bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of colour patterns for the recognition of flowers by bees
Authors: Hempel de Ibarra Natalie , Holtze Susanne , Bäucker Cornelia , Sprau Philipp , Vorobyev Misha 
Published: September 2022

Bees discriminate between many different colours of flower petals, but it is not well understood how they perceive and learn patterns frequently found in flowers with colourful structures. We used multi-spectral imaging to explore chromatic cues in concentric flower patterns as they are seen through the low-resolution eyes of the honeybee. We find a diversity of colour combinations, which suggests that plants might exploit the sensory capabilities of pollinators, like bees, that learn colours easily. A consistent feature is that the surround of the pattern has a stronger chromatic contrast to the foliage background than the centre. This can potentially facilitate the fast identification of floral objects within colourful scenes when a foraging bee moves through a flower patch. In behavioural experiments we trained and tested bees with three types of concentric patterns. They recognized and discriminated patterns accurately in most tests, relying flexibly on both chromatic and spatial cues. Only rarely, depending on the training stimulus, chromatic cues determined their choices whilst pattern cues were ignored. The variability of floral designs and the bees' flexibility in recalling colour and spatial information suggest a role for colour vision in pattern processing. Implications for the signalling strategies of flowers are discussed.
This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
Understanding insect colour constancy
Authors: Werner Annette 
Published: September 2022

Colour constancy is the ability to recognize the colour of objects despite spectral changes in the natural illumination. As such, this phenomenon is important for most organisms with good colour vision, and it has been intensively studied in humans and primates. Colour constancy is also documented for several species of insects, which is not surprising given the ecological importance of colour vision. But how do insects, with their small brains, solve the complex problem of colour vision and colour constancy? In an interspecies approach, this review reports on behavioural studies on colour constancy in bees, butterflies, moths and humans, corresponding computational models and possible neurophysiological correlates.This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
Crustacean conundrums: a review of opsin diversity and evolution
Authors: Palecanda Sitara , Iwanicki Thomas , Steck Mireille , Porter Megan L. 
Published: September 2022

Knowledge of crustacean vision is lacking compared to the more well-studied vertebrates and insects. While crustacean visual systems are typically conserved morphologically, the molecular components (i.e. opsins) remain understudied. This review aims to characterize opsin diversity across crustacean lineages for an integrated view of visual system evolution. Using publicly available data from 95 species, we identified opsin sequences and classified them by clade. Our analysis produced 485 putative visual opsins and 141 non-visual opsins. The visual opsins were separated into six clades: long wavelength sensitive (LWS), middle wavelength sensitive (MWS) 1 and 2, short wavelength or ultraviolet sensitive (SWS/UVS) and a clade of thecostracan opsins, with multiple LWS and MWS opsin copies observed. The SWS/UVS opsins were relatively conserved in most species. The crustacean classes Cephalocarida, Remipedia and Hexanauplia exhibited reduced visual opsin diversity compared to others, with the malacostracan decapods having the highest opsin diversity. Non-visual opsins were identified from all investigated classes except Cephalocarida. Additionally, a novel clade of non-visual crustacean-specific, R-type opsins (Rc) was discovered. This review aims to provide a framework for future research on crustacean vision, with an emphasis on the need for more work in spectral characterization and molecular analysis.This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
Colour vision in ants (Formicidae, Hymenoptera)
Authors: Yilmaz Ayse , Spaethe Johannes 
Published: September 2022

Ants are ecologically one of the most important groups of insects and exhibit impressive capabilities for visual learning and orientation. Studies on numerous ant species demonstrate that ants can learn to discriminate between different colours irrespective of light intensity and modify their behaviour accordingly. However, the findings across species are variable and inconsistent, suggesting that our understanding of colour vision in ants and what roles ecological and phylogenetic factors play is at an early stage. This review provides a brief synopsis of the critical findings of the past century of research by compiling studies that address molecular, physiological and behavioural aspects of ant colour vision. With this, we aim to improve our understanding of colour vision and to gain deeper insights into the mysterious and colourful world of ants.
This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
Systematic Engineering of Virus-Like Particles to Identify Self-Assembly Rules for Shifting Particle Size
Authors: Ikwuagwu Bon , Hartman Emily , Mills Carolyn , Tullman-Ercek Danielle 
Published: September 2022

