bluuebunny/crossref_metadata_2025 huggingface dataset:
Fasciclin 2 functions as an expression-level switch on EGFR to control organ shape and size inDrosophila
Authors: Garcia-Alonso Luis
Published: May 2024

Fasciclin 2 (DrosophilaNCAM) is a homophilic Cell Adhesion Molecule expressed at moderate levels in the proliferating epithelial cells of imaginal discs, where it engages EGFR in a cell autonomous auto-stimulatory loop that promotes growth along larval development. In addition, Fasciclin 2 is expressed at high levels in the pre-differentiating cells of imaginal discs. Gain-of-function genetic analysis shows that Fasciclin 2 acts as a non-cell autonomous repressor of EGFR when high expression levels are induced during imaginal disc growth. Loss-of-function genetic analysis shows that this Fasciclin 2 functional facet is required at the end of larval development and it is mediated by interaction with IgCAMs CG15630 (Fipi) and CG33543 (Elff). Thus, Fasciclin 2 bears two complementary functional roles which correspond with different levels of expression. The combined results from loss- and gain-of-function analyses suggest a scenario where the Fasciclin 2/EGFR cell autonomous auto-stimulatory loop promotes cell proliferation until reaching a Fasciclin 2 expression threshold where its non-cell autonomous function stops growth. Thus, cellular integration of Fasciclin 2 autonomous and non-cell autonomous signaling from neighbor cells may be a key regulator component to orchestrate the rate of intercalary cell proliferation and the final size and shape of an organ.

Author Summary

How organ size and shape are controlled during development is a central and still unsolved problem in developmental biology. Growth control must be precise and local to account for the vast variation of organ shapes and sizes during evolution. Here I show that the expression of Fasciclin 2 (DrosophilaNCAM) controls whether to grow or not to grow by controlling EGFR activity in epithelial organs. Fasciclin 2 homophilic binding promotes cell autonomous activity of EGFR at low and medium levels of expression, which in turn causes a cell autonomous increase of Fasciclin 2 expression. In addition, at high expression levels, Fasciclin 2 function switches to a non-cell autonomous repressor of EGFR by interacting with its heterophilic partner IgCAMs Fipi and Elff. Thus, the two functional facets of Fasciclin 2, as cell autonomous activator and non-cell autonomous repressor of EGFR, constitute an expression-level switch for growth in the control of organ shape and size.
Machine learning strategies to tackle data challenges in mass spectrometry-based proteomics
Authors: Dens Ceder , Adams Charlotte , Laukens Kris , Bittremieux Wout
Published: May 2024

In computational proteomics, machine learning (ML) has emerged as a vital tool for enhancing data analysis. Despite significant advancements, the diversity of ML model architectures and the complexity of proteomics data present substantial challenges in the effective development and evaluation of these tools. Here, we highlight the necessity for high-quality, comprehensive datasets to train ML models and advocate for the standardization of data to support robust model development. We emphasize the instrumental role of key datasets like ProteomeTools and MassIVE-KB in advancing ML applications in proteomics and discuss the implications of dataset size on model performance, highlighting that larger datasets typically yield more accurate models. To address data scarcity, we explore algorithmic strategies such as self-supervised pretraining and multi-task learning. Ultimately, we hope that this discussion can serve as a call to action for the proteomics community to collaborate on data standardization and collection efforts, which are crucial for the sustainable advancement and refinement of ML methodologies in the field.
Selective predation by ants against less-honeydew secreting aphids
Authors: Matsuura Takumi , Handa Chihiro , Takahashi Satobu , Itino Takao
Published: May 2024

Many ant-aphid interactions illustrate the concept of a mutually beneficial association between two organisms: aphids provide ants with honeydew; in return, ants defend aphids from enemies. However, ants also often prey on the aphids they attend, and we do not know if the predation pressure causes any adaptations on the side of aphids. The aphidStomaphis japonicahas an obligate mutualistic association withLasiusants. Here, we report evidence of selective predation of less-honeydew secretingStomaphisaphids by the tendingLasiusants. We show that 1. the aphids are severely preyed on by the ants – up to half of the aphids’ standing population per day. 2. the ants selectively prey on the aphids which do not deliver honeydew when attacked, and 3. the frequency of aphids’ honeydew secretion is heritable. These results suggest selective predation by ants against less-honeydew secreting aphids takes place and it is heritable.
Modulation of H3K4 trimethylation by KDM5A and MLLs impacts metabolic adaptability in prostate and cervical cancer cells
Authors: Kirtana R. , Manna Soumen , Patra Samir Kumar
Published: May 2024

