Ultraviolet vision in anemonefish improves colour discrimination.

In many animals, ultraviolet (UV) vision guides navigation, foraging, and communication, but few studies have addressed the contribution of UV signals to colour vision, or measured UV discrimination thresholds using behavioural experiments. Here, we tested UV colour vision in an anemonefish (Amphiprion ocellaris) using a five-channel (RGB-V-UV) LED display. We first determined that the maximal sensitivity of the A. ocellaris UV cone was ∼386 nm using microspectrophotometry. Three additional cone spectral sensitivities had maxima at ∼497, 515 and ∼535 nm. We then behaviourally measured colour discrimination thresholds by training anemonefish to distinguish a coloured target pixel from grey distractor pixels of varying intensity. Thresholds were calculated for nine sets of colours with and without UV signals. Using a tetrachromatic vision model, we found that anemonefish were better (i.e. discrimination thresholds were lower) at discriminating colours when target pixels had higher UV chromatic contrast. These colours caused a greater stimulation of the UV cone relative to other cone types. These findings imply that a UV component of colour signals and cues improves their detectability, which likely increases the prominence of anemonefish body patterns for communication and the silhouette of zooplankton prey.

Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data.

Single-cell technologies enable high-resolution studies of phenotype-defining molecular mechanisms. However, data sparsity and cellular heterogeneity make modeling biological variability across single-cell samples difficult. Here we present SCORPION, a tool that uses a message-passing algorithm to reconstruct comparable gene regulatory networks from single-cell/nuclei RNA-sequencing data that are suitable for population-level comparisons by leveraging the same baseline priors. Using synthetic data, we found that SCORPION outperformed 12 existing gene regulatory network reconstruction techniques. Using supervised experiments, we show that SCORPION can accurately identify differences in regulatory networks between wild-type and transcription factor-perturbed cells. We demonstrate SCORPION's scalability to population-level analyses using a single-cell RNA-sequencing atlas containing 200,436 cells from colorectal cancer and adjacent healthy tissues. The differences between tumor regions detected by SCORPION are consistent across multiple cohorts as well as with our understanding of disease progression, and elucidate phenotypic regulators that may impact patient survival.

Physical-Chemical Assessment of Azo Dye Basic Violet I (BVI) Discoloration Using the Corona Plasma in Batch and Flow Systems.

The decolorization of the Basic violet I (BVI) dye when interacted with a corona discharge is studied in the present work, taking in account two systems, batch and flux. The current and voltage were measured during the whole process in which a corona plasma was generated, with an applied power of 51.9 and 167.72 W where the transport gas was air. A batch reactor and a flow reactor were used, where 500 and 5000 mL of samples were treated, respectively. Optical emission spectra (OES) were measured where the oxidizing species ·OH were at wavelengths of 307.597 and 310.148 nm, associated with the A2∑+ - X2Π transition. The absorption spectra for the batch system showed a discoloration of 85.7% in the first 10 min, while in the flow system, the absorption was 93.9% at the same time and 4.5% at the same time by conventional heating. Characteristics of the final sample included an acidic solution with an electrical conductivity of 449.20 ± 55.44 and 313.6 ± 39.58 µS/cm, a dissolved oxygen concentration of 7.74 ± 0.2 and 6.37 ± 0.23 mg/L, an absorbance of 0.04 ± 0.01 and 0.03 ± 0.01 au, with turbidity measuring 1.22 ± 1.59 and 10.34 ± 4.96 NTU, and an energy cost of 1.1 × 10-1 and 6.3 × 10-1 g/kWh in the batch and continuous flow systems, respectively. The interaction of the corona plasma with water promoted the production of reactive species, resulting in the discoloration of the Basic Violet I dye.

Cephalopods and the law.

In this My word Daniel Osorio explains why cephalopod molluscs were protected by a European Union directive on laboratory animal legislation in 2013, and how the scientific community responded to the challenges posed by this development.

Mapping oto-pharyngeal development in a human inner ear organoid model.