ABSTRACTVirus-like particles (VLPs) are promising scaffolds for biomaterials as well as diagnostic and therapeutic applications. However, there are some key challenges to be solved, such as the ability to engineer alternate sizes for varied use cases. To this end, we created a library of MS2 VLP variants at two key residues in the coat protein which have been implicated as important to controlling VLP size and geometry. By adapting a method for systematic mutagenesis coupled with size-based selections and high-throughput sequencing as a readout, we developed a quantitative assessment of two residues in MS2 coat protein that govern the size shift in MS2 VLPs. We then applied the strategy to the equivalent residues in Qβ VLPs, an MS2 homolog, and demonstrate that the analogous pair of residues are also able to impact VLP size and shape. These results underscore the power of fitness landscapes in identifying critical features for assembly.
Membrane cholesterol regulates inhibition and substrate transport by the glycine transporter, GlyT2
Authors: Frangos Zachary J. , Wilson Katie A. , Aitken Heather M. , Chater Ryan Cantwell , Vandenberg Robert J. , O’Mara Megan L. 
Published: September 2022

AbstractMembrane cholesterol binds to and modulates the function of the specific SLC6 transporters. Here we investigate how cholesterol binds to and modulates the rate of glycine transport by the SLC6 glycine transporter GlyT2, and how this impacts lipid inhibition of GlyT2. Bioactive lipid inhibitors of GlyT2 are analgesics that bind to the lipid allosteric site of the outward facing GlyT2 conformation that is accessible from the extracellular solution. Using molecular dynamics simulations, mutagenesis and cholesterol depletion experiments, we show that bioactive lipid inhibition of glycine transport is modulated by the recruitment of membrane cholesterol to a cholesterol binding site formed by transmembrane helices 1, 5 and 7. Recruitment involves cholesterol flipping from its membrane orientation, and insertion of the 3’ hydroxyl group into the cholesterol binding cavity to interact with the base of the lipid allosteric site and the bound inhibitor. The recruitment of membrane cholesterol by allosteric GlyT2 inhibitors is a potential avenue for the development of high-potency, specific pain analgesics and could provide alternative therapeutics that target GlyT2 and other SLC6 neurotransmitter transporters.
Cortical Circuit Mechanisms of Multimodal Temporal Pattern Discrimination
Authors: Post Sam , Mol William , Abu-Wishah Omar , Ali Shazia , Rahmatullah Noorhan , Goel Anubhuti 
Published: September 2022

AbstractDiscriminating between temporal features in sensory stimuli is critical to complex behavior and decision making. However, how sensory cortical circuit mechanisms contribute to discrimination between subsecond temporal components in sensory events is unclear. To elucidate the mechanistic underpinnings of timing in primary visual cortex (V1), we recorded from V1 using 2-photon calcium imaging in awake-behaving mice performing a go/no-go discrimination timing task, which was composed of patterns of subsecond audio-visual stimuli. In both conditions, activity during the early stimulus period was temporally coordinated with the preferred stimulus. However, while network activity increased in the preferred condition, network activity was increasingly suppressed in the nonpreferred condition over the stimulus period. Our results demonstrate that discrimination between subsecond intervals that are contained in rhythmic patterns can be accomplished by local networks and suggest the contribution of neural resonance as a mechanism.
Endogenous tagging of Unc-13 reveals nanocluster reorganization at active zones during presynaptic homeostatic potentiation
Authors: Dannhäuser Sven , Mrestani Achmed , Gundelach Florian , Pauli Martin , Komma Fabian , Kollmannsberger Philip , Sauer Markus , Heckmann Manfred , Paul Mila M. 
Published: September 2022

