bluuebunny/crossref_metadata_2025 huggingface dataset:
Nimbolide Targets RNF114 to Induce the Trapping of PARP1 and Poly-ADP-Ribosylation-Dependent DNA Repair Factors
Authors: Li Peng , Zhen Yuanli , Kim Chiho , Deng Heping , Deng Hejun , Wang Xu-Dong , Qin Tian , Yu Yonghao
Published: October 2022

PARP1 is an abundant nuclear enzyme that is critically involved in DNA damage response. Its main enzymatic function is to catalyze a protein post-translational modification known as poly-ADP-ribosylation (PARylation). Despite the tremendous progresses of PARP1 inhibitors (PARPi) in the clinic, the basic mechanism of action of PARPi is poorly understood. Recent studies point to PARP1 trapping as a key factor driving the cytotoxic and immunomodulatory functions of PARPi. However, the molecular underpinnings of PARP1 trapping remain elusive. Here, using an unbiased, quantitative proteomic screen, we identified RING finger protein 114 (RNF114), as a PARylation-dependent, ubiquitin E3 ligase involved in DNA damage response. Upon sensing DNA damage, RNF114 was recruited, in a PAR-dependent manner, to the DNA lesions, where it specifically targeted PARylated-PARP1 for ubiquitin-proteasomal degradation. The blockade of this pathway interfered with the removal of PARP1 from the DNA damage site, leading to profound PARP1 trapping. We show that a natural product, Nimbolide, targeted RNF114 to block the degradation and removal of PARylated-PARP1 from DNA lesions. Unlike conventional PARPi, nimbolide treatment induced the trapping of both PARP1 and PARylation-dependent DNA repair factors. This unique mechanism of action of nimbolide translated into its superior cytotoxic effects against BRCA-deficient cancers. Furthermore, we demonstrated that, as a super trapper of both PARylated-PARP1 and PARylation-dependent DNA repair factors, nimbolide was able to overcome the intrinsic and acquired resistance to PARPi. Finally, we showed that nimbolide treatment activated innate immune signaling and was able to synergize with various cytotoxic agents. These results point to the exciting possibility of targeting homologous recombination-deficient cancers using nimbolide and its analogs.
Treatment of pancreatic cancer with irreversible electroporation and intratumoral CD40 antibody stimulates systemic immune responses that inhibit liver metastasis in an orthotopic model
Authors: Narayanan Jayanth S. Shankara , Hayashi Tomoko , Erdem Suna , McArdle Sara , Tiriac Herve , Ray Partha , Pu Minya , Mikulski Zbigniew , Miller Aaron , Messer Karen , Carson Dennis , Schoenberger Stephen P. , White Rebekah R.
Published: October 2022

Background

Pancreatic cancer (PC) has a poor prognosis, and most patients present with either locally advanced or distant metastatic disease. Irreversible Electroporation (IRE) is a non-thermal method of ablation used clinically in locally advanced PC, but most patients eventually develop distant recurrence. We have previously shown that IRE alone is capable of generating protective, neoantigen-specific immunity. Here we aim to generate meaningful therapeutic immune effects by combining IRE with local (intratumoral) delivery of a CD40 agonistic antibody (CD40Ab).

Methods

KPC46 organoids were generated from a tumor-bearing male KrasLSL-G12D-p53LSL-R172H-Pdx-1-Cre (KPC) mouse. Orthotopic tumors were established in the pancreatic tail of B6/129 F1J mice via laparotomy. Mice were randomized to treatment with either sham laparotomy, IRE alone, CD40Ab alone, or IRE followed immediately by CD40Ab injection. Metastatic disease and immune infiltration in the liver were analyzed 14 days post-procedure using flow cytometry and multiplex immunofluorescence imaging with spatial analysis. Candidate neoantigens were identified by mutanome profiling of tumor tissue for ex vivo functional analyses.

Results

The combination of IRE+CD40Ab improved median survival to greater than 35 days, significantly longer than IRE (21 days) or CD40Ab (24 days) alone (p<0.01). CD40Ab decreased metastatic disease burden, with less disease in the combination group than in the sham group or IRE alone. Immunohistochemistry of liver metastases revealed a more than two-fold higher infiltration of CD8+ T-cells in the IRE+CD40Ab group than in any other group (p<0.01). Multiplex immunofluorescence imaging revealed a 4-6-fold increase in the density of CD80+CD11c+ activated dendritic cells (p<0.05), which were spatially distributed throughout the tumor unlike the sham group, where they were restricted to the periphery. In contrast, CD4+FoxP3+ T-regulatory cells (p<0.05) and Ly6G+ MDSCs (P<0.01) were reduced and restricted to the tumor periphery in the IRE+CD40Ab group. T-cells from the IRE+CD40Ab group recognized significantly more peptides representing candidate neoantigens than did T-cells from the IRE or untreated control groups.

Conclusions

IRE can induce local tumor regression and neoantigen-specific immune responses. Addition of CD40Ab to IRE improved dendritic cell activation and neoantigen recognition, while generating a strong systemic anti-tumor T-cell response that inhibited metastatic disease progression.

