Variance in odds ratios for estimating the deterrent effect of darkness on cycling: Variation due to the choice of case and control hours.

Comparing the counts of cyclists travelling at specific times of day is one approach to measuring the impact of ambient light level. Here we investigate one source of variance in the magnitude of change seen in previous research-the choice of case and control hour. This was done through an analysis of cyclist flows using data from multiple automated cyclist counters in five cities (Arlington, Bergen, Berlin, Birmingham and Leeds) to determine the odds ratios (OR) for each combination of case and control hour. The results tend to reveal odds ratios above 1.0 indicating that cycling can be deterred by darkness. The odds ratios varied with the choice of case and control hour. For two cities (Birmingham and Leeds), the impact was small, with little difference in ORs between any case and control hour combination. For three cities the variance in ORs was larger. To represent the impact of darkness on cycling flows across the range of case and control hours we suggest the Mantel-Haenszel pooled odds ratio is used, in which the odds ratio for each combination of case and control hour is weighted by the total number of cyclists in that combination. This suggested a statistically significant (p<0.001) deterrent effect of darkness in all five cities.

Natural variation in photosynthetic electron transport of wheat flag leaves in response to dark-induced senescence.

Early leaf senescence affects photosynthetic efficiency and limits growth during the late production stage of winter wheat (Triticum aestivum). Natural variation in photosystem response to senescence represents a valuable resource for improving the aging traits of flag leaves. To explore the natural variation of different phases of photosynthetic electron transport in modern wheat cultivars during senescence, we exposed the flag leaves of 32 wheat cultivars to dark conditions to induce senescence process, and simultaneously measured prompt fluorescence and modulated 820 nm reflection. The results showed that the chlorophyll content, activity of PSII donor side, PSI and electron transfer between PSII and PSI were all decreased during dark-induced senescence, but they showed different sensitivity to dark-induced senescence. Furthermore, natural variation in photosynthetic parameters among the 32 wheat cultivars were also observed and showed by variation coefficient of the different parameters. We observed that PSII and PSI activity showed less sensitivity to dark-induced senescence than electron transfer between them, while PSII and PSI activity exhibit greater natural variation than electron transport between PSII and PSI. It suggests that Cytb6f might degrade faster and have less variation than PSII and PSI during dark-induced senescence.

Transcriptome-Wide Identification of Dark- and Salt-Induced Senescence-Related NAC Gene Family Members in Alfalfa.

Leaves are a key forage part for livestock, and the aging of leaves affects forage biomass and quality. Preventing or delaying premature leaf senescence leads to an increase in pasture biomass accumulation and an improvement in alfalfa quality. NAC transcription factors have been reported to affect plant growth and abiotic stress responses. In this study, 48 NAC genes potentially associated with leaf senescence were identified in alfalfa under dark or salt stress conditions. A phylogenetic analysis divided MsNACs into six subgroups based on similar gene structure and conserved motif. These MsNACs were unevenly distributed in 26 alfalfa chromosomes. The results of the collinearity analysis show that all of the MsNACs were involved in gene duplication. Some cis-acting elements related to hormones and stress were screened in the 2-kb promoter regions of MsNACs. Nine of the MsNAC genes were subjected to qRT-PCR to quantify their expression and Agrobacterium-mediated transient expression to verify their functions. The results indicate that Ms.gene031485, Ms.gene032313, Ms.gene08494, and Ms.gene77666 might be key NAC genes involved in alfalfa leaf senescence. Our findings extend the understanding of the regulatory function of MsNACs in leaf senescence.

Efficient dark-fermentation biohydrogen production by Shigella flexneri SPD1 from biowaste-derived sugars through green solvents approach.