Abstract

Chemical modifications of chromatin modulate gene expression and induce essential metabolic plasticity for tumor growth. Accumulation of H3K4me3 in the promoter of a gene activates transcription by making the promoter accessible to the polymerases. Methylation of H3K4 is catalysed by MLLs and demethylation of H3K4me3 is catalysed by KDM5 family proteins. Herein, we investigated if genes encoding the enzymes involved in glucose metabolism are dependent on KDM5A and MLL1, and if targeting the H3K4me3 would help in modulating the resilience of cancer cells. We present that KDM5A modulates most of the metabolic genes in a demethylase dependent manner as assesses by H3K4me3 occupancy on G6PD and catalase promoters. Targeting its expression would indeed help in sensitizing cancer cells to ROS dependent apoptotic cell death. We elucidated the differences in the epigenetic regulation in cancerous cells originated from cervical and prostate tissues and used a normal skin keratinocyte for comparison. In cervical and prostate cancers - KDM5A activated glycolysis but downregulates other metabolic processes. In cervical cancer, which majorly depends on PPP, changes in KDM5A did not modulate the G6PD expression. Further, we have shown that curcumin treatment enhanced KDM5A expression and downregulated MLL2 in cancer cell lines but not in keratinocyte cells. Curcumin inhibited metabolic pathways and enhanced apoptosis in cancer cells without affecting keratinocyte cells by modulating KDM5A and MLL levels. This work also strengthens the basic concept that, epigenetic modulations of genes in a tissue precisely depends on signal and sites of modification(s).
Multilevel irreversibility reveals higher-order organisation of non-equilibrium interactions in human brain dynamics
Authors: Nartallo-Kaluarachchi Ramón , Bonetti Leonardo , Fernández-Rubio Gemma , Vuust Peter , Deco Gustavo , Kringelbach Morten L. , Lambiotte Renaud , Goriely Alain
Published: May 2024

Information processing in the human brain can be modelled as a complex dynamical system operating out of equilibrium with multiple regions interacting nonlinearly. Yet, despite extensive study of the global level of non-equilibrium in the brain, quantifying the irreversibility of interactions among brain regions at multiple levels remains an unresolved challenge. Here, we present the Directed Multiplex Visibility Graph Irreversibility framework, a method for analysing neural recordings using network analysis of time-series. Our approach constructs directed multi-layer graphs from multivariate time-series where information about irreversibility can be decoded from the marginal degree distributions across the layers, which each represents a variable. This framework is able to quantify the irreversibility of every interaction in the complex system. Applying the method to magnetoencephalography recordings during a long-term memory recognition task, we quantify the multivariate irreversibility of interactions between brain regions and identify the combinations of regions which showed higher levels of non-equilibrium in their interactions. For individual regions, we find higher irreversibility in cognitive versus sensorial brain regions whilst for pairs, strong relationships are uncovered between cognitive and sensorial pairs in the same hemisphere. For triplets and quadruplets, the most non-equilibrium interactions are between cognitive-sensorial pairs alongside medial regions. Finally, for quintuplets, our analysis finds higher irreversibility when the prefrontal cortex is included in the interaction. Combining these results, we show that multilevel irreversibility offers unique insights into the higher-order, hierarchical organisation of neural dynamics and presents a new perspective on the analysis of brain network dynamics.
Phylogenomics supports a single origin of terrestriality in Isopods
Authors: Thomas Thorpe Jessica A.
Published: May 2024

Terrestriality, the adaptation to life on land, is one of the key evolutionary transitions, having occurred numerous times across the tree of life. Within Arthropoda, there have been several independent transitions in hexapods, myriapods, arachnids and isopods. Isopoda is a morphologically diverse order within Crustacea, with species adapted to almost every environment on Earth. The order is divided into 11 suborders with the most speciose, Oniscidea, including terrestrial isopods such as woodlice and sea-slaters. Recent molecular phylogenetic studies have challenged traditional isopod morphological taxonomy, suggesting that several well-accepted suborders, including Oniscidea, may be non-monophyletic. This implies that terrestriality may have evolved more than once within Isopoda. Current molecular hypotheses, however, are based on limited sequence data. Here, I collate available transcriptome and genome datasets for 33 isopods and four peracarid crustaceans from public sources, generate assemblies, and use 960 single-copy orthologues to estimate isopod relationships and the timing of divergences with molecular dating. The resulting phylogenetic analyses support monophyly of terrestrial isopods and suggest that conflicting relationships based on nuclear ribosomal sequences may be caused by long-branch attraction. Dating analyses suggest a Carboniferous-Permian origin of isopod terrestriality, much more recently than other terrestrial arthropods.
“Tumor-selective treatment of metastatic pancreatic cancer with an engineered, probiotic living drug”
Authors: Decker-Farrell Amanda R. , Sastra Stephen A. , Harimoto Tetsuhiro , Hasselluhn Marie C. , Palermo Carmine F. , Ballister Edward R. , Badgley Michael A. , Danino Tal , Olive Kenneth P.
Published: May 2024

Pancreatic ductal adenocarcinoma (PDAC) poses significant challenges for effective treatment, with systemic chemotherapy often proving inadequate due to poor drug delivery and the tumor’s immunosuppressive microenvironment. Engineered bacteria present a novel approach to target PDAC, leveraging their ability to colonize tumors and deliver therapeutic payloads. Here, we engineered probioticEscherichia coliNissle 1917 (EcN) to produce the pore-forming Theta toxin (Nis-Theta) and evaluated its efficacy in a preclinical model of PDAC. Probiotic administration resulted in selective colonization of tumor tissue, leading to improved overall survival compared to standard chemotherapy. Moreover, this strain exhibited cytotoxic effects on both primary and distant tumor lesions while sparing normal tissues. Importantly, treatment also modulated the tumor microenvironment by increasing anti-tumor immune cell populations and reducing immunosuppressive markers. These findings demonstrate the potential of engineered probiotic bacteria as a safe and effective therapeutic approach for PDAC, offering promise for improved patient outcomes.
Mixtures of phthalates disrupt expression of genes related to lipid metabolism and peroxisome proliferator-activated receptor signaling in mouse granulosa cells
Authors: Alahmadi Hanin , Martinez Stephanie , Farrell Rivka , Bikienga Rafiatou , Arinzeh Nneka , Potts Courtney , Li Zhong , Warner Genoa R.
Published: May 2024