Inner ear development requires the coordination of cell types from distinct epithelial, mesenchymal and neuronal lineages. Although we have learned much from animal models, many details about human inner ear development remain elusive. We recently developed an in vitro model of human inner ear organogenesis using pluripotent stem cells in a 3D culture, fostering the growth of a sensorineural circuit, including hair cells and neurons. Despite previously characterizing some cell types, many remain undefined. This study aimed to chart the in vitro development timeline of the inner ear organoid to understand the mechanisms at play. Using single-cell RNA sequencing at ten stages during the first 36 days of differentiation, we tracked the evolution from pluripotency to various ear cell types after exposure to specific signaling modulators. Our findings showcase gene expression that influences differentiation, identifying a plethora of ectodermal and mesenchymal cell types. We also discern aspects of the organoid model consistent with in vivo development, while highlighting potential discrepancies. Our study establishes the Inner Ear Organoid Developmental Atlas (IODA), offering deeper insights into human biology and improving inner ear tissue differentiation.

Anillin forms linear structures and facilitates furrow ingression after septin and formin depletion.

During cytokinesis, a contractile ring consisting of unbranched filamentous actin (F-actin) and myosin II constricts at the cell equator. Unbranched F-actin is generated by formin, and without formin no cleavage furrow forms. In Caenorhabditis elegans, depletion of septin restores furrow ingression in formin mutants. How the cleavage furrow ingresses without a detectable unbranched F-actin ring is unknown. We report that, in this setting, anillin (ANI-1) forms a meshwork of circumferentially aligned linear structures decorated by non-muscle myosin II (NMY-2). Analysis of ANI-1 deletion mutants reveals that its disordered N-terminal half is required for linear structure formation and sufficient for furrow ingression. NMY-2 promotes the circumferential alignment of the linear ANI-1 structures and interacts with various lipids, suggesting that NMY-2 links the ANI-1 network with the plasma membrane. Collectively, our data reveal a compensatory mechanism, mediated by ANI-1 linear structures and membrane-bound NMY-2, that promotes furrowing when unbranched F-actin polymerization is compromised.

Birds multiplex spectral and temporal visual information via retinal On- and Off-channels.

In vertebrate vision, early retinal circuits divide incoming visual information into functionally opposite elementary signals: On and Off, transient and sustained, chromatic and achromatic. Together these signals can yield an efficient representation of the scene for transmission to the brain via the optic nerve. However, this long-standing interpretation of retinal function is based on mammals, and it is unclear whether this functional arrangement is common to all vertebrates. Here we show that male poultry chicks use a fundamentally different strategy to communicate information from the eye to the brain. Rather than using functionally opposite pairs of retinal output channels, chicks encode the polarity, timing, and spectral composition of visual stimuli in a highly correlated manner: fast achromatic information is encoded by Off-circuits, and slow chromatic information overwhelmingly by On-circuits. Moreover, most retinal output channels combine On- and Off-circuits to simultaneously encode, or multiplex, both achromatic and chromatic information. Our results from birds conform to evidence from fish, amphibians, and reptiles which retain the full ancestral complement of four spectral types of cone photoreceptors.

A single-cell level comparison of human inner ear organoids with the human cochlea and vestibular organs.

Inner ear disorders are among the most common congenital abnormalities; however, current tissue culture models lack the cell type diversity to study these disorders and normal otic development. Here, we demonstrate the robustness of human pluripotent stem cell-derived inner ear organoids (IEOs) and evaluate cell type heterogeneity by single-cell transcriptomics. To validate our findings, we construct a single-cell atlas of human fetal and adult inner ear tissue. Our study identifies various cell types in the IEOs including periotic mesenchyme, type I and type II vestibular hair cells, and developing vestibular and cochlear epithelium. Many genes linked to congenital inner ear dysfunction are confirmed to be expressed in these cell types. Additional cell-cell communication analysis within IEOs and fetal tissue highlights the role of endothelial cells on the developing sensory epithelium. These findings provide insights into this organoid model and its potential applications in studying inner ear development and disorders.

A model of colour appearance based on efficient coding of natural images.

