospora, revealing that from ∼10% to as much 40% of the transcriptome can be expressed under circadian control. Functional classifications of these genes revealed strong enrichment in pathways involving metabolism, protein synthesis, and stress responses; in broad terms, daytime metabolic potential favors catabolism, energy production, and precursor assembly, whereas night activities favor biosynthesis of cellular components and growth. Discriminative regular expression motif elicitation (DREME) identified key promoter motifs highly correlated with the temporal regulation of ccgs. Correlations between ccg abundance from RNA-Seq, the degree of ccg-promoter activation as reported by ccg-promoter-luciferase fusions, and binding of WCC as measured by ChIP-Seq, are not strong. Therefore, although circadian activation is critical to ccg rhythmicity, posttranscriptional regulation plays a major role in determining rhythmicity at the mRNA level

Long Days Enhance Recognition Memory and Increase Insulin-like Growth Factor 2 in the Hippocampus

Light improves cognitive function in humans; however, the neurobiological mechanisms underlying positive effects of light remain unclear. One obstacle is that most rodent models have employed lighting conditions that cause cognitive deficits rather than improvements. Here we have developed a mouse model where light improves cognitive function, which provides insight into mechanisms underlying positive effects of light. To increase light exposure without eliminating daily rhythms, we exposed mice to either a standard photoperiod or a long day photoperiod. Long days enhanced long-term recognition memory, and this effect was abolished by loss of the photopigment melanopsin. Further, long days markedly altered hippocampal clock function and elevated transcription of Insulin-like Growth Factor2 (Igf2). Up-regulation of Igf2 occurred in tandem with suppression of its transcriptional repressor Wilm’s tumor1. Consistent with molecular de-repression of Igf2, IGF2 expression was increased in the hippocampus before and after memory training. Lastly, long days occluded IGF2-induced improvements in recognition memory. Collectively, these results suggest that light changes hippocampal clock function to alter memory, highlighting novel mechanisms that may contribute to the positive effects of light. Furthermore, this study provides insight into how the circadian clock can regulate hippocampus-dependent learning by controlling molecular processes required for memory consolidation

NOX2 inhibition enables retention of the circadian clock in BV2 microglia and primary macrophages

IntroductionSustained neuroinflammation is a major contributor to the progression of neurodegenerative diseases such as Alzheimer’s (AD) and Parkinson’s (PD) diseases. Neuroinflammation, like other cellular processes, is affected by the circadian clock. Microglia, the resident immune cells in the brain, act as major contributors to neuroinflammation and are under the influence of the circadian clock. Microglial responses such as activation, recruitment, and cytokine expression are rhythmic in their response to various stimuli. While the link between circadian rhythms and neuroinflammation is clear, significant gaps remain in our understanding of this complex relationship. To gain a greater understanding of this relationship, the interaction between the microglial circadian clock and the enzyme NADPH Oxidase Isoform 2 (NOX2) was studied; NOX2 is essential for the production of reactive oxygen species (ROS) in oxidative stress, an integral characteristic of neuroinflammation.MethodsBV2 microglia were examined over circadian time, demonstrating oscillations of the clock genes Per2 and Bmal1 and the NOX2 subunits gp91phox and p47phox.ResultsThe BV2 microglial clock exerted significant control over NOX2 expression and inhibition of NOX2 enabled the microglia to retain a functional circadian clock while reducing levels of ROS and inflammatory cytokines. These trends were mirrored in mouse bone marrow-derived primary macrophages.ConclusionsNOX2 plays a crucial role in the interaction between the circadian clock and the activation of microglia/macrophages into their pro-inflammatory state, which has important implications in the control of neuroinflammation