Phthalates are a class of known endocrine disrupting chemicals that are found in common everyday products. Several studies associate phthalate exposure with detrimental effects on ovarian functions, including growth and development of the follicle and production of steroid hormones. We hypothesized that dysregulation of the ovary by phthalates may be mediated by phthalate toxicity towards granulosa cells, a major cell type in ovarian follicles responsible for key steps of hormone production and nourishing the developing oocyte. To test the hypothesis that phthalates target granulosa cells, we harvested granulosa cells from adult CD-1 mouse ovaries and cultured them for 96 hours in vehicle control, a phthalate mixture, or a phthalate metabolite mixture (0.1-100 μg/mL). After culture, we measured metabolism of the phthalate mixture into monoester metabolites by the granulosa cells, finding that granulosa cells do not significantly contribute to ovarian metabolism of phthalates. Immunohistochemistry of phthalate metabolizing enzymes in whole ovaries confirmed that these enzymes are not strongly expressed in granulosa cells of antral follicles and that ovarian metabolism of phthalates likely occurs primarily in the stroma. RNA sequencing of treated granulosa cells identified 407 differentially expressed genes, with overrepresentation of genes from lipid metabolic processes, cholesterol metabolism, and peroxisome proliferator-activated receptor (PPAR) signaling pathways. Expression of significantly differentially expressed genes related to these pathways were confirmed using qPCR. Our results agree with previous findings that phthalates and phthalate metabolites have different effects on the ovary and interfere with PPAR signaling in granulosa cells.
Bayesian Functional Connectivity and Graph Convolutional Network for Working Memory Load Classification
Authors: Gangapuram Harshini , Manian Vidya
Published: May 2024

Brain responses related to working memory originate from distinct brain areas and oscillate at different frequencies. EEG signals with high temporal correlation can effectively capture these responses. Therefore, estimating the functional connectivity of EEG for working memory protocols in different frequency bands plays a significant role in analyzing the brain dynamics with increasing memory and cognitive loads, which remains largely unexplored. The present study introduces a Bayesian structure learning algorithm to learn the functional connectivity of EEG in sensor space. Next, the functional connectivity graphs are taken as input to the graph convolutional network to classify the working memory loads. The intrasubject (subject-specific) classification performed on 154 subjects for six different verbal working memory loads produced the highest classification accuracy of 96% and average classification accuracy of 89%, outperforming state-of-the-art classification models proposed in the literature. Furthermore, the proposed Bayesian structure learning algorithm is compared with state-of-the-art functional connectivity estimation methods through intersubject and intrasubject statistical analysis of variance. The results also show that the alpha and theta bands have better classification accuracy than the beta band.
Characterization and Engineering of the Type 3 Secretion System Needle Monomer fromSalmonellaThrough the Construction and Screening of a Comprehensive Mutagenesis Library
Authors: Burdette Lisa Ann , Leach Samuel Alexander , Kennedy Nolan , Ikwuagwu Bon C. , Summers Jordan S. , Tullman-Ercek Danielle
Published: May 2024

Protein production strategies in bacteria are often limited due to the need for cell lysis and complicated purification schemes. To avoid these challenges, researchers have developed bacterial strains capable of secreting heterologous protein products outside the cell, but secretion titers often remain too low for commercial applicability. Improved understanding of the link between secretion system structure and its secretory abilities can help overcome the barrier to engineering higher secretion titers. Here we investigated this link with the PrgI protein, the monomer of the secretory channel of the Type 3 Secretion System (T3SS) ofSalmonella enterica. Despite detailed knowledge of the PrgI needle’s assembly and structure, little is known about how its structure influences its secretory capabilities. To study this, we recently constructed a comprehensive codon mutagenesis library of the PrgI protein utilizing a novel one pot recombineering approach. We then screened this library for functional T3SS assembly and secretion titer by measuring the secretion of alkaline phosphatase using a high-throughput activity assay. This allowed us to construct a first-of-its-kind secretion fitness landscape (SFL) to characterize the PrgI needle’s mutability at each position as well as the mutations which lead to enhanced T3SS secretion. We discovered new design rules for building a functional T3SS as well as identified hypersecreting mutants. This work can be used to increase understanding of the T3SS’s assembly and identify further targets for engineering. This work also provides a blueprint for future efforts to engineer other complex protein assemblies through the construction of fitness landscapes.