Abstract Figure
Unified and standardized mass spectrometry data processing in Python using spectrum_utils
Authors: Bittremieux Wout , Levitsky Lev , Pilz Matteo , Sachsenberg Timo , Huber Florian , Wang Mingxun , Dorrestein Pieter C.
Published: October 2022

spectrum_utils is a Python package for mass spectrometry data processing and visualization. Since its introduction, spectrum_utils has grown into a fundamental software solution that powers various applications in proteomics and metabolomics, ranging from spectrum preprocessing prior to spectrum identification and machine learning applications, to spectrum plotting from online data repositories, and assisting data analysis tasks for dozens of other projects. Here we present updates to spectrum_utils, which include new functionality to integrate mass spectrometry community data standards, enhanced mass spectral data processing, and unified mass spectral data visualization in Python. spectrum_utils is freely available as open source at https://github.com/bittremieux/spectrum_utils.
Auditory biases in cognitive assessment – Insights from hearing-loss simulation for dementia screening
Authors: Füllgrabe Christian
Published: October 2022

Cognitive-screening tests are used to detect pathological changes in mental abilities. Many use orally presented instructions and test items. Hence, hearing loss (HL), whose prevalence increases with age, may bias cognitive-test performance in the target population for dementia screening. To study the effect of the test format, an impairment-simulation approach was used in normal-hearing listeners to compare performance on the Hopkins Verbal Learning Test when test items were unprocessed and processed to simulate age-related HL. Immediate verbal recall declined with simulated HL, suggesting that auditory factors are confounding variables in cognitive assessment and result in the underestimation of cognitive functioning.
Defining the in vivo mechanism of air pollutant toxicity using murine stress response biomarkers
Authors: Inesta-Vaquera Francisco , Miyasita Lisa , Grigg Jonathan , Henderson Colin J. , Wolf C. Roland
Published: October 2022

Background

Air pollution can cause a wide range of serious human diseases. For the informed instigation of interventions which prevent these outcomes there is an urgent need to develop robust in vivo biomarkers which provide insights into mechanisms of toxicity and relate pollutants to specific adverse outcomes.

Objective

To exemplify the application of in vivo stress response reporters in establishing mechanisms of air pollution toxicity and the application of this knowledge in epidemiological studies and potentially in disease prevention.

Methods

Murine stress-reporter models (oxidative stress/inflammation, DNA damage and Ah receptor -AhR-activity) and primary mouse and primary human nasal cells were exposed to chemicals present in diesel exhaust emissions, particulate matter (PM) standards (PM2.5-SRM2975, PM10-SRM1648b) or fresh roadside PM10. Stress reporter activity was analysed by luminescence assays and histochemical approaches in a panel of murine tissues. Biochemical, genetic and pharmacological approaches were used to establish the mechanism of the stress responses observed. Pneumococcal adhesion was assessed in exposed primary human nasal epithelial cells (HPNEpC).

Results

Nitro-PAHs induced Hmox1 and CYP1a1 reporters in a time- and dose-dependent, cell- and tissue-specific manner. NRF2 pathway mediated this Hmox1-reporter induction. SRM1658b, but not SRM2975, was a potent inducer of NRF2-dependent Hmox1 reporter activity in lung macrophages. Combined use of HPNEpC and in vivo reporters demonstrated that London roadside PM10 particles induced pneumococcal infection in HPNEpC mediated by oxidative stress responses.

Discussion

The combined use of in vivo reporter models with HPNEpC provides a robust approach to define the relationship between air pollutant exposure and health risks. These models can be used to hazard ranking environmental pollutants by considering the complexity of mechanisms of toxicity. These data will facilitate the relationship between toxic potential and the level of pollutant exposure in populations to be established and potentially extremely valuable tools for intervention studies.
Guitarfishes are plucked: undermanaged in global fisheries despite declining populations and high volume of unreported international trade
Authors: Sherman C. Samantha , Simpfendorfer Colin A. , Haque Alifa B. , Digel Eric D. , Zubick Patrick , Eged Jonathan , Matsushiba Jay H. , Sant Glenn , Dulvy Nicholas K.
Published: October 2022

Some sharks and rays are subject to fisheries catch and international trade regulations. However, the Guitarfishes (family Rhinobatidae) are a highly threatened group with minimal regulations. Substantial underreporting of catch and broad commodity codes for traded products are masking the true volume of Guitarfishes included in international trade. Here, we collate international trade information for Guitarfishes that have not readily been documented in trade, possibly due to poor resolution of molecular genetic markers, to begin to document the extent of trade. We assess the shortfall in fisheries management (M-Risk) for all species of Guitarfish based on 99 assessments across 28 countries. Globally, Guitarfishes are inadequately managed, with an average M-Risk of 45% of an ideal score, resulting in 76% of species being threatened globally. The high and unregulated catch and trade volume, paired with the management shortfalls, require global integrated improvement in fisheries management, supported by regulating international trade to sustainable levels.
Revaluation of old data with new techniques reveals novel insights into the celiac microbiome
Authors: Colgan John J , Burns Michael B
Published: October 2022

Celiac disease is an autoimmune disorder of the small intestine in which gluten, an energy-storage protein expressed by wheat and other cereals, elicits an immune response leading to villous atrophy. Despite a strong genetic component, the disease arises sporadically throughout life, leading us to hypothesize the the microbiome might be a trigger for celiac disease. Here, we took microbiome data from 3 prior studies examining celiac disease and the microbiome and analyzed this data with newer computational tools and databases: the dada2 and PICRUSt2 pipelines and the SILVA database. Our results both confirmed findings of previous studies and generated new data regarding the celiac microbiome of India and Mexico. Our results showed that, while some aspects of prior reports are robust, older datasets must be reanalyzed with new tools to ascertain which findings remain accurate while also uncovering new findings.