This study evaluated the dark-fermentative hydrogen (H2) production potential of isolated and identified Shigella flexneri SPD1 from various pure (glucose, fructose, sucrose, lactose, and galactose) and biowastes (coconut coir, cotton fiber, groundnut shells, rice-, and wheat-straws)-derived sugars. Among sugars, S. flexneri SPD1 exhibited high H2 production of up to 3.20 mol/mole of hexose using glucose (5.0 g/L). The pre-treatment of various biowastes using green solvents (choline chloride and lactic acid mixture) and enzymatic hydrolysis resulted in the generation of up to 36.0 g/L of sugars. The maximum H2 production is achieved up to 2.92 mol/mol of hexose using cotton-hydrolysate. Further, the upscaling of bioprocess up to 5 L of capacity resulted in a maximum yield of up to 3.06 mol/mol of hexose. These findings suggested that S. flexneri SPD1, a novel H2-producer, can be employed to develop a circular economy-based approach to produce clean energy.

The natural variance of Arabidopsis secondary metabolism on extended darkness.

In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0-and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the Zenodo database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.

Dark-DSAR: Lightweight one-step pipeline for action recognition in dark videos.

Dark video human action recognition has a wide range of applications in the real world. General action recognition methods focus on the actor or the action itself, ignoring the dark scene where the action happens, resulting in unsatisfied accuracy in recognition. For dark scenes, the existing two-step action recognition methods are stage complex due to introducing additional augmentation steps, and the one-step pipeline method is not lightweight enough. To address these issues, a one-step Transformer-based method named Dark Domain Shift for Action Recognition (Dark-DSAR) is proposed in this paper, which integrates the tasks of domain migration and classification into a single step and enhances the model's functional coherence with respect to these two tasks, making our Dark-DSAR has low computation but high accuracy. Specifically, the domain shift module (DSM) achieves domain adaption from dark to bright to reduce the number of parameters and the computational cost. Besides, we explore the matching relationship between the input video size and the model, which can further optimize the inference efficiency by removing the redundant information in videos through spatial resolution dropping. Extensive experiments have been conducted on the datasets of ARID1.5, HMDB51-Dark, and UAV-human-night. Results show that the proposed Dark-DSAR obtains the best Top-1 accuracy on ARID1.5 with 89.49%, which is 2.56% higher than the state-of-the-art method, 67.13% and 61.9% on HMDB51-Dark and UAV-human-night, respectively. In addition, ablation experiments reveal that the action classifiers can gain ≥1% in accuracy compared to the original model when equipped with our DSM.

Light sensitivity of the circadian system in the social Highveld mole-rat Cryptomys hottentotus pretoriae.

Highveld mole-rats (Cryptomys hottentotus pretoriae) are social rodents that inhabit networks of subterranean tunnels. In their natural environment, they are rarely exposed to light, and consequently their visual systems have regressed over evolutionary time. However, in the laboratory they display nocturnal activity, suggesting that they are sensitive to changes in ambient illumination. We examined the robustness of the Highveld mole-rat circadian system by assessing its locomotor activity under decreasing light intensities. Mole-rats were subjected to seven consecutive light cycles commencing with a control cycle (overhead fluorescent lighting at 150 lx), followed by decreasing LED lighting (500, 300, 100, 10 and 1 lx) on a 12 h light:12 h dark (L:D) photoperiod and finally a constant darkness (DD) cycle. Mole-rats displayed nocturnal activity under the whole range of experimental lighting conditions, with a distinct spike in activity at the end of the dark phase in all cycles. The mole-rats were least active during the control cycle under fluorescent light, locomotor activity increased steadily with decreasing LED light intensities, and the highest activity was exhibited when the light was completely removed. In constant darkness, mole-rats displayed free-running rhythms with periods (τ) ranging from 23.77 to 24.38 h, but was overall very close to 24 h at 24.07 h. Our findings confirm that the Highveld mole-rat has a higher threshold for light compared with aboveground dwelling rodents, which is congruent with previous neurological findings, and has implications for behavioural rhythms.

Intervening dark periods negatively affect the photosynthetic performance of Chlamydomonas reinhardtii during growth under fluctuating high light.