Importance

Protein secretion offers a simplified alternative method for protein purification from bacterial hosts. However, the current state-of-the-art methods for protein secretion in bacteria are still hindered by low yields relative to traditional protein purification strategies. Engineers are now seeking strategies to enhance protein secretion titers from bacterial hosts, often through genetic manipulations. In this study, we demonstrate that protein engineering strategies focused on altering the secretion apparatus can be a fruitful avenue toward this goal. Specifically, this study focuses on how changes to the PrgI needle protein from the type 3 secretion system fromSalmonella entericacan impact secretion titer. We demonstrate that this complex is amenable to comprehensive mutagenesis studies and that this can yield both PrgI variants with increased secretory capabilities and insight into the normal functioning of the type 3 secretion system.
Dissecting neurofilament tail sequence-phosphorylation-structure relationships with multicomponent reconstituted protein brushes
Authors: Ding Erika A. , Yokokura Takashi J. , Wang Rui , Kumar Sanjay
Published: May 2024

Neurofilaments (NFs) are multi-subunit, bottlebrush-shaped intermediate filaments abundant in the axonal cytoskeleton, with “bristles” composed of the subunits’ disordered tail domains. Precisely how the tails’ variable charge patterns and repetitive phosphorylation sites mediate their conformation within the brush remains an open question in axonal biology. We address this problem by grafting recombinant NF tail protein constructs (NFL, NFM, and NFH) to functionalized substrates, forming phosphorylatable brushes of defined stoichiometry. Atomic force microscopy reveals that NFM-based brushes are highly extended, while brushes incorporating the much larger NFH are surprisingly compact even after multisite phosphorylation. A self-consistent field theory predicts multilayered brush morphologies for NFM and phosphorylated NFH brushes. Further experiments with designed mutants reveal that N-terminal negative charges in NFH repel phosphorylated residues to generate the multilayer morphology and that charge segregation in NFM promotes collapsed conformations, lending new insight into how NF tail sequence features determine protein brush conformation.
Circulating inflammatory proteins and risk of Parkinson’s disease and other neurodegenerative disorders: a two-sample Mendelian randomization study
Authors: Chen Zhichun , Li Guanglu , Zhou Liche , Zhang Lina , You Yong , Liu Jun
Published: May 2024

Background

Accumulating studies have suggested associations between peripheral inflammation and neurodegenerative disorders, including Parkinson’s disease (PD).

Objective

To evaluate the causal associations between 91 plasma inflammatory proteins and 4 neurodegenerative disorders.

Methods

Two-sample Mendelian randomization studies were performed using summary statistics extracted from genome-wide association studies of 91 plasma inflammatory proteins and 4 neurodegenerative disorders.

Results

Genetically proxied tumor necrosis factor receptor superfamily member 9 levels were causally associated with reduced risk of PD (odds ratio [OR] = 0.82, 95% confidence interval [CI] = 0.74-0.92,p= 4.18 x 10−4, Bonferroni-correctedp< 0.05 for 91 proteins). Additionally, we identified potential causal associations between the levels of C-C motif chemokine 20 (OR = 1.14, 95%CI = 1.03-1.25,p= 1.29 x 10−2) and Alzheimer’s disease, between levels of leukemia inhibitory factor receptor (OR = 0.91, 95%CI = 0.84-0.98,p= 1.12 x 10−2) and tumor necrosis factor-β (OR = 0.95, 95%CI = 0.93-0.98,p= 1.01 x 10−3) and amyotrophic lateral sclerosis, between levels of adenosine deaminase (OR = 0.81, 95%CI = 0.71-0.94,p= 5.14 x 10−3) and interleukin-18 (OR = 0.81, 95%CI = 0.69-0.96,p= 1.68 x 10−2) and multiple sclerosis.

Conclusions

Our study unveils plausible causal associations between circulating inflammatory factors and risk of 4 neurodegenerative disorders. These findings hold promise for promoting risk assessment and prevention of neurodegenerative disorders, meriting further exploration.
Molecular correlates of swarming behaviour inAedes aegyptimales
Authors: Devilliers Julien , Marshall Hollie , Warren Ben , Kyriacou Charalambos P. , Araripe Luciana Ordunha , Bruno Rafaela V. , Rosato Ezio , Feuda Roberto
Published: May 2024

Mosquitoes are the deadliest vectors of disease. They impose a huge health burden on human populations spreading parasites as disparate as protozoans (malaria), viruses (yellow fever and more), and nematodes (filariasis), which cause life-threatening conditions. In recent years, mating has been proposed as a putative target for population control. Mosquitoes mate mid-air in swarms initiated by males and triggered by a combination of internal and external stimuli. As the number of females in a swarm is limited, there is intense competition among males. Indeed, males ‘retune’ their physiology for this demanding behaviour but the underlying genetic changes are largely unknown. Interestingly, recent evidence indicates that the upregulation of circadian clock genes may be involved in the swarming of malaria mosquitoes of the genusAnopheles. Here, we use whole-head RNA-seq to identify gene expression changes inAedes aegyptimales who are engaged in swarming in a laboratory setting. Our results suggest that swarming males tend to lower some housekeeping functions while increasing the remodelling of the cytoskeleton and neuronal connectivity; the transcription of circadian clock genes is unaffected.
Identification of Fasnall as a therapeutically effective Complex I inhibitor
Authors: Mukha Dzmitry , Dessain Jena , O’Connor Seamus , Pniewski Katherine , Bertolazzi Fabrizio , Patel Jeet , Mullins Mary , Schug Zachary T.
Published: May 2024