IMPORTANCE

Bioinformatics is a rapidly developing field, with new computational tools released yearly. It is thus important to revisit results generated using older tools to determine whether they are also revealed by currently available technology. Celiac disease is an autoimmune disorder that affects up to 2% of the world’s population. While the ultimate cause of celiac disease is unknown, many researchers hypothesize that changes to the intestinal microbiome play a role in the disease’s progression. Here, we have re-analyzed 16S rRNA data from several previous celiac studies to determine whether previous results are also uncovered using new computational tools.
Patterns of Ongoing Thought in the Real-World
Authors: Mulholland Bridget , Goodall-Halliwell Ian , Wallace Raven , Chitiz Louis , Mckeown Brontë , Rastan Aryanna , Poerio Giulia , Leech Robert , Turnbull Adam , Klein Arno , Van Auken Wil , Milham Michael , Wammes Jeffrey , Jefferies Elizabeth , Smallwood Jonathan
Published: October 2022

Previous research has indicated that health and well-being are impacted on by both the way we think, and the things we do. In the laboratory, studies suggest that specific task contexts affect this process because the people we are with, the places we are in, and the activities we perform may influence our thought patterns. In our study participants completed multi-dimensional experience-sampling surveys eight times per day for 5 days to generate thought data across a variety of dimensions in daily life. Principal component analysis was used to decompose the experience sampling data, and linear mixed modelling related these patterns to the activity in daily life in which they emerged. Our study replicated the influence of socializing on patterns of ongoing thought observed in our prior study and established that this is part of a broader set of relationship that links our current activities to how our thoughts are organised in daily life. We also found that factors such as time of day and the physical location are associated with reported patterns of thought, factors that are important for future studies to explore. Our study suggests that sampling thinking in the real world may be able to provide a set of comprehensive thinking-activity mappings that will be useful to researchers and health care professionals interested in health and well-being.
Selective inhibition of somatostatin-positive dentate hilar interneurons induces age-related cellular changes and cognitive dysfunction
Authors: Lyu Jinrui , Nagarajan Rajasekar , Kambali Maltesh , Wang Muxiao , Rudolph Uwe
Published: October 2022

The cellular basis of age-related impairments of hippocampal function is not fully understood. In order to evaluate the role of somatostatin-positive (Sst+) interneurons in the dentate gyrus hilus in this process, we chemogenetically inhibited Sst+interneurons in the dentate gyrus (DG) hilus. Chronic chemogenetic inhibition (CCI) of these neurons resulted in increased c-Fos staining in the DG hilus, a decrease in the percentage of Gad67- and of Sst-expressing interneurons in the DG, and increased microglial activation in DG, CA3, and CA1. Total dendritic length and spine density were reduced in DG and CA1, suggesting reduced dendritic complexity. Behaviorally, the recognition index in an object recognition task and the percentage of spontaneous alternations in the Y maze were decreased, while in both initial and reversal learning in the Morris water maze the latencies to find the hidden platform were increased, suggesting cognitive dysfunction. Our findings establish a causal role for a reduced function of Sst+interneurons in the DG hilus for cognitive decline and suggest that this reduced function may contribute to age-related impairments of learning and memory. Furthermore, our CCI mice may represent a cellularly defined model of hippocampal aging.

SIGNIFICANCE STATEMENT

Neuronal circuits and cellular processes underlying age-related cognitive dysfunction are not well understood. We observed that chronic chemogenetic inhibition of a defined cell type, somatostatin-positive interneurons in the dentate gyrus hilus, which have previously been found to be associated with cognitive dysfunction in aged rodents, is necessary and sufficient to elicit changes in expression of interneuronal markers, an increase in the activity of dentate gyrus granule cells, increased microglial activation across the entire hippocampus and an impairment of learning and memory-related tasks. Thus, inhibition of somatostatin-positive interneurons in the dentate gyrus hilus replicates changes that are also seen with normal aging, representing a novel cellularly defined animal model of hippocampal aging.
GESIAP: A Versatile Genetically Encoded Sensor-based Image Analysis Program
Authors: Zheng W. Sharon , Zhang Yajun , Zhu Roger E. , Zhang Peng , Gupta Smriti , Huang Limeng , Sahoo Deepika , Guo Kaiming , Glover Matthew E. , Vadodaria Krishna C. , Li Mengyao , Qian Tongrui , Jing Miao , Feng Jiesi , Wan Jinxia , Borden Philip M. , Ali Farhan , Kwan Alex C. , Gan Li , Lin Li , Gage Fred H. , Venton B. Jill , Marvin Jonathan S. , Podgorski Kaspar , Clinton Sarah M. , Zhang Miaomiao , Looger Loren L. , Li Yulong , Zhu J. Julius
Published: October 2022