The acclimation of the green algae Chlamydomoas reinhardtii to high light (HL) has been studied predominantly under continuous illumination of the cells. Here, we investigated the impact of fluctuating HL in alternation with either low light (LL) or darkness on photosynthetic performance and on photoprotective responses. Compared to intervening LL phases, dark phases led to (1) more pronounced reduction of the photosystem II quantum efficiency, (2) reduced degradation of the PsbS protein, (3) lower energy dissipation capacity and (4) an increased pool size of the xanthophyll cycle pigments. These characteristics indicate increased photo-oxidative stress when HL periods are interrupted by dark phases instead of LL phases. This overall trend was similar when comparing long (8 h) and short (30 min) HL phases being interrupted by long (16 h) and short (60 min) phases of dark or low light, respectively. Only the degradation of PsbS was clearly more efficient during long (16 h) LL phases when compared to short (60 min) LL phases.

Adaptation to photoperiod via dynamic neurotransmitter segregation.

Changes in the amount of daylight (photoperiod) alter physiology and behaviour1,2. Adaptive responses to seasonal photoperiods are vital to all organisms-dysregulation associates with disease, including affective disorders3 and metabolic syndromes4. The circadian rhythm circuitry is implicated in such responses5,6, yet little is known about the precise cellular substrates that underlie phase synchronization to photoperiod change. Here we identify a brain circuit and system of axon branch-specific and reversible neurotransmitter deployment that are critical for behavioural and sleep adaptation to photoperiod. A type of neuron called mrEn1-Pet17 in the mouse brainstem median raphe nucleus segregates serotonin from VGLUT3 (also known as SLC17A8, a proxy for glutamate) to different axonal branches that innervate specific brain regions involved in circadian rhythm and sleep-wake timing8,9. This branch-specific neurotransmitter deployment did not distinguish between daylight and dark phase; however, it reorganized with change in photoperiod. Axonal boutons, but not cell soma, changed neurochemical phenotype upon a shift away from equinox light/dark conditions, and these changes were reversed upon return to equinox conditions. When we genetically disabled Vglut3 in mrEn1-Pet1 neurons, sleep-wake periods, voluntary activity and clock gene expression did not synchronize to the new photoperiod or were delayed. Combining intersectional rabies virus tracing and projection-specific neuronal silencing, we delineated a preoptic area-to-mrEn1Pet1 connection that was responsible for decoding the photoperiodic inputs, driving the neurotransmitter reorganization and promoting behavioural synchronization. Our results reveal a brain circuit and periodic, branch-specific neurotransmitter deployment that regulates organismal adaptation to photoperiod change.

Do body colour and sociability impact scototaxis response of fish?

Scototaxis test is an anxiety-like test used by behavioural neuroscientists consisting in the assessment of dark/light preference of laboratory animals. This test has been widely used in fish. Most of the species have been shown to express a preference for the dark environment. However, the majority of the investigated species has a dark body colour, thus making a clear contrast with a white/bright background. Also, while in nature fish tend to be highly social, studies in the scototaxis literature tested single fish. Yet, individual vs. group behaviour might interact with scototaxis response. In experiment 1, we assessed the individual response to test the hypothesis that the different colours of the body might modulate the dark/light preference. We found that species with a dark body colour (Hyphessobrycon megalopterus) and a largely transparent body colour (Kryptopterus bicirrhis) strongly preferred the darker environment. Instead, the preference for darkness of a species with a luminescent part of the body (Paracheirodon axelrodi) was less pronounced. Lastly, a species with a white body colour (Corydoras albini) did not prefer either a bright or a dark sector. In experiment 2, we explored the behaviour of these species when inserted in shoals of 20 individuals in the experimental apparatus. While H. megalopterus and K. bichirrhis confirmed their robust preference for darker environments, the other two species changed their preference. Taken together, these results suggest that scototaxis response is context-dependent, as it appears to be modulated by the body colour and the presence/absence of other conspecifics in the surrounding.