Proliferating cancer cells actively utilize anabolic processes for biomass production, includingde novobiosynthesis of amino acids, nucleotides, and fatty acids. The key enzyme of the fatty acid biosynthesis pathway, fatty acid synthase (FASN), is widely recognized as a promising therapeutic target in cancer and other health conditions1,2. Here, we establish a metabolic signature of FASN inhibition using a panel of pharmacological inhibitors (GSK2194069, TVB-2640, TVB-3166, C75, cerulenin, and Fasnall). We find that the activity of commonly used FASN inhibitors is inconsistent with the metabolic signature of FASN inhibition (accumulation of malonate, succinate, malonyl coenzyme A, succinyl coenzyme A, and other metabolic perturbations). Moreover, we show that one of these putative FASN inhibitors, Fasnall, is a respiratory Complex I inhibitor that mimics FASN inhibition through NADH accumulation and consequent depletion of the tricarboxylic acid cycle metabolites. We demonstrate that Fasnall impairs tumor growth in several oxidative phosphorylation-dependent cancer models, including combination therapy-resistant melanoma patient-derived xenografts. Fasnall administration does not reproduce neurological side effects in mice reported for other Complex I inhibitors3,4. Our results have significant implications for understanding the FASN role in human health and disease and provide evidence of therapeutic potential for Complex I inhibitors with fast systemic clearance. Our findings also highlight the continuing need for validation of small molecule inhibitors to distinguish high-quality chemical probes and to expand the understanding of their application.
mTOR dysregulation induces IL6 and paracrine AT2 cell senescence impeding lung repair in lymphangioleiomyomatosis
Authors: Babaei-Jadidi Roya , Clements Debbie , Wu Yixin , Chen Ken , Miller Suzanne , Plate Manuela , Lim Kyungtae , Chambers Rachel , Rawlins Emma L , Xu Yan , Johnson Simon R
Published: May 2024

Lymphangioleiomyomatosis (LAM) is a rare disease which causes lung cysts and respiratory failure. TSC2 deficient ‘LAM cells’ with dysregulated mTOR signalling form nodules with fibroblasts causing lung injury. We examined if mTOR dysregulation could induce senescence and impair responses to lung injury. Senescence markers p21 and p16 were increased in LAM lungs and co-localised with alveolar type 2 cells. The SenMayo senescence gene panel was upregulated in LAM alveolar type 2 cells with senescence supressed by mTOR inhibition in patients. LAM cell / fibroblast spheroid cultures induced senescence markers in alveolar type 2 cell organoids, altered their growth and delayed epithelial scratch wound repair. Upstream regulator analysis predicted alveolar type 2 cell IL6 receptor activation. IL6 was produced by LAM cells, induced p16 and p21 in alveolar type 2 cells, inhibited epithelial wound resolution and was overexpressed in LAM patient serum where it was related to lung function. Wound repair in the presence of TSC2 null LAM cell / fibroblast spheroids was enhanced by the IL6 receptor antagonist Tocilizumab. Our findings show TSC2 loss induces senescence and IL6 production which are associated with impaired lung repair. Targeting IL6 signalling in parallel with mTOR inhibition, may reduce lung damage in LAM.
Conditional language models enable the efficient design of proficient enzymes
Authors: Munsamy Geraldene , Illanes-Vicioso Ramiro , Funcillo Silvia , Nakou Ioanna T. , Lindner Sebastian , Ayres Gavin , Sheehan Lesley S. , Moss Steven , Eckhard Ulrich , Lorenz Philipp , Ferruz Noelia
Published: May 2024

The design of functional enzymes holds promise for transformative solutions across various domains but presents significant challenges. Inspired by the success of language models in generating nature-like proteins, we explored the potential of an enzyme-specific language model in designing catalytically active artificial enzymes. Here, we introduce ZymCTRL (’enzyme control’), a conditional language model trained on the enzyme sequence space, capable of generating enzymes based on user-defined specifications. Experimental validation at diverse data regimes and for different enzyme families demonstrated ZymCTRL’s ability to generate active enzymes across various sequence identity ranges. Specifically, we describe the design of carbonic anhydrases and lactate dehydrogenases in zero-shot, without requiring further training of the model, and showcasing activity at sequence identities below 40% compared to natural proteins. Biophysical analysis confirmed the globularity and well-folded nature of the generated sequences. Furthermore, fine-tuning the model enabled the generation of lactate dehydrogenases outside of natural sequence space but with activity comparable to their natural counterparts. Two of the artificial lactate dehydrogenases were selected for scale production and successfully lyophilised, maintaining activity and demonstrating preliminary conversion in one-pot enzymatic cascades under extreme conditions. Our findings open a new door towards the rapid and cost-effective design of artificial proficient enzymes. The model and dataset are freely available to the community.
The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired
Authors: Ritter Eleanore J , Cochetel Noe , Minio Andrea , Cousins Peter , Cantu Dario , Niederhuth Chad
Published: May 2024