An object's colour, brightness and pattern are all influenced by its surroundings, and a number of visual phenomena and "illusions" have been discovered that highlight these often dramatic effects. Explanations for these phenomena range from low-level neural mechanisms to high-level processes that incorporate contextual information or prior knowledge. Importantly, few of these phenomena can currently be accounted for in quantitative models of colour appearance. Here we ask to what extent colour appearance is predicted by a model based on the principle of coding efficiency. The model assumes that the image is encoded by noisy spatio-chromatic filters at one octave separations, which are either circularly symmetrical or oriented. Each spatial band's lower threshold is set by the contrast sensitivity function, and the dynamic range of the band is a fixed multiple of this threshold, above which the response saturates. Filter outputs are then reweighted to give equal power in each channel for natural images. We demonstrate that the model fits human behavioural performance in psychophysics experiments, and also primate retinal ganglion responses. Next, we systematically test the model's ability to qualitatively predict over 50 brightness and colour phenomena, with almost complete success. This implies that much of colour appearance is potentially attributable to simple mechanisms evolved for efficient coding of natural images, and is a well-founded basis for modelling the vision of humans and other animals.

Assessment of cognitive impairment and depressive signs in patients with type 2 diabetes treated with metformin from Southeast Mexico: A cross-sectional study.

Multiple factors associate diabetes with cognitive impairment and depression. Antidiabetic drugs have reported antidepressant and pro-cognitive effects in diabetic and non-diabetic subjects. Antidepressant and pro-cognitive effects of metformin are reported in various studies; however, these effects are not consistent among researches. We designed a cross-sectional study. We recruited patients with T2D diagnosis from the Diabetes Clinic of the Regional Hospital of High Specialty "Dr. Gustavo A. Rovirosa Pérez" from January 2019 to May 2022. We included 431 subjects with T2D, 374 patients with metformin treatment and 57 subjects without metformin. These patients were on intensive therapies and had not a previous diagnosis of cognitive impairment or depression. We applied Mini-Mental State Examination (MMSE) to evaluate cognitive impairment, and Hamilton Depression Rating Scale (HAM-D) to assess depressive signs. Our sample had a mean age of 53.77 ± 13.43 years. Metformin users were 374 individuals, and 57 subjects didn't use metformin. MMSE found cognitive impairment in 8.3% (n = 31) of metformin users, and 14.8% (n = 8) of patients without metformin. HAM-D scale showed that 39.5% (n = 147) of patients with metformin had depression signs, subjects without metformin and depressive signs were 44.6% (n = 25). We found no differences between groups for cognitive impairment and depression grades. We did not find associations between metformin treatment, cognitive impairment measures and depression sign measures. However, chronic metformin treatment, insulin use, glycemic control and age could influence our results.

Rabies, the cause of fatal encephalitis.

To describe the clinical progression and medical protocols applied in a 41 year old man who was bited by a bat three months before. The patient did not ask for medical care until acute tremor and pain in the right thoracic limb and hydro-phobia started. For a history of a wild animal bite associated with a unique clinical condition, we suspected of rabies encephalitis, confirming the diagnostic by pathology after his death. This case ocurred in Guadalajara, Jalisco, México, in April, 2022. The last case of human rabies reported in Jalisco secondary to bat bite was almost 30 years ago. As an uncomon disease, medical personnel and facilities should be prepared to attend this sort of cases after clinical suspicion. For the present case, the medical history was the key for diagnosis. Rabies is a disease caused by the neurotropic virus belonging to the Rhabdoviridae family whose prognosis is bleak, with mortality close to 100% and therapeutic options limited. This case emphasizes the high mortality of rabies virus infection and the importance of increasing awareness and education to the public in general, with regard to applying the vaccine as post-exposure prophylaxis.

Ablation of long noncoding RNA MALAT1 activates antioxidant pathway and alleviates sepsis in mice.