SUMMARYNeurotransmitter release at presynaptic active zones (AZs) requires concerted protein interactions within a dense 3D nano-hemisphere. Among the complex protein mesh-work the (M)unc-13 family member Unc-13 of Drosophila melanogaster is essential for docking of synaptic vesicles and transmitter release.We employ MiMIC-based gene editing using GFSTF (EGFP-FlAsH-StrepII-TEV-3xFlag) to endogenously tag all annotated Drosophila Unc-13 isoforms enabling visualization of endogenous Unc-13 expression within the central and peripheral nervous system. Electrophysiological characterization using two-electrode voltage clamp (TEVC) reveals that evoked and spontaneous synaptic transmission remain unaffected in unc-13GFSTF 3rd instar larvae and acute presynaptic homeostatic potentiation (PHP) can be induced at control levels. Furthermore, multi-color structured-illumination shows precise co-localization of Unc-13GFSTF, Bruchpilot and GluRIIA-receptor subunits within the synaptic mesoscale. Localization microscopy in combination with HDBSCAN algorithms detect Unc-13GFSTF nanoclusters that move towards the AZ center during PHP with unaltered Unc-13GFSTF protein levels.
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
Authors: Song Yabing , Wang Jianbin 
Published: September 2022

AbstractSummaryVisualizing genome coverage is of vital importance to inspect and interpret various next-generation sequencing (NGS) data. However, existing tools that perform such visualizations remain inflexible, complicated, lack necessary annotations and the figures generated are not publication-quality. Here, we introduce ggcoverage, an R package with the grammar of graphics implemented in ggplot2, providing a flexible, programmable and user-friendly way to visualize genome coverage, multiple available annotations to adapt to different NGS data, and generating publication-quality plots.Availability and Implementationggcoverage is an R package available via CRAN (https://cran.r-project.org/web/packages/ggcoverage/index.html) under MIT license. Support is available via GitHub (https://github.com/showteeth/ggcoverage/issues). Data used to generate figures are available on GitHub as example data.Contactsongyb18@mails.tsinghua.edu.cn, jianbinwang@tsinghua.edu.cn.
A deep learning and digital archaeology approach for mosquito repellent discovery
Authors: Wei Jennifer N. , Ruiz Carlos , Vlot Marnix , Sanchez-Lengeling Benjamin , Lee Brian K. , Berning Luuk , Vos Martijn W. , Henderson Rob W.M. , Qian Wesley W. , Ando D. Michael , Groetsch Kurt M. , Gerkin Richard C. , Wiltschko Alexander B. , Riffel Jeffrey , Dechering Koen J. 
Published: September 2022

AbstractInsect-borne diseases kill >0.5 million people annually. Currently available repellents for personal or household protection are limited in their efficacy, applicability, and safety profile. Here, we describe a machine-learning-driven high-throughput method for the discovery of novel repellent molecules. To achieve this, we digitized a large, historic dataset containing ∼19,000 mosquito repellency measurements. We then trained a graph neural network (GNN) to map molecular structure and repellency. We applied this model to select 317 candidate molecules to test in parallelizable behavioral assays, quantifying repellency in multiple pest species and in follow-up trials with human volunteers. The GNN approach outperformed a chemoinformatic model and produced a hit rate that increased with training data size, suggesting that both model innovation and novel data collection were integral to predictive accuracy. We identified >10 molecules with repellency similar to or greater than the most widely used repellents. We analyzed the neural responses from the mosquito antennal (olfactory) lobe to selected repellents and found a limited correlation between these responses and our GNN representation. This approach enables computational screening of billions of possible molecules to identify empirically tractable numbers of candidate repellents, leading to accelerated progress towards solving a global health challenge.
A Principal Odor Map Unifies Diverse Tasks in Human Olfactory Perception
Authors: Lee Brian K. , Mayhew Emily J. , Sanchez-Lengeling Benjamin , Wei Jennifer N. , Qian Wesley W. , Little Kelsie , Andres Matthew , Nguyen Britney B. , Moloy Theresa , Parker Jane K. , Gerkin Richard C. , Mainland Joel D. , Wiltschko Alexander B. 
Published: September 2022