Ribosome Pausing Negatively Regulates Protein Translation in Maize Seedlings during Dark-to-Light Transitions.

Regulation of translation is a crucial step in gene expression. Developmental signals and environmental stimuli dynamically regulate translation via upstream small open reading frames (uORFs) and ribosome pausing. Recent studies have revealed many plant genes that are specifically regulated by uORF translation following changes in growth conditions, but ribosome-pausing events are less well understood. In this study, we performed ribosome profiling (Ribo-seq) of etiolated maize (Zea mays) seedlings exposed to light for different durations, revealing hundreds of genes specifically regulated at the translation level during the early period of light exposure. We identified over 400 ribosome-pausing events in the dark that were rapidly released after illumination. These results suggested that ribosome pausing negatively regulates translation from specific genes, a conclusion that was supported by a non-targeted proteomics analysis. Importantly, we identified a conserved nucleotide motif downstream of the pausing sites. Our results elucidate the role of ribosome pausing in the control of gene expression in plants; the identification of the cis-element at the pausing sites provides insight into the mechanisms behind translation regulation and potential targets for artificial control of plant translation.

Altered Metabolism during the Dark Period in Drosophila Short Sleep Mutants.

Sleep is regulated via circadian mechanisms, but effects of sleep disruption on physiological rhythms, in particular metabolic cycling, remain unclear. To examine this question, we probed diurnal metabolic alterations of two Drosophila short sleep mutants, fumin and sleepless. Samples were collected with high temporal sampling (every 2 h) over 24 h under a 12:12 light:dark cycle, and profiling was done using an ion-switching LCMS/MS method. Fewer metabolites with 24 h oscillations were noted with short sleep (50 and 46 in fumin and sleepless, BH. Q < 0.2 by RAIN analysis) compared to a wild-type control (iso31, 63 with BH. Q < 0.2), and peak phases of the sleep mutants were consolidated into two major phase peaks at mid-day and middle of night. Overall, altered nicotinate/nicotinamide, alanine/aspartate/glutamate, acetylcholine, glyoxylate/dicarboxylate, and TCA cycle metabolism were observed in the short sleep mutants, indicative of increased energetic demand and oxidative stress compared to wild type. Both changes in cycling and discriminant models suggest unique alterations in the dark period indicative of constrained metabolic networks. Thus, we conclude that sleep loss alters metabolic function uniquely throughout the day, and further examination of specific mechanisms is warranted.

Finotypic plasticity: Predator-induced plasticity in fin size, darkness and display behaviour in a teleost fish.

Fish fins are remarkable devices of propulsion. Fin morphology is intimately linked to locomotor performance, and hence to behaviours that influence fitness, such as foraging and predator avoidance. This foreshadows a connection between fin morphology and variation in predation risk. Yet, whether prey can adjust fin morphology according to changes in perceived risk within their lifetime (a.k.a. predator-induced plasticity) remains elusive. Here, we quantify the structural size of five focal fins in crucian carp (Carassius carassius) following controlled manipulations to perceived predation risk (presence/absence of pike Esox lucius). We also assess if crucian carp respond to increased predation risk by shifts in dorsal fin colouration, and test for differences in how fish actively use their dorsal fins by quantifying the area of the fin displayed in behavioural trials. We find that crucian carp show phenotypic plasticity with regards to fin size as predator-exposed fish consistently have larger fins. Individuals exposed to perceived predation risk also increased dorsal fin darkness and actively displayed a larger area of the fin to potential predators. Our results thus provide compelling evidence for predator-induced fin enlargement, which should result in enhanced escape swimming performance. Moreover, fin-size plasticity may evolve synergistically with fin colouration and display behaviour, and we suggest that the adaptive value of this synergy is to enhance the silhouette of deep-bodied and hard-to-capture prey to deter gape-limited predators prior to attack. Together, our results provide new perspectives on the role of predation risk in development and evolution of fins.