Intercellular communication mediated by a large number of neuromodulators diversifies physiological actions, yet neuromodulation remains poorly understood despite the recent upsurge of genetically encoded transmitter sensors. Here, we report the development of a versatile genetically encoded sensor-based image analysis program (GESIAP) that utilizes MATLAB-based algorithms to achieve high-throughput, high-resolution processing of sensor-based functional imaging data. GESIAP enables delineation of fundamental properties (e.g., transmitter spatial diffusion extent, quantal size, quantal content, release probability, pool size, and refilling rate at single release sites) of transmission mediated by various transmitters (i.e., monoamines, acetylcholine, neuropeptides, and glutamate) at various cell types (i.e., neurons, astrocytes, and other non-neuronal cells) of various animal species (i.e., mouse, rat, and human). Our analysis appraises a dozen of newly developed transmitter sensors, validates a conserved model of restricted non-volume neuromodulatory synaptic transmission, and accentuates a broad spectrum of presynaptic release properties that variegate neuromodulation.
Neural representational geometries correlate with behavioral differences in monkeys and recurrent neural networks
Authors: Fascianelli Valeria , Battista Aldo , Stefanini Fabio , Tsujimoto Satoshi , Genovesio Aldo , Fusi Stefano
Published: October 2022

Animals likely use a variety of strategies to solve laboratory tasks. Traditionally, combined analysis of behavioral and neural recording data across subjects employing different strategies may obscure important signals and give confusing results. Hence, it is essential to develop techniques that can infer strategy at the single-subject level. We analyzed an experiment in which two monkeys performed a visually cued rule-based task. The analysis of their performance shows no indication that they used a different strategy. However, when we examined the geometry of stimulus representations in the state space of the neural activities recorded in dorsolateral prefrontal cortex, we found striking differences between the two monkeys. Our purely neural results induced us to reanalyze the behavior. The new analysis showed that the differences in representational geometry correlate with differences in the reaction times, revealing behavioral differences we were unaware of. All these analyses indicate that the monkeys are using different strategies. Finally, using recurrent neural network models trained to perform the same task, we show that these strategies correlate with the amount of training, suggesting a possible explanation for the observed neural and behavioral differences.
Alternative designs lead to similar performance when traits and performance vary on different axes
Authors: Nolting Kristen M. , Holsinger Kent E.
Published: October 2022

Plants differ from one another in size, architecture, water relations, and resource uptake, and these differences often lead to differences in performance. Yet within a community species that differ markedly in these traits often have similar performance. Here we use a simple model to show that when the major axes of trait covariation do not align with the axis of performance variation, large differences among species in structural traits may have similar performance, i.e., ‘alternative designs.’ We further illustrate this phenomenon using trait and performance data from co-occurringProteaspecies in the Cape Floristic Region, South Africa. Long-term coexistence of species within a community requires both similar levels of performance, so that some species are not excluded by competition, and niche differentiation, so that multiple species can coexist. Thus, misalignment between the axis of performance variation and the major axes of trait variation may be common, just as genetic variation may be maintained within a population when the selection gradient does not align with the major axes of the genetic variance-covariance matrix.
The prophylactic value of TNF-α inhibitors against retinal cell apoptosis and optic nerve axon loss after corneal surgery or trauma
Authors: Paschalis Eleftherios I. , Zhou Chengxin , Sharma Jyoti , Dohlman Thomas H. , Kim Sarah , Lei Fengyang , Chodosh James , Vavvas Demetrios , Urtti Arto , Papaliodis George , Dohlman Claes H.
Published: October 2022

Abstract

Background and Purpose

Late secondary glaucoma is an often-severe complication after acute events like anterior segment surgery, trauma, infection, etc. TNF-α is a major mediator that is rapidly upregulated, diffusing also to the retina and causes apoptosis of the ganglion cells and degeneration of their optic nerve axons (mediating steps to glaucomatous damage). Anti-TNF-α antibodies are in animals very effective in protecting the retinal cells and the optic nerve—and might therefore be useful prophylactically against secondary glaucoma in future such patients.Here we evaluate 1)toxicityand 2)efficacyof two TNF-α inhibitors (adalimumab and infliximab), in rabbits bysubconjunctivaladministration.

Methods

For drugtoxicity, animals withnormal, unburnedcorneas were injected with adalimumab (0.4, 4, or 40 mg), or infliximab (1, 10, or 100 mg). For drugefficacy, other animals were subjected to alkali burn before such injection, or steroids (for control). The rabbits were evaluated clinically with slit lamp and photography, electroretinography, optical coherence tomography, and intraocular pressure manometry. A sub-set of eyes were stainedex vivoafter 3 days for retinal cell apoptosis (TUNEL). In other experiments the optic nerves were evaluated by paraphenylenediamine staining after 50 or 90 days. Loss of retinal cells and optic nerve degeneration were quantified.

Results

Subconjunctival administration of 0.4 mg or 4.0 mg adalimumab were well tolerated, whereas 40.0 mg was toxic to the retina. 1, 10, or 100 mg infliximab were also well tolerated.Analysis of the optic nerve axons after 50 days confirmed the safety of 4.0 mg adalimumab and of 100 mg infliximab.

Forefficacy, 4.0 mg adalimumab subconjunctivally in 0.08 mLprovided practically full protection against retinal cell apoptosis 3 days following alkali burn, and infliximab 100 mg only slightly less. At 90 days following burn injury, control optic nerves showed about 50% axon loss as compared to 8% in the adalimumab treatment group.