The metastasis-associated lung adenocarcinoma transcript1 (MALAT1) is a long noncoding RNA (lncRNA) and is known for its role in cancer development and prognosis. In this study, we report that MALAT1 plays an important role in regulating acute inflammatory responses in sepsis. In patient samples, MALAT1 expression was positively correlated with severity of sepsis. In cultured macrophages, LPS treatment significantly induced MALAT1 expression, while genetic ablation of MALAT1 greatly reduced proinflammatory cytokine levels. Furthermore, MALAT1-ablated mice had significantly increased survival rates in cecal ligation and puncture (CLP)-induced sepsis and LPS-induced endotoxemia. One novel and salient feature of MALAT1-ablated mice is greatly reduced ROS level in macrophages and other cell types and increased glutathione/oxidized glutathione (GSH/GSSG) ratio in macrophages, suggesting an increased antioxidant capacity. We showed a mechanism for MALAT1 ablation leading to enhanced antioxidant capacity is through activation of methionine cycle by epitranscriptomical regulation of methionine adenosyltransferase 2A (MAT2A). MAT2A 3'UTR can be methylated by METTL16 which was known to directly bind to MALAT1. MALAT1 ablation was found to reduce methylation in MAT2A hairpin1 and increase MAT2A protein levels. Our results suggest a MALAT1-METTL16-MAT2A interactive axis which may be targeted for treatments of sepsis.

scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation.

Gene knockout (KO) experiments are a proven, powerful approach for studying gene function. However, systematic KO experiments targeting a large number of genes are usually prohibitive due to the limit of experimental and animal resources. Here, we present scTenifoldKnk, an efficient virtual KO tool that enables systematic KO investigation of gene function using data from single-cell RNA sequencing (scRNA-seq). In scTenifoldKnk analysis, a gene regulatory network (GRN) is first constructed from scRNA-seq data of wild-type samples, and a target gene is then virtually deleted from the constructed GRN. Manifold alignment is used to align the resulting reduced GRN to the original GRN to identify differentially regulated genes, which are used to infer target gene functions in analyzed cells. We demonstrate that the scTenifoldKnk-based virtual KO analysis recapitulates the main findings of real-animal KO experiments and recovers the expected functions of genes in relevant cell types.

Multi-level control of adaptive camouflage by European cuttlefish.

To camouflage themselves on the seafloor, European cuttlefish Sepia officinalis control the expression of about 30 pattern components to produce a range of body patterns.1 If each component were under independent control, cuttlefish could produce at least 230 patterns. To examine how cuttlefish deploy this vast potential, we recorded cuttlefish on seven experimental backgrounds, each designed to resemble a pattern component, and then compared their responses to predictions of two models of sensory control of component expression. The body pattern model proposes that cuttlefish integrate low-level sensory cues to categorize the background and co-ordinate component expression to produce a small number of overall body patterns.2-4 The feature matching model proposes that each component is expressed in response to one (or more) local visual features, and the overall pattern depends upon the combination of features in the background. Consistent with the feature matching model, six of the backgrounds elicited a specific set of one to four components, whereas the seventh elicited eleven components typical of a disruptive body pattern. This evidence suggests that both modes of control are important, and we suggest how they can be implemented by a recent hierarchical model of the cuttlefish motor system.5,6.

A genetic algorithm approach to design job rotation schedules ensuring homogeneity and diversity of exposure in the automotive industry.

Job rotation is a work organization strategy with increasing popularity, given its benefits for workers and companies, especially those working with manufacturing. This study proposes a formulation to help the team leader in an assembly line of the automotive industry to achieve job rotation schedules based on three major criteria: improve diversity, ensure homogeneity, and thus reduce exposure level. The formulation relied on a genetic algorithm, that took into consideration the biomechanical risk factors (EAWS), workers' qualifications, and the organizational aspects of the assembly line. Moreover, the job rotation plan formulated by the genetic algorithm formulation was compared with the solution provided by the team leader in a real life-environment. The formulation proved to be a reliable solution to design job rotation plans for increasing diversity, decreasing exposure, and balancing homogeneity within workers, achieving better results in all of the outcomes when compared with the job rotation schedules created by the team leader. Additionally, this solution was less time-consuming for the team leader than a manual implementation. This study provides a much-needed solution to the job rotation issue in the manufacturing industry, with the genetic algorithm taking less time and showing better results than the job rotations created by the team leaders.