A Light-Responsive Neural Circuit Suppresses Feeding.

Light plays an essential role in a variety of physiological processes, including vision, mood, and glucose homeostasis. However, the intricate relationship between light and an animal's feeding behavior has remained elusive. Here, we found that light exposure suppresses food intake, whereas darkness amplifies it in male mice. Interestingly, this phenomenon extends its reach to diurnal male Nile grass rats and healthy humans. We further show that lateral habenula (LHb) neurons in mice respond to light exposure, which in turn activates 5-HT neurons in the dorsal Raphe nucleus (DRN). Activation of the LHb→5-HTDRN circuit in mice blunts darkness-induced hyperphagia, while inhibition of the circuit prevents light-induced anorexia. Together, we discovered a light-responsive neural circuit that relays the environmental light signals to regulate feeding behavior in mice.

Maize smart-canopy architecture enhances yield at high densities.

Increasing planting density is a key strategy for enhancing maize yields1-3. An ideotype for dense planting requires a 'smart canopy' with leaf angles at different canopy layers differentially optimized to maximize light interception and photosynthesis4-6, among other features. Here we identified leaf angle architecture of smart canopy 1 (lac1), a natural mutant with upright upper leaves, less erect middle leaves and relatively flat lower leaves. lac1 has improved photosynthetic capacity and attenuated responses to shade under dense planting. lac1 encodes a brassinosteroid C-22 hydroxylase that predominantly regulates upper leaf angle. Phytochrome A photoreceptors accumulate in shade and interact with the transcription factor RAVL1 to promote its degradation via the 26S proteasome, thereby inhibiting activation of lac1 by RAVL1 and decreasing brassinosteroid levels. This ultimately decreases upper leaf angle in dense fields. Large-scale field trials demonstrate that lac1 boosts maize yields under high planting densities. To quickly introduce lac1 into breeding germplasm, we transformed a haploid inducer and recovered homozygous lac1 edits from 20 diverse inbred lines. The tested doubled haploids uniformly acquired smart-canopy-like plant architecture. We provide an important target and an accelerated strategy for developing high-density-tolerant cultivars, with lac1 serving as a genetic chassis for further engineering of a smart canopy in maize.

Altered pupil light and darkness reflex and eye-blink responses in late-life depression.

BACKGROUND: Late-life depression (LLD) is a prevalent neuropsychiatric disorder in the older population. While LLD exhibits high mortality rates, depressive symptoms in older adults are often masked by physical health conditions. In younger adults, depression is associated with deficits in pupil light reflex and eye blink rate, suggesting the potential use of these responses as biomarkers for LLD. METHODS: We conducted a study using video-based eye-tracking to investigate pupil and blink responses in LLD patients (n = 25), older (OLD) healthy controls (n = 29), and younger (YOUNG) healthy controls (n = 25). The aim was to determine whether there were alterations in pupil and blink responses in LLD compared to both OLD and YOUNG groups. RESULTS: LLD patients displayed significantly higher blink rates and dampened pupil constriction responses compared to OLD and YOUNG controls. While tonic pupil size in YOUNG differed from that of OLD, LLD patients did not exhibit a significant difference compared to OLD and YOUNG controls. GDS-15 scores in older adults correlated with light and darkness reflex response variability and blink rates. PHQ-15 scores showed a correlation with blink rates, while MoCA scores correlated with tonic pupil sizes. CONCLUSIONS: The findings demonstrate that LLD patients display altered pupil and blink behavior compared to OLD and YOUNG controls. These altered responses correlated differently with the severity of depressive, somatic, and cognitive symptoms, indicating their potential as objective biomarkers for LLD.

Stability of individual anthocyanins from black carrots stored in light and darkness - Impact of acylation.