Conclusions

Subconjunctival injection of 4.0 mg adalimumabin rabbits shows no eye toxicity and provides excellent neuroprotection, both short (3 days) and long-term (90 days).Ourtotal accumulated data from several of our studies, combined with the present paper, suggest that corneal injuries, including surgery, might benefit from routine administration of anti-TNF-α biologics to reduce inflammation and future secondary glaucoma.
Bridging the neural and algorithmic correlates of action-stopping
Authors: Jana Sumitash
Published: October 2022

Rapid stopping of actions is crucial for survival. The algorithm underlying action-stopping is often described using the independent race model, where the race between independent go- and stop-processes determines whether one is able to stop. However, it is unclear whether humans have neural correlates of these processes. Here, using scalp potentials from three studies, we show that the mu (8-13 Hz) desynchronization over the contralateral motor cortex follows the predictions of a go-process: the activity builds up till an action is made. We also show that the low beta (13-20 Hz) activity over the frontal areas follows the predictions of a stop-process: the activity builds up after the stop signal and prior to the stopping latency. Using these neural correlates, we observed that: 1) The failure to stop mostly results from a rapid go-process, 2) The go-process seems to be influenced by the stop-process during the late stages of action-stopping, 3) Intrinsic prefrontal beta activity has a retardive effect on movement, 4) Violations of independence assumption in the failed stop trials may result from the activity of the stop-process. Future studies may use these neural correlates to resolve the mimicry between models of action-stopping.
RNAcontacts, a pipeline for predicting contacts from RNA proximity ligation assays
Authors: Margasyuk Sergey , Vlasenok Mariia , Li Guo , Cao Changchang , Pervouchine Dmitri D.
Published: October 2022

Background

High-throughput RNA proximity ligation assays are molecular methods that simultaneously analyze spatial proximity of many RNAs in living cells. Their principle is based on cross-linking, fragmentation, and consequent religation of RNAs followed by high-throughput sequencing. The generated fragments have two distinct types of splits, one resulting from pre-mRNA splicing, and the other resulting from ligating spatially close RNA strands.

Findings

Here, we present RNAcontacts, a universal pipeline for detecting RNA-RNA contacts in high-throughput RNA proximity ligation assays. It circumvents the inherent problem of mapping sequences with two distinct split types using a two-pass alignment, in which splice junctions are inferred from a control RNA-seq experiment on the first pass and then provided to the aligner on the second pass as bona fide introns. This approach allows for a more sensitive detection of RNA contacts and has higher specificity with respect to splice junctions that are present in the biological sample in comparison to previously developed methods. RNAcontacts extracts contacts, clusters their ligation points, computes the read support, and generates tracks for the visualization through the UCSC Genome Browser. It is implemented in a reproducible and scalable workflow management system Snakemake that allows fast and uniform processing of multiple datasets.

Conclusions

RNAcontacts represents a generic pipeline for the detection of RNA contacts that can be used with any proximity ligation method as long as one of the interacting partners is RNA.

RNAcontacts is available via github at https://github.com/smargasyuk/RNAcontacts/
A Hybrid Learning Method with High Specificity for Excluding Non-chromosome Objects Problem
Authors: Kao E-Fong , Hsieh Ya-Ju , Ke Chien-Chih , Lin Wan-Chi , Yang Fang-Yu Ou , Wu Jain-Shing
Published: October 2022

Background

For automated analysis of metaphase chromosome images, the chromosome objects on the images need to be segmented in advance. However, the segmentation results often contain a lot of non-chromosome objects in the images. Hence, elimination of non-chromosome objects is an essential process in automated chromosome image analysis. This study aims to exclude non-chromosome objects and preserve as many chromosomes as possible. In this paper, we propose a hybrid deep learning method to exclude non-chromosome objects from metaphase chromosome images.

Method

The proposed method consists of two phases. In the first phase, two classification results are obtained from feature-based and image-based convolutional neural networks (CNN) separately (the feature-based CNN uses the features of the images as input; the image-based CNN uses the images as input directly). In the second phase, the prediction results from the above two CNNs are combined and resent to another CNN to obtain final classification results.

Results

The proposed method uses 18,757 non-chromosome objects and 43,398 chromosomes (including single and multiple overlapped chromosomes) from 1038 chromosome images to evaluate the performance. The experimental results show that the proposed method can detect and exclude 99.61% (18,683/18,757) of the non-chromosome objects and preserve 99.95% (43,375/43,398) of the chromosomes for further analysis.

Conclusions

The proposed method has a high effectiveness on excluding non-chromosome objects and could be used as a preprocessing procedure for chromosome image analysis.