Background: Teinturier grapevine varieties were first described in the 16th century and have persisted due to their deep pigmentation. Unlike most other grapevine varieties, teinturier varieties produce berries with pigmented flesh due to anthocyanin production within the flesh. As a result, teinturier varieties are of interest not only for their ability to enhance the pigmentation of wine blends but also for their health benefits. Here, we assembled and annotated the Dakapo and Rubired genomes, two teinturier varieties. Findings: For Dakapo, we used a combination of Nanopore sequencing, Illumina sequencing, and scaffolding to the existing grapevine genome assembly to generate a final assembly of 508.5 Mbp with an N50 scaffold length of 25.6 Mbp and a BUSCO score of 98.0%. A combination approach of de novo annotation and lifting over annotations from the existing grapevine reference genome resulted in the annotation of 36,940 genes in the Dakapo assembly. For Rubired, PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long. The diploid genome has an N50 scaffold length of 24.9 Mbp and a BUSCO score of 98.7%, and both haplotype-specific genomes are of similar quality. De novo annotation of the diploid Rubired genome yielded annotations for 56,681 genes. Conclusions: The Dakapo and Rubired genome assemblies and annotations will provide genetic resources for future investigations into berry flesh pigmentation and other traits of interest in grapevine.
Multi-trait modeling and machine learning discover new markers associated with stem traits in alfalfa
Authors: Medina Cesar A. , Heuschele Deborah J. , Zhao Dongyan , Lin Meng , Beil Craig T. , Sheehan Moira J. , Xu Zhanyou
Published: May 2024

Alfalfa biomass can be fractionated into leaf and stem components. Leaves comprise a protein-rich and highly digestible portion of biomass for ruminant animals, while stems constitute a high fiber and less digestible fraction, representing 50 to 70% of the biomass. However, little attention has focused on stem-related traits, which are a key aspect in improving the nutritional value and intake potential of alfalfa. This study aimed to identify molecular markers associated with four morphological traits in a panel of five populations of alfalfa generated over two cycles of divergent selection based on 16-h and 96-h in vitro neutral detergent fiber digestibility in stems. Phenotypic traits of stem color, presence of stem pith cells, winter standability, and winter injury were modeled using univariate and multivariate spatial mixed linear models (MLM), and the predicted values were used as response variables in genome-wide association studies (GWAS). The alfalfa panel was genotyped using a 3K DArTag SNP markers for the evaluation of the genetic structure and GWAS. Principal component and population structure analyses revealed differentiations between populations selected for high- and low-digestibility. Thirteen molecular markers were significantly associated with stem traits using either univariate or multivariate MLM. Additionally, support vector machine (SVM) and random forest (RF) algorithms were implemented to determine marker importance scores for stem traits and validate the GWAS results. The top-ranked markers from SVM and RF aligned with GWAS findings for solid stem pith, winter standability, and winter injury. Additionally, SVM identified additional markers with high variable importance for solid stem pith and winter injury. Most molecular markers were located in coding regions. These markers can facilitate marker-assisted selection to expedite breeding programs to increase winter hardiness or stem palatability.

Author Summary

The alfalfa stem constitutes a significant portion of forage yield, accounting for 50 to 70% of biomass yield, and influences various traits including plant height, standability, and digestibility. In our study, we identified thirteen molecular markers associated with stem color, presence of stem pith parenchyma, winter standability, and winter injury in a panel of five divergent stem digestibility populations. Multivariate trait modeling enhances the correlation among traits, thereby expanding the number of markers associated via GWAS. Similarly, machine learning algorithms increase the confidence of markers initially identified by GWAS and uncover new candidate regions that could serve as associated markers. Genes harboring markers associated to the four stem traits play roles in plant growth, response to plant injury, or tolerance to cold, underscoring their potential utility in enhancing traits such as cold tolerance and forage quality in alfalfa.
Multi-Drug Artificial Neural Network Models for Predicting HIV-1 RTI Resistance
Authors: Yilmaz Sumeyye , Tunc Huseyin , Sari Murat
Published: May 2024

Drug resistance is a major barrier to effectively treating HIV/AIDS, necessitating the exploration of novel drugs and an understanding of resistance mechanisms. Genotypic and phenotypic tests, while common, are costly and time-consuming. To address these challenges, machine learning models that effectively generalize available data have been leveraged. This study aims to create multi-drug artificial neural network (MD-ANN) models based on drug-isolate-fold change (DIF) to predict the drug resistance profiles of HIV-1 reverse transcriptase inhibitors (RTIs) using the Stanford HIV Drug Resistance Database. Unlike existing isolate-fold change (IF) models, the DIF-based models can test novel RTIs against a given mutant strain. It has been shown that the DIF-based models have competitive predictive capabilities in single-drug benchmarks compared to IF-based models while taking advantage of molecular learning to test novel RTIs. The DIF-based models can rank ten FDA-approved inhibitor pairs according to their drug resistance scores. We validate our observations with an external test set consisting of drug resistance scores for novel RTIs in the CheMBL database. By combining the Stanford dataset and the external dataset, our DIF model achieves impressive classification and regression results with an accuracy of 0.774, AUC of 0.859, androf 0.701 on the test set. To demonstrate how our DIF models learn from drug molecules, we construct a null model that only takes into account isolate representations. This null model yields an accuracy of 0.641, AUC of 0.701, androf 0.470. We highlight the significant contribution of drug information in improving the predictive accuracy and reliability of the DIF model. The DIF models have the potential to facilitate the testing of new inhibitors across various isolates.
Adaptive sampling-based structural prediction reveals opening of a GABAAreceptor through theαβinterface
Authors: Haloi Nandan , Howard Rebecca J. , Lindahl Erik
Published: May 2024