AbstractMapping molecular structure to odor perception is a key challenge in olfaction. Here, we use graph neural networks (GNN) to generate a Principal Odor Map (POM) that preserves perceptual relationships and enables odor quality prediction for novel odorants. The model is as reliable as a human in describing odor quality: on a prospective validation set of 400 novel odorants, the model-generated odor profile more closely matched the trained panel mean (n=15) than did the median panelist. Applying simple, interpretable, theoretically-rooted transformations, the POM outperformed chemoinformatic models on several other odor prediction tasks, indicating that the POM successfully encoded a generalized map of structure-odor relationships. This approach broadly enables odor prediction and paves the way toward digitizing odors.One-Sentence SummaryAn odor map achieves human-level odor description performance and generalizes to diverse odor-prediction tasks.
Deep autoregressive generative models capture the intrinsics embedded in T-cell receptor repertoires
Authors: Jiang Yuepeng , Li Shuai Cheng 
Published: September 2022

ABSTRACTT-cell receptors (TCRs) play an essential role in the adaptive immune system. Probabilistic models for TCR repertoires can help decipher the underlying complex sequence patterns and provide novel insights into understanding the adaptive immune system. In this work, we develop TCRpeg, a deep autoregressive generative model to unravel the sequence patterns of TCR repertoires. TCRpeg outperforms state-of-the-art methods in estimating the probability distribution of a TCR repertoire, boosting the accuracy from 0.672 to 0.906 measured by the Pearson correlation coefficient. Furthermore, with promising performance in probability inference, TCRpeg improves on a range of TCR-related tasks: revealing TCR repertoire-level discrepancies, classifying antigen-specific TCRs, validating previously discovered TCR motifs, generating novel TCRs, and augmenting TCR data. Our results and analysis highlight the flexibility and capacity of TCRpeg to extract TCR sequence information, providing a novel approach to decipher complex immunogenomic repertoires.
Energy Crisis after Inter-System Mitochondria Transfer is the Direct Cause of Death by Sepsis
Authors: Tang Michael 
Published: September 2022

AbstractSepsis is one of the leading causes of death worldwide. With nearly 50 million incidences per year, it causes 11 million deaths worldwide annually, exceeding the 10 million total deaths caused by all tumors. Surprisingly, there is no specific drug available on market, explaining why it has a mortality rate as high as 22.5%. The lack of specific drug is mainly caused by the lack of understanding of how sepsis causes death. In this paper, I hypothesized that since energy production by mitochondria through respiration is not sustainable because the high level of reactive oxygen species (ROS) produced during respiration damages mitochondria themselves, mitochondria in the immune system cannot meet the dramatic and long-lasting high level of energy requirement of the system during sepsis. The immune system uses up all the functional mitochondria in the body by inter-system mitochondria transfer (ISMT), which dumps its used, unfunctional, or oxidized mitochondria to and recruits functional mitochondria from other systems. ISMT leads to the lack of functional mitochondria, hence energy, in the brain and the heart, and eventually causes death of the body. The hypothesis was supported by three key results: First, 2.5 hours after sepsis induction, mtDNA copy number increased dramatically in the spleen, brain, muscle, and blood, but decreased dramatically in the liver, kidneys, and skin. Second, mice died from sepsis showed a severe decline of mitochondria function in the brain and the heart. Finally, a single injection of isolated functional mitochondria to mice with sepsis reduced the mortality rate compared to mice received inactivated mitochondria.
Balancing true and false detection of intermittent sensory targets by adjusting the inputs to the evidence accumulation process
Authors: Geuzebroek Anna C. , Craddock Hannah , O’Connell Redmond G. , Kelly Simon P. 
Published: September 2022