Abstract Figure

Graphic Abstract
Advancing Antibiotic Resistance Classification with Deep Learning Using Protein Sequence and Structure
Authors: Qabel Aymen , Ennadir Sofiane , Nikolentzos Giannis , Lutzeyer Johannes F. , Chatzianastasis Michail , Bostrom Henrik , Vazirgiannis Michalis
Published: October 2022

Background: Antibiotic resistance is a major global health concern, as bacteria can develop immunity to drugs rendering them ineffective. To address this problem, it is crucial to identify and classify the genes that are responsible for antibiotic resistance, i.e. antibiotic resistant genes (ARGs). Previous methods for gene classification have mainly focused on the sequence of proteins and have ignored their structure. Recently, the AlphaFold model has made significant progress in predicting the 3D structure of proteins. Since the sequence and the structure can complement each other, having access to both of them can allow machine learning models to more accurately classify novel ARGs. In this paper, we develop two deep learning models to classify novel Antibiotic Resistant Genes (ARGs) using information from both protein sequence and structure. The first architecture is a graph neural network (GNN) model equipped with node features derived from a large language model, while the second model is a convolutional neural network (CNN) applied to images extracted from the protein structures. Results: Evaluation of the proposed models on a standard benchmark dataset of ARGs over 18 antibiotic resistance categories demonstrates that both models can achieve high accuracy in classifying ARGs (> 73%). The GNN model outperformed state-of-the-art methods and provided rich protein embeddings that could be also utilized in other tasks involving proteins, while the CNN model achieved competitive performance. With larger datasets, it is expected that the performance would further increase due to the nature of the underlying neural networks. Conclusions: The proposed deep learning methods offer a more accurate approach for antibiotic resistance classification and hold significant potential for improving our understanding of the mechanisms underlying antibiotic resistance.
The primordial knot: the deep-rooted origin of the disulfide-rich spider venom toxins
Authors: Shaikh Naeem Yusuf , Sunagar Kartik
Published: October 2022

Spider venoms are a complex concoction of enzymes, polyamines, inorganic salts and disulfide-rich peptides (DRPs). Although DRPs are widely distributed and abundant, their evolutionary origin has remained elusive. This knowledge gap stems from the extensive molecular divergence of DRPs and a lack of sequence and structural data from diverse lineages. By evaluating DRPs under a comprehensive phylogenetic, structural and evolutionary framework, we have not only identified over 70 novel spider toxin superfamilies but also provide the first evidence for their common origin. We trace the origin of these toxin superfamilies to a primordial knot - the ‘Adi Shakti’ - nearly ∼375 MYA in the common ancestor of Araneomorphae and Mygalomorphae. As these lineages constitute over 50% of the extant spiders, our findings provide fascinating insights into the early evolution and diversification of the spider venom arsenal. Reliance on a single molecular toxin scaffold by nearly all spiders is in complete contrast to most other venomous animals that have recruited into their venoms diverse toxins with independent origins. Moreover, by comparatively evaluating araneomorph and mygalomorph spiders that differentially depend on their ability to secrete silk for prey capture, we highlight the prominent role of predatory strategies in driving the evolution of spider venom.

Significance Statement

Venoms are concoctions of biochemicals that function in concert to incapacitate prey or predators of venom-producing animals. Most venomous animals secrete a complex venom cocktail, constituted by toxins with independent evolutionary origins. In complete contrast, we trace the origin of diverse toxin superfamilies in spiders to a single molecular scaffold. The common origin of these disulphide-rich peptides that constitute three-quarters of nearly all spider venoms, therefore, represents a unique scenario of weaponization, where a single motif was recruited and extensively diversified to generate a plethora of superfamilies with distinct activities. Remarkably, the evolution of spider venom was also found to be driven by prey capture (i.e., reliance on silk versus venom) and venom deployment (predation or self-defence) strategies.
Synthetically engineered IgG1 antibody Fc fragments presenting influenza A virus receptor sialic acid inhibit viral haemagglutination activity, but enhance virus replication in cultured A549 cells
Authors: Vrettou Christina , Blundell Patricia , Gaunt Eleanor R , Pleass Richard J
Published: October 2022

Many clinically important viruses, including influenza A, SARS-CoV-1, adenoviruses, and DNA tumour viruses such as Kaposi’s sarcoma herpesvirus use multivalent binding to sialic acid (SA) to infect cells, or to modulate immune responses through interactions with sialylated attachment factors that facilitate virus infectivity and/or host survival. Molecular scaffolds rich in SA that bind virions with high avidity may therefore be useful as anti-infective medicines. We generated a panel of 12 of these molecules using fragment-crystallisable scaffolds in CHO-S cells that are rich in SA. The viral surface protein of influenza A virus (IAV), haemagglutinin, binds SA for cell entry, and so we tested the activity of these compounds against this virus. Two of the sialylated Fc-molecules reduced IAV haemagglutination activity by up to 64-fold. However, the same molecules enhanced virus infectivity of A549 cultured cells. To explain the increased viral titres, we postulated that sialylated Fcs may be anti-inflammatory. However, sialylated Fc multimers were instead pro-inflammatory; they induced chemokine/cytokine responses from differentiated human THP-1 derived macrophages, including raised IL-8 and MIP-1α/β, that mimicked responses driven by universal type I interferon. Steric targeting of SA to block virus entry may therefore have unexpected effects in target cells that currently preclude their use for medical intervention.
Feedback-based motor control can guide plasticity and drive rapid learning
Authors: Feulner Barbara , Perich Matthew G. , Miller Lee E. , Clopath Claudia , Gallego Juan A.
Published: October 2022