GABAAreceptors are ligand-gated ion channels in the central nervous system with largely inhibitory function. Despite being a target for drugs including general anesthetics and benzodiazepines, experimental structures have yet to capture an open state of canonicalα1β2γ2 GABAAreceptors. Here, we use a goal-oriented adaptive sampling strategy in molecular dynamics simulations followed by Markov state modeling to capture an energetically stable putative open state of the receptor. The model conducts chloride ions with comparable conductance as in electrophysiology measurements. The channel desensitizes by narrowing at both the cytoplasmic (−2′) and central (9′) gates, a motion primarily mediated by transmembraneαβsubunit interface. Consistent with previous experiments, targeted substitutions disrupting interactions at this interface slowed the open-to-desensitized transition rate. This work demonstrates the capacity of advanced simulation techniques to investigate a computationally and experimentally plausible functionally critical of a complex membrane protein, yet to be resolved by experimental methods.
Down-regulation of AKT proteins slows the growth of mutant-KRAS pancreatic tumors
Authors: Chen Chuankai , Jiang Ya-Ping , You Inchul , Gray Nathanael S. , Lin Richard Z.
Published: May 2024

Serine/threonine kinase AKT isoforms play a well-established role in cell metabolism and growth. Most pancreatic adenocarcinoma (PDAC) harbors activation mutations of KRAS, which activates the PI3K/AKT signaling pathway. However, AKT inhibitors are not effective in the treatment of pancreatic cancer. To better understand the role of AKT signaling in mutant-KRAS pancreatic tumors, this study utilizes proteolysis-targeting chimeras (PROTACs) and CRISPR-Cas9-genome editing to investigate AKT proteins. PROTAC down-regulation of AKT proteins markedly slowed the growth of three pancreatic tumor cell lines harboring mutant KRAS. In contrast, inhibition of AKT kinase activity alone had very little effect on the growth of these cell lines. Concurrent genetic deletion of all AKT isoforms (AKT1, AKT2, and AKT3) in the KPC (KrasG12D;Trp53R172H;Pdx1-Cre) pancreatic cancer cell line also dramatically slowed its growthin vitroand when orthotopically implanted in syngeneic mice. Surprisingly, insulin-like growth factor-1 (IGF-1), but not epidermal growth factor (EGF), restored KPC cell growth in serum-deprived conditions and the IGF-1 growth stimulation effect was AKT dependent. RNA-seq analysis of AKT1/2/3-deficient KPC cells suggested that reduced cholesterol synthesis may be responsible for the decreased response to IGF-1 stimulation. These results indicate that the presence of all three AKT isoforms supports pancreatic tumor cell growth and pharmacological degradation of AKT proteins may be more effective than AKT catalytic inhibitors for treating pancreatic cancer.
Host-derived Interleukin 1α induces an immunosuppressive tumor microenvironment via regulating monocyte-to-macrophage differentiation
Authors: Keerthi Raja Manikanda Raja , Gupta Gourab , Atkinson Grace , Kathrein Katie , Armstrong Alissa , Gower Michael , Roninson Igor , Broude Eugenia , Chen Menqiang , Ji Hao , Lim Chang-uk , Wang Hongjun , Fan Daping , Xu Peisheng , Li Jie , Zhou Gang , Chen Hexin
Published: May 2024

Tumor-associated macrophages exhibit high heterogeneity and contribute to the establishment of an immunosuppressive tumor microenvironment (TME). Although numerous studies have demonstrated that extracellular factors promote macrophage proliferation and polarization, the regulatory mechanisms governing the differentiation process to generate phenotypically, and functionally diverse macrophage subpopulations remain largely unexplored. In this study, we examined the influence of interleukin 1α (IL-1α) on the development of an immunosuppressive TME using orthotopic transplantation murine models of breast cancer. Deletion of host Il1α led to the rejection of inoculated congenic tumors. Single-cell sequencing analysis revealed that CX3CR1+ macrophage cells were the primary sources of IL-1α in the TME. The absence of IL-1α reprogrammed the monocyte-to-macrophage differentiation process within the TME, characterized by a notable decrease in the subset of CX3CR+ ductal-like macrophages and an increase in iNOS-expressing inflammatory cells. Comparative analysis of gene signatures in both human and mouse macrophage subsets suggested that IL-1α deficiency shifted the macrophage polarization from M2 to M1 phenotypes, leading to enhanced cytotoxic T lymphocyte activity in the TME. Importantly, elevated levels of IL-1α in human cancers were associated with worse prognosis following immunotherapy. These findings underscore the pivotal role of IL-1α in shaping an immune-suppressive TME through the regulation of macrophage differentiation and activity, highlighting IL-1α as a potential target for breast cancer treatment.