Black carrot anthocyanins have gained increasing attention as natural coloring agent, owing to their higher stability than anthocyanins from berries. The stability has been attributed to their higher degree of acylation. This study investigated the impact of acylation on the stability of individual anthocyanins during storage in light and darkness. We hypothesized that the acylated anthocyanins would be more stable than the non-acylated ones. The major five anthocyanins were fractioned by semi-preparative HPLC and stored at pH 4.5 in light and darkness to investigate how acylation affected the stability. The stability was evaluated by absorption spectroscopy and mass spectrometry (MS). Two of the anthocyanins were non-acylated; 3-xylosyl(glucosyl)galactoside and cyanidin 3-xylosylgalactoside, and three were acylated; cyanidin 3-xylosyl(sinapolyglucosyl)galacto-side, cyanidin 3-xylosyl(feruloylglu-cosyl)galactoside, and cyanidin 3-xylosyl(coumaroyl-glucosyl)galactoside. Both methods (spectroscopy and MS) showed a clear effect of acylation when stored in light, but surprisingly the two non-acylated anthocyanins, showed higher stability than the three acylated ones.

Dark continuous noise from mutant G90D-rhodopsin predominantly underlies congenital stationary night blindness.

Congenital stationary night blindness (CSNB) is an inherited retinal disease that causes a profound loss of rod sensitivity without severe retinal degeneration. One well-studied rhodopsin point mutant, G90D-Rho, is thought to cause CSNB because of its constitutive activity in darkness causing rod desensitization. However, the nature of this constitutive activity and its precise molecular source have not been resolved for almost 30 y. In this study, we made a knock-in (KI) mouse line with a very low expression of G90D-Rho (equal in amount to ~0.1% of normal rhodopsin, WT-Rho, in WT rods), with the remaining WT-Rho replaced by REY-Rho, a mutant with a very low efficiency of activating transducin due to a charge reversal of the highly conserved ERY motif to REY. We observed two kinds of constitutive noise: one being spontaneous isomerization (R*) of G90D-Rho at a molecular rate (R* s-1) 175-fold higher than WT-Rho and the other being G90D-Rho-generated dark continuous noise comprising low-amplitude unitary events occurring at a very high molecular rate equivalent in effect to ~40,000-fold of R* s-1 from WT-Rho. Neither noise type originated from G90D-Opsin because exogenous 11-cis-retinal had no effect. Extrapolating the above observations at low (0.1%) expression of G90D-Rho to normal disease exhibited by a KI mouse model with RhoG90D/WTand RhoG90D/G90D genotypes predicts the disease condition very well quantitatively. Overall, the continuous noise from G90D-Rho therefore predominates, constituting the major equivalent background light causing rod desensitization in CSNB.

Diurnal predators in dim light: the ability of mantids to prey for supper.

Many insects rely heavily on visual cues in foraging and other life activities. Mantids are insect predators that usually ambush prey. The sophisticated visual system of mantids allows them to spot, track, and strike at prey with high accuracy. Mantids are categorized as diurnal animals in most cases, while our field observations suggested that they were active in foraging both day and night. Therefore, we hypothesize that predation in dim light is possible for mantids, while mantids are unable to capture prey in complete darkness. In this study, we experimentally examined whether different light conditions could affect the predation success and efficiency of mantid nymphs and adults, Hierodula chinensis Werner (Mantodea: Mantidae), through behavioral observations. Individual mantids were placed in individual chambers in complete darkness, simulated moonlight (0.1 lux), or simulated dusk (50 lux) conditions and were allowed to forage for prey items for 10 min. Our observations showed no evidence that H. chinensis could capture any prey in complete deprivation of light. The proportion of nymphs with successful predation in simulated moonlight was 50% higher than that in complete darkness and 45.83% lower than that in simulated dusk. The proportion of adults with successful predation in simulated moonlight was 42.11% higher than that in complete darkness and 57.89% lower than that in simulated dusk. Overall, the results provide new insights into the behavioral ecology of diurnal predators at night, with potential association with moonlight, starlight, and light pollution.