Animals use afferent feedback to rapidly correct ongoing movements in the presence of a perturbation. Repeated exposure to a predictable perturbation leads to behavioural adaptation that counteracts its effects. Primary motor cortex (M1) is intimately involved in both processes, integrating inputs from various sensorimotor brain regions to update the motor output. Here, we investigate whether feedback-based motor control and motor adaptation may share a common implementation in M1 circuits. We trained a recurrent neural network to control its own output through an error feedback signal, which allowed it to recover rapidly from external perturbations. Implementing a biologically plausible plasticity rule based on this same feedback signal also enabled the network to learn to counteract persistent perturbations through a trial-by-trial process, in a manner that reproduced several key aspects of human adaptation. Moreover, the resultant network activity changes were also present in neural population recordings from monkey M1. Online movement correction and longer-term motor adaptation may thus share a common implementation in neural circuits.
GLUT1 ablation in astrocytes paradoxically improves central and peripheral glucose metabolism via enhanced insulin-stimulated ATP release
Authors: Ardanaz Carlos G. , de la Cruz Aida , Elizalde-Horcada Marcos , Puerta Elena , Ramírez María J. , Ortega Jorge E. , Urbiola Ainhoa , Ederra Cristina , Ariz Mikel , Ortiz-de-Solórzano Carlos , Irigoyen Joaquín Fernández- , Santamaría Enrique , Karsenty Gerard , Brüning Jens C. , Solas Maite
Published: October 2022

Astrocytes are considered an essential source of blood-borne glucose or its metabolites to neurons. Nonetheless, the necessity of the main astrocyte glucose transporter, i.e. GLUT1, for brain glucose metabolism has not been defined. Unexpectedly, we found that brain glucose metabolism was paradoxically augmented in mice with astrocytic GLUT1 ablation (GLUT11′GFAPmice). These mice also exhibited improved peripheral glucose metabolism especially in obesity, rendering them metabolically healthier. Importantly, GLUT11′GFAPmice did not present cognitive alterations. Mechanistically, we observed that GLUT1-ablated astrocytes exhibited increased insulin receptor-dependent ATP release, and both astrocyte insulin signalling and brain purinergic signalling are essential for improved brain function and systemic glucose metabolism. Collectively, we demonstrate that astrocytic GLUT1 is central to the regulation of brain energetics, yet its ablation triggers a reprogramming of brain metabolism sufficient to sustain energy requirements, peripheral glucose homeostasis and cognitive function.
Using SuperClomeleon to measure changes in intracellular chloride during development and after early life stress
Authors: Herstel L.J. , Peerboom C. , Uijtewaal S. , Selemangel D. , Karst H. , Wierenga C.J.
Published: October 2022

Intraneuronal chloride concentrations ([Cl-]i) decrease during development resulting in a shift from depolarizing to hyperpolarizing y-aminobutyric acid (GABA) responses via chloride-permeable GABAAreceptors. This GABA shift plays a pivotal role in postnatal brain development, and can be strongly influenced by early life experience. Here, we assessed the applicability of the recently developed fluorescent SuperClomeleon (SClm) sensor to examine changes in [Cl-]iusing two-photon microscopy in brain slices. We used SClm mice of both sexes to monitor the developmental decrease in neuronal chloride levels in organotypic hippocampal cultures. We could discern a clear reduction in [Cl-]ibetween DIV3 and DIV9 (equivalent to the second postnatal weekin vivo)and a further decrease in some cells until DIV22. In addition, we assessed alterations in [Cl-]iin the medial prefrontal cortex (mPFC) of P9 male SClm mouse pups after early life stress (ELS). ELS was induced by limiting nesting material between P2 and P9. ELS induced a shift towards higher (i.e. immature) chloride levels in layer 2/3 cells in the mPFC. Although conversion from SClm fluorescence to absolute chloride concentrations proved difficult, our study underscores that the SClm sensor is a powerful tool to measure physiological changes in [Cl-]iin brain slices.

Significance Statement

The reduction of intraneuronal chloride concentrations is crucial for brain development, as it ensures a shift from the initial excitatory action of the neurotransmitter GABA in immature neurons to the inhibitory GABA signaling in the adult brain. Despite the significance of chloride maturation, it has been difficult to study this phenomenon in experiments. Recent development of chloride sensors enable direct imaging of intracellular chloride signaling in neurons. Here we assessed the applicability of the SuperClomeleon chloride sensor to measure physiologically relevant changes in chloride levels using two-photon microscopy in cultured and acute brain slices. Although we also point out some limitations, we conclude that the SuperClomeleon sensor is a powerful tool to measure physiological changes in intracellular chloride.
The Neural Correlates of Continuous Feedback Processing
Authors: Hassall Cameron D. , Yan Yan , Hunt Laurence T.
Published: October 2022

Feedback processing is commonly studied by analyzing the brain’s response to discrete rather than continuous events. Such studies have led to the hypothesis that rapid phasic midbrain dopaminergic activity tracks reward prediction errors (RPEs), the effects of which are measurable at the scalp via electroencephalography (EEG). Although studies using continuous feedback are sparse, recent animal work suggests that moment-to-moment changes in reward are tracked byslowly rampingmidbrain dopaminergic activity. Some have argued that these ramping signals index state values rather than RPEs. Our goal here was to develop an EEG measure of continuous feedback processing in humans, then test whether its behaviour could be accounted for by the RPE hypothesis. Participants completed a stimulus-response learning task in which a continuous reward cue gradually increased or decreased over time. A regression-based unmixing approach revealed EEG activity with a topography and timecourse consistent with the stimulus-preceding negativity (SPN), a scalp potential previously linked to reward anticipation and tonic dopamine release. Importantly, this reward-related activity depended on outcome expectancy: as predicted by the RPE hypothesis, activity for expected reward cues was reduced compared to unexpected reward cues. These results demonstrate the possibility of using human scalp-recorded potentials to track continuous feedback processing, and test candidate hypotheses of this activity.
Larval density in the invasive Drosophila suzukii: immediate and delayed effects on life-history traits
Authors: Reyes-Ramírez Alicia , Belgaidi Zaïnab , Gibert Patricia , Pommier Thomas , Siberchicot Aurélie , Mouton Laurence , Desouhant Emmanuel
Published: October 2022