Teaser

Interleukin 1α dictates macrophage behavior, influencing an immunosuppressive microenvironment in breast cancer, suggesting it as a treatment target.
Cardiovascular responses to natural and auditory evoked slow waves predict post-sleep cardiac function
Authors: Alessandrelli Giulia , Huwiler Stephanie , Bernardi Giulio , Carro-Domínguez Manuel , Stich Fabia , Sala Rossella , Aziri Florent , Trippel Anna , Markendorf Susanne , Niederseer David , Bohm Philipp , Cerveri Pietro , Siclari Francesca , Huber Reto , Wenderoth Nicole , Schmied Christian , Lustenberger Caroline
Published: May 2024

The interplay between slow-wave sleep and cardiovascular health is increasingly recognized. Our prior research showed that auditory-enhanced slow waves can boost cardiac function, yet the mechanisms behind this remain unclear. Advancing these findings, our current analysis dissected the effects of two slow wave types on cardiovascular function, using data from 18 middle-aged men across three nights. We found that the strength of heart rate and blood pressure responses concurrent with slow waves predicts cardiac function post-sleep. Notably, we identified that highly synchronized type I slow waves, as opposed to lower-amplitude type II slow waves, primarily co-occur with these cardiovascular pulsations. While auditory stimulation enhances both types of slow waves, they exhibit distinct temporal dynamics, pointing to different underlying biological mechanisms. This study crucially addresses how distinct slow wave types can affect cardiovascular function, implying that targeted slow wave stimulation could be a strategic approach to improve heart health.
Insulin evokes release of endozepines from astrocytes of the NTS to modulate glucose metabolism
Authors: New Lauryn E. , Wang Niannian , Khan Shabbir , Griffiths Joanne C. , Hains Ryan , Johnston Jamie , Filippi Beatrice M.
Published: May 2024

The central nervous system (CNS) plays a key role in regulating metabolic functions, but conditions like obesity and diabetes can disrupt this balance. Within the CNS, the nucleus of the solitary tract (NTS) in the dorsal vagal complex (DVC) controls glucose metabolism and feeding behaviour. In rodents, the NTS senses insulin and communicates with the liver to regulate glucose production. Even short-term exposure to a high-fat diet (HFD) can lead to insulin resistance and impair NTS function. However, we still know little about which cells in the NTS are sensitive to insulin. Our study aimed to identify these insulin-sensitive cells and understand how they affect glucose metabolism.

We found that insulin receptors in astrocytes are crucial for the NTS’s ability to regulate glucose production in the liver. Insulin evokes the release of endozepines from astrocytes, and injecting endozepines into the NTS reduces glucose production. The effect of endozepines within the NTS is mimicked by GABAA antagonists and prevented by an agonist, suggesting that insulin prompts astrocytes to release endozepines, which then attenuate GABAA receptor activity, ultimately reducing glucose production in the liver.

Our study is the first to show that insulin–dependent release of endozepines from NTS- astrocytes is fundamental to control blood glucose levels, providing valuable insights into the mechanisms underlying insulin function within this specific region of the CNS.
Salmonids elicit an acute behavioral response to heterothermal environments
Authors: Naudascher Robert , Brizzolara Stefano , Slomka Jonasz , Boes Robert M. , Holzner Markus , Silva Luiz G. M. , Stocker Roman
Published: May 2024

Most fish species are ectothermic and rely on behavioral strategies to control their body temperature in heterothermal environments. Both thermotaxis and thermokinesis have been suggested as important underlying mechanisms. However, to what extent these behaviors allow fish to respond to rapid (timescales of minutes) and strong thermal disturbances, like those caused by anthropogenic water releases into natural freshwater systems, is poorly understood. Here, we quantify this response for a salmonid species with a novel laboratory approach coupled with image-based tracking. We exposed brown trout parr (Salmo trutta), acclimated to 12 °C, to rapidly forming cold- and warm-water interfaces with temperatures ranging from 4 to 20 °C. We found that fish actively avoided colder water (≤8 °C) through a rapid response that combined thermotaxis and thermokinesis. In contrast, fish did not avoid warmer water and frequently crossed interfaces having temperature contrasts of up to 8 °C. This study shows that brown trout parr swiftly deploy multiple behavioral strategies to minimize exposure to cold water and take advantage of warm water, illustrating their capability to cope with rapidly occurring thermal alterations.
HER4 is a high affinity dimerization partner for all EGFR/HER/ErbB-family proteins
Authors: Singh Pradeep Kumar , Kim Soyeon , Smith Adam W.
Published: May 2024

Human epidermal growth factor receptors (HER) – also known as EGFR or ErbB receptors – are a subfamily of receptor tyrosine kinases (RTKs) that play crucial roles in cell growth, division, and differentiation. HER4 (ErbB4) is the least studied member of this family, partly because its expression is lower in later stages of development. Recent work has suggested that HER4 can play a role in metastasis through cell migration and invasiveness; however, unlike EGFR and HER2, the precise role that HER4 plays in tumorigenesis is still unresolved. Early work on HER family proteins suggested that there are direct interactions between the four members, but to date, there has been no single study of all four receptors in the same cell line studied with the same biophysical method. Here, we quantitatively measure the degree of association between HER4 and the other HER-family proteins in live cells with a time-resolved fluorescence technique called pulsed interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS). PIE-FCCS is sensitive to the oligomerization state of membrane proteins in live cells, while simultaneously measuring protein expression levels and diffusion coefficients. Our PIE-FCCS results demonstrate that HER4 interacts directly with all HER family members in the cell plasma membrane. The interaction between HER4 and other HER family members intensified in the presence of a HER4-specific ligand. Our work suggests that HER4 is a preferred dimerization partner for all HER family proteins, even in the absence of ligands.