Inter-relationships among alternative definitions of feed efficiency in grazing lactating dairy cows

peer-reviewedInternational interest in feed efficiency, and in particular energy intake and residual energy intake (REI), is intensifying due to a greater global demand for animal-derived protein and energy sources. Feed efficiency is a trait of economic importance, and yet is overlooked in national dairy cow breeding goals. This is due primarily to a lack of accurate data on commercial animals, but also a lack of clarity on the most appropriate definition of the feed intake and utilization complex. The objective of the present study was to derive alternative definitions of energetic efficiency in grazing lactating dairy cows and to quantify the inter-relationships among these alternative definitions. Net energy intake (NEI) from pasture and concentrate intake was estimated up to 8 times per lactation for 2,693 lactations from 1,412 Holstein-Friesian cows. Energy values of feed were based on the French Net Energy system where 1 UFL is the net energy requirements for lactation equivalent of 1 kg of air-dry barley. A total of 8,183 individual feed intake measurements were available. Energy balance was defined as the difference between NEI and energy expenditure. Efficiency traits were either ratio-based or residual-based; the latter were derived from least squares regression models. Residual energy intake was defined as NEI minus predicted energy to fulfill the requirements for the various energy sinks. The energy sinks (e.g., NEL, metabolic live weight) and additional contributors to energy kinetics (e.g., live weight loss) combined, explained 59% of the variation in NEI, implying that REI represented 41% of the variance in total NEI. The most efficient 10% of test-day records, as defined by REI (n = 709), on average were associated with a 7.59 UFL/d less NEI (average NEI of the entire population was 16.23 UFL/d) than the least efficient 10% of test-day records based on REI (n = 709). Additionally, the most efficient 10% of test-day records, as defined by REI, were associated with superior energy conversion efficiency (ECE, i.e., NEL divided by NEI; ECE = 0.55) compared with the least efficient 10% of test-day records (ECE = 0.33). Moreover, REI was positively correlated with energy balance, implying that more negative REI animals (i.e., deemed more efficient) are expected to be, on average, in greater negative energy balance. Many of the correlations among the 14 defined efficiency traits differed from unity, implying that each trait is measuring a different aspect of efficiency.The authors gratefully acknowledge funding from the Irish Department of Agriculture, Food and Marine (Dublin, Ireland) Research Stimulus Fund project GENCOST, and funding from the Marie Curie project International Research Staff Exchange Scheme SEQSE

Characteristics of feed efficiency within and across lactation in dairy cows and the effect of genetic selection

peer-reviewedThe objective of the present study was to investigate the phenotypic inter- and intra-relationships within and among alternative feed efficiency metrics across different stages of lactation and parities; the expected effect of genetic selection for feed efficiency on the resulting phenotypic lactation profiles was also quantified. A total of 8,199 net energy intake (NEI) test-day records from 2,505 lactations on 1,290 cows were used. Derived efficiency traits were either ratio based or residual based; the latter were derived from least squares regression models. Residual energy intake (REI) was defined as NEI minus predicted energy requirements based on lactation performance; residual energy production (REP) was defined as net energy for lactation minus predicted energy requirements based on lactation performance. Energy conversion efficiency was defined as net energy for lactation divided by NEI. Pearson phenotypic correlations among traits were computed across lactation stages and parities, and the significance of the differences was determined using the Fisher r-to-z transformation. Sources of variation in the feed efficiency metrics were investigated using linear mixed models, which included the fixed effects of contemporary group, breed, parity, stage of lactation, and the 2-way interaction of parity by stage of lactation. With the exception of REI, parity was associated with all efficiency and production traits. Stage of lactation, as well as the 2-way interaction of parity by stage of lactation, were associated with all efficiency and production traits. Phenotypic correlations among the efficiency and production traits differed not only by stage of lactation but also by parity. For example, the strong phenotypic correlation between REI and energy balance (EB; 0.89) for cows in parity 3 or greater and early lactation was weaker for parity 1 cows at the same lactation stage (0.81), suggesting primiparous cows use the ingested energy for both milk production and growth. Nonetheless, these strong phenotypic correlations between REI and EB suggested negative REI animals (i.e., more efficient) are also in more negative EB. These correlations were further supported when assessing the effect on phenotypic performance of animals genetically divergent for feed intake and efficiency based on parental average. Animals genetically selected to have lower REI resulted in cows who consumed less NEI but were also in negative EB throughout the entire lactation. Nonetheless, such repercussions of negative EB do not imply that selection for negative REI (as defined here) should not be practiced, but instead should be undertaken within the framework of a balanced breeding objective, which includes traits such as reproduction and health.Funding from the Irish Department of Agriculture, Food and Marine (Dublin, Ireland) Research Stimulus Fund project Genetics of cost production traits (GENCOST), and funding from the Horizon 2020 Marie Curie project International Research Staff Exchange Scheme Global cooperation to develop next generation whole genome sequence selection tools for novel traits (SEQSEL) are greatly appreciated