The immediate and delayed effects of density are key in determining population dynamics, since they can positively or negatively affect the fitness of individuals. These effects have great relevance for polyphagous insects for which immature stages develop within a single site of finite feeding resources. Drosophila suzukii is a crop pest that induces severe economic losses for agricultural production, however little is known about the effects of density on its life-history traits. In the present study, we (i) investigated the egg distribution resulting from females’ egg-laying strategy and (ii) tested the immediate and delayed effects of larval density on emergence rate, development time, sex ratio of offspring, fecundity and adult size (a range of 1 to 50 larvae was used). We showed that most of fruits contain several eggs and aggregate of eggs of high density can be found in some fruits. This high density has no immediate effects on the emergence rate, but has effect on larval developmental time. This trait was involved in a trade-off with adult life-history traits: the larval development was reduced as larval density increased, but smaller and less fertile adults were produced. Our results should help to better understand the population dynamics of this species and to develop more successful control programs.
The mesoglea buffers the physico-chemical microenvironment of photosymbionts in the upside-down jellyfishCassiopeasp
Authors: Lyndby Niclas Heidelberg , Murray Margaret Caitlyn , Trampe Erik , Meibom Anders , Kühl Michael
Published: October 2022

The jellyfishCassiopeahas a conspicuous lifestyle, positioning itself upside-down on sediments in shallow waters thereby exposing its photosynthetic endosymbionts (Symbiodiniaceae) to light. Several studies have shown how the photosymbionts benefit the jellyfish host in terms of nutrition and O2availability, but little is known about the internal physico-chemical microenvironment ofCassiopeaduring light-dark periods. Here, we used fiber-optic sensors to investigate how light is modulated at the water-tissue interface ofCassiopeasp. and how light is scattered inside host tissue. We additionally used electrochemical and fiber-optic microsensors to investigate the dynamics of O2and pH in response to changes in the light availability in intact living specimens ofCassiopeasp.

Mapping of photon scalar irradiance revealed a distinct spatial heterogeneity over different anatomical structures of the host, where oral arms and the manubrium had overall higher light availability, while shaded parts underneath the oral arms and the bell had less light available. White host pigmentation, especially in the bell tissue, showed higher light availability relative to similar bell tissue without white pigmentation. Microprofiles of scalar irradiance into white pigmented bell tissue showed intense light scattering and enhanced light penetration, while light was rapidly attenuated over the upper 0.5 mm in tissue with symbionts only.

Depth profiles of O2concentration into bell tissue of intact, healthy/living jellyfish showed increasing concentration with depth into the mesoglea, with no apparent saturation point during light periods. O2was slowly depleted in the mesoglea in darkness, and O2concentration remained higher than ambient water in large (> 6 cm diameter) individuals, even after 50 min in darkness. Light-dark shifts in large medusae showed that the mesoglea slowly turns from a net sink during photoperiods into a net source of O2during darkness. In contrast, small medusae showed a more dramatic change in O2concentration, with rapid O2buildup/consumption in response to light-dark shifts; in a manner similar to corals. These effects on O2production/consumption were also reflected in moderate pH fluctuations within the mesoglea. The mesoglea thus buffers O2and pH dynamics during dark-periods.
Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator
Authors: Westbury Michael V. , Brown Stuart C. , Lorenzen Julie , O’Neill Stuart , Scott Michael B. , McCuaig Julia , Cheung Christina , Armstrong Edward , Valdes Paul J. , Samaniego Castruita Jose Alfredo , Cabrera Andrea A. , Blom Stine Keibel , Dietz Rune , Sonne Christian , Louis Marie , Galatius Anders , Fordham Damien A. , Ribeiro Sofia , Szpak Paul , Lorenzen Eline D.
Published: October 2022

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea-ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modelling, we investigate how Holocene environmental changes affected the evolutionary ecology of polar bears around Greenland. We show that throughout the last ∼11,000 years, Greenlandic polar bears have been heavily influenced by changes in sea-surface temperature (SST) and sea-ice cover. Most notable are major reductions in effective population size at the beginning of the Holocene and during the Holocene Thermal Maximum ∼6 kya, which coincide with increases in annual mean SST, reduction in sea-ice covers, declines in suitable habitat, and shifts in suitable habitat northwards. Furthermore, we show how individuals sampled from west and east Greenland are genetically, morphologically, and ecologically distinct. We find bears sampled in west Greenland to be larger, more genetically diverse and have diets dominated by ringed seals, whereas bears from east Greenland are smaller and less diverse with more varied diets, putatively driven by regional biotic differences. Taken together, we provide novel insights into the vulnerability of polar bears to environmental change, and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.

Teaser

Multivariate investigations of the environment’s role in the evolutionary ecology of Greenlandic polar bears.