AbstractDecisions about noisy stimuli are widely understood to be made by accumulating evidence up to a decision bound that can be adjusted according to task demands. However, relatively little is known about how such mechanisms operate in continuous monitoring contexts requiring intermittent target detection. Here, we examined neural decision processes underlying detection of 1-second coherence-targets within continuous random dot motion, and how they are adjusted across contexts with Weak, Strong, or randomly Mixed weak/strong targets. Our prediction was that decision bounds would be set lower when weak targets are more prevalent. Behavioural hit and false alarm rate patterns were consistent with this, and were well-captured by a bound-adjustable leaky accumulator model. However, beta-band EEG signatures of motor preparation contradicted this, instead indicating lower bounds in the Strong-target context. We thus tested two alternative models in which decision bound dynamics were constrained directly by Beta measurements, respectively featuring leaky accumulation with adjustable leak, and non-leaky accumulation of evidence referenced to an adjustable sensory-level criterion. We found that the latter model best explained both behaviour and neural dynamics, highlighting novel means of decision policy regulation and the importance of neurally-informed modelling.
IL-10 inhibits STAT1-dependent macrophage accumulation during microbiota-induced colitis
Authors: Patik Izabel , Redhu Naresh S. , Eran Alal , Bao Bin , Nandy Anubhab , Tang Ying , El Sayed Shorouk , Shen Zeli , Glickman Jonathan , Fox James G. , Snapper Scott B. , Horwitz Bruce H. 
Published: September 2022

AbstractLoss of IL-10R function leads to severe early onset colitis and in murine models is associated with the accumulation of immature inflammatory colonic macrophages. We have shown that IL-10R-deficient colonic macrophages exhibit increased STAT1-dependent gene expression, suggesting that IL-10R-mediated inhibition of STAT1 signaling in newly recruited colonic macrophages might interfere with the development of an inflammatory phenotype. Indeed Stat1-/- mice exhibit defects in colonic macrophage accumulation following Helicobacter hepaticus infection and IL-10R blockade, and this was phenocopied in mice lacking IFNGR, an inducer of STAT1 activation. Radiation chimeras demonstrated that reduced accumulation of STAT1-deficient macrophages was based on a cell-intrinsic defect. Unexpectedly, mixed radiation chimeras generated with both WT and IL-10R-deficient bone marrow indicated that rather than directly interfering with STAT1 function, IL-10R prevents the generation of a cell extrinsic signal that promotes the accumulation of immature macrophages. These results define essential mechanisms controlling inflammatory macrophage accumulation in inflammatory bowel diseases.SummaryIntrinsic STAT1-function drives the accumulation of macrophages within the colon following the loss of IL-10R signaling. IL-10R prevents this STAT1-dependent process through a non-cell autonomous mechanism.
LRRK2-G2019S Synergizes with Ageing and Low-Grade Inflammation to Promote Gut and Peripheral Immune Cell Activation that Precede Nigrostriatal Degeneration
Authors: Giachino Carmela , Tirolo Cataldo , Caniglia Salvatore , Serapide Maria F. , L’Episcopo Francesca , Bertoli Federico , Giuliano Claudio , Mearelli Marika , Jakobi Meike , Schneiderhan-Marra Nicole , Deleidi Michela , Marchetti Bianca 
Published: September 2022

AbstractBackgroundMutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most frequent cause of familial Parkinson’s disease (PD). The incomplete penetrance ofLRRK2mutations suggest that additional hits are required for disease onset. We hypothesized that chronic low-grade inflammation interacts with LRRK2 G2019S, the most frequent PD-associated mutation, to activate peripheral and central immune reactions and drive age-dependent neurodegeneration.Methods and ResultsWe exposed wild-type and LRRK2 G2019S mice to a low chronic dose of lipopolysaccharide, and we performed a longitudinal analysis of central and peripheral immune reactions and neurodegeneration. Low-dose inflammation triggered nigrostriatal degeneration, macrophage/monocyte brain infiltration, and astro-/microgliosis. LRRK2 G2019S mice showed an early dysregulation of peripheral cytokines, increased CD4+T-cell infiltration and α-synuclein aggregation in the colon. Interestingly, peripheral immune activation and colonic α-synuclein aggregation precede astro-/microgliosis and neurodegeneration.ConclusionsOur study suggests an early role of the peripheral immune system and the gut in LRRK2 PD and provides a novel model to study early therapeutic immune targets and biomarkers.