AMI-LA radio continuum observations of Spitzer c2d small clouds and cores: Perseus region

We present deep radio continuum observations of the cores identified as deeply embedded young stellar objects in the Perseus molecular cloud by the Spitzer c2d programme at a wavelength of 1.8 cm with the Arcminute Microkelvin Imager Large Array (AMI-LA). We detect 72% of Class 0 objects from this sample and 31% of Class I objects. No starless cores are detected. We use the flux densities measured from these data to improve constraints on the correlations between radio luminosity and bolometric luminosity, infrared luminosity and, where measured, outflow force. We discuss the differing behaviour of these objects as a function of protostellar class and investigate the differences in radio emission as a function of core mass. Two of four possible very low luminosity objects (VeLLOs) are detected at 1.8 cm.Comment: 18 pages, 9 figures, accepted MNRA

Physiotherapy for sleep disturbance in chronic low back pain: a feasibility randomised controlled trial

<p>Abstract</p> <p>Background</p> <p>Sleep disturbance is becoming increasingly recognised as a clinically important symptom in people with chronic low back pain (CLBP, low back pain >12 weeks), associated with physical inactivity and depression. Current research and international clinical guidelines recommend people with CLBP assume a physically active role in their recovery to prevent chronicity, but the high prevalence of sleep disturbance in this population may be unknowingly limiting their ability to participate in exercise-based rehabilitation programmes and contributing to poor outcomes. There is currently no knowledge concerning the effectiveness of physiotherapy on sleep disturbance in people with chronic low back pain and no evidence of the feasibility of conducting randomized controlled trials that comprehensively evaluate sleep as an outcome measure in this population.</p> <p>Methods/Design</p> <p>This study will evaluate the feasibility of a randomised controlled trial (RCT), exploring the effects of three forms of physiotherapy (supervised general exercise programme, individualized walking programme and usual physiotherapy, which will serve as the control group) on sleep quality in people with chronic low back pain. A presenting sample of 60 consenting patients will be recruited in the physiotherapy department of Beaumont Hospital, Dublin, Ireland, and randomly allocated to one of the three groups in a concealed manner. The main outcomes will be sleep quality (self-report and objective measurement), and self-reported functional disability, pain, quality of life, fear avoidance, anxiety and depression, physical activity, and patient satisfaction. Outcome will be evaluated at baseline, 3 months and 6 months. Qualitative telephone interviews will be embedded in the research design to obtain feedback from a sample of participants' about their experiences of sleep monitoring, trial participation and interventions, and to inform the design of a fully powered future RCT. Planned analysis will explore trends in the data, effect sizes and clinically important effects (quantitative data), and thematic analysis (qualitative data).</p> <p>Discussion</p> <p>This study will evaluate the feasibility of a randomised controlled trial exploring the effects of three forms of physiotherapy (supervised general exercise programme, individualized walking programme and usual physiotherapy, which will serve as the control group) on sleep quality in people with chronic low back pain.</p> <p>Trial Registration</p> <p>Current controlled trial ISRCTN54009836</p

Biochemical adaptations of the retina and retinal pigment epithelium support a metabolic ecosystem in the vertebrate eye

Here we report multiple lines of evidence for a comprehensive model of energy metabolism in the vertebrate eye. Metabolic flux, locations of key enzymes, and our finding that glucose enters mouse and zebrafish retinas mostly through photoreceptors support a conceptually new model for retinal metabolism. In this model, glucose from the choroidal blood passes through the retinal pigment epithelium to the retina where photoreceptors convert it to lactate. Photoreceptors then export the lactate as fuel for the retinal pigment epithelium and for neighboring Mu ̈ ller glial cells. We used human retinal epithelial cells to show that lactate can suppress consumption of glucose by the retinal pigment epithelium. Suppression of glucose consumption in the retinal pigment epithelium can increase the amount of glucose that reaches the retina. This framework for understanding metabolic relationships in the vertebrate retina provides new insights into the underlying causes of retinal disease and age-related vision loss