Colour discrimination thresholds vary throughout colour space in a reef fish (Rhinecanthus aculeatus).

Animals use colour vision in a range of behaviours. Visual performance is limited by thresholds, which are set by noise in photoreceptors and subsequent neural processing. The receptor noise limited (RNL) model of colour discrimination is widely used for modelling colour vision and accounts well for experimental data from many species. In one of the most comprehensive tests yet of colour discrimination in a non-human species, we used Ishihara-style stimulus patterns to examine thresholds for 21 directions at five locations in colour space for the fish Rhinecanthus aculeatus. Thresholds matched RNL model predictions most closely for stimuli near the achromatic point, but exceeded predictions (indicating a decline in sensitivity) with distance from this point. Thresholds were also usually higher for saturation than for hue differences. These changes in colour threshold with colour space location and direction may give insight into photoreceptor non-linearities and post-receptoral mechanisms of colour vision in fish. Our results highlight the need for a cautious interpretation of the RNL model - especially for modelling colours that differ from one another in saturation (rather than hue), and for highly saturated colours distant from the achromatic point in colour space.

scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation.

Trajectory inference (TI) or pseudotime analysis has dramatically extended the analytical framework of single-cell RNA-seq data, allowing regulatory genes contributing to cell differentiation and those involved in various dynamic cellular processes to be identified. However, most TI analysis procedures deal with individual genes independently while overlooking the regulatory relations between genes. Integrating information from gene regulatory networks (GRNs) at different pseudotime points may lead to more interpretable TI results. To this end, we introduce scInTime-an unsupervised machine learning framework coupling inferred trajectory with single-cell GRNs (scGRNs) to identify master regulatory genes. We validated the performance of our method by analyzing multiple scRNA-seq data sets. In each of the cases, top-ranking genes predicted by scInTime supported their functional relevance with corresponding signaling pathways, in line with the results of available functional studies. Overall results demonstrated that scInTime is a powerful tool to exploit pseudotime-series scGRNs, allowing for a clear interpretation of TI results toward more significant biological insights.

Gag-like proteins: Novel mediators of prenatal alcohol exposure in neural development.

BACKGROUND: We previously showed that ethanol did not kill fetal neural stem cells (NSCs), but that their numbers nevertheless are decreased due to aberrant maturation and loss of self-renewal. To identify mechanisms that mediate this loss of NSCs, we focused on a family of Gag-like proteins (GLPs), derived from retroviral gene remnants within mammalian genomes. GLPs are important for fetal development, though their role in brain development is virtually unexplored. Moreover, GLPs may be transferred between cells in extracellular vesicles (EVs) and thereby transfer environmental adaptations between cells. We hypothesized that GLPs may mediate some effects of ethanol in NSCs. METHODS: Sex-segregated male and female fetal murine cortical NSCs, cultured ex vivo as nonadherent neurospheres, were exposed to a dose range of ethanol and to mitogen-withdrawal-induced differentiation. We used siRNAs to assess the effects of NSC-expressed GLP knockdown on growth, survival, and maturation and in silico GLP knockout, in an in vivo single-cell RNA-sequencing dataset, to identify GLP-mediated developmental pathways that were also ethanol-sensitive. RESULTS: PEG10 isoform-1, isoform-2, and PNMA2 were identified as dominant GLP species in both NSCs and their EVs. Ethanol-exposed NSCs exhibited significantly elevated PEG10 isoform-2 and PNMA2 protein during differentiation. Both PEG10 and PNMA2 were mediated apoptosis resistance and additionally, PEG10 promoted neuronal and astrocyte lineage maturation. Neither GLP influenced metabolism nor cell cycle in NSCs. Virtual PEG10 and PNMA2 knockout identified gene transcription regulation and ubiquitin-ligation processes as candidate mediators of GLP-linked prenatal alcohol effects. CONCLUSIONS: Collectively, GLPs present in NSCs and their EVs may confer apoptosis resistance within the NSC niche and contribute to the abnormal maturation induced by ethanol.