bluuebunny/crossref_metadata_2025 huggingface dataset:
WITHDRAWN: I feel your pain: Higher empathy is associated with higher posterior default mode network activity
Authors: Oliva Valeria , Riegner Gabriel , Dean Jon , Khatib Lora A. , Allen Alessandro , Barrows Daniel , Chen Conan , Fuentes Richard , Jacobson Aaron , Lopez Carolina , Mosbey Dwayne , Reyes Mikaila , Ross Jacob , Uvarova Alexandra , Liu Thomas , Mobley William , Zeidan Fadel
Published: August 2023

Withdrawal Statement

The authors discovered an error in the primary analysis and have withdrawn the results from this version of the investigation.
Antigen presentation by tumor-associated macrophages drives tumor-infiltrating T cells from a progenitor exhaustion state to terminal exhaustion
Authors: Waibl Polania Jessica , Hoyt-Miggelbrink Alexandra , Tomaszewski William H. , Wachsmuth Lucas P. , Lorrey Selena J. , Wilkinson Daniel S. , Lerner Emily , Woroniecka Karolina , Finlay John B. , Ayasoufi Katayoun , Fecci Peter E.
Published: August 2023

Whereas terminally exhausted T (Tex_term) cells retain anti-tumor cytotoxic functions, the frequencies of stem-like progenitor exhausted T (Tex_prog) cells better reflect immunotherapeutic responsivity. Here, we examined the intratumoral cellular interactions that govern the transition to terminal T cell exhaustion. We defined a metric reflecting the intratumoral progenitor exhaustion-to-terminal exhaustion ratio (PETER), which decreased with tumor progression in solid cancers. Single cell analyses of Tex_prog cells and Tex_term cells in glioblastoma (GBM), a setting of severe T cell exhaustion, revealed disproportionate loss of Tex_prog cells over time. Exhaustion concentrated within tumor-specific T cell subsets, with cognate antigen exposure requisite for acquisition of the Tex_term phenotype. Tumor-associated macrophages (TAM) - not tumor cells - were the primary source of antigenic exposure governing the Tex_prog to Tex_term transition. TAM depletion increased frequencies of Tex_prog cells in multiple tumor models, increased PETER, and promoted responsiveness to αPD-1 immunotherapy. Thus, targeting TAM – T cell interactions may further license checkpoint blockade responses.
Competition-driven eco-evolutionary feedback reshapes bacterio-phage lambda’s fitness landscape and enables speciation
Authors: Doud Michael B. , Gupta Animesh , Li Victor , Medina Sarah J. , De La Fuente Caesar A. , Meyer Justin R.
Published: August 2023

A major challenge in evolutionary biology is explaining how populations navigate rugged fitness landscapes without getting trapped on local optima. One idea illustrated by adaptive dynamics theory is that as populations adapt, their newly enhanced capacities to exploit resources alter fitness payoffs and restructure the landscape in ways that promote speciation by opening new adaptive pathways. While there have been indirect tests of this theory, none have measured how fitness landscapes deform during adaptation, or test whether these shifts promote diversification. Here, we achieve this by studying bacteriophage ⋋, a virus that readily speciates into co-existing receptor specialists under controlled laboratory conditions. We used a high-throughput gene editing-phenotyping technology to measure ⋋’s fitness landscape in the presence of different evolved-⋋ competitors and found that the fitness effects of individual mutations, and their epistatic interactions, depend on the competitor. Using these empirical data, we simulated ⋋’s evolution on an un-changing landscape and one that recapitulates how the landscape deforms during evolution. ⋋ heterogeneity only evolved in the shifting landscape regime. This study provides a test of adaptive dynamics, and, more broadly, shows how fitness landscapes dynamically change during adaptation, potentiating phenomena like speciation by opening new adaptive pathways.
Co-evolution of gene transfer agents and their alphaproteobacterial hosts
Authors: Kogay Roman , Zhaxybayeva Olga
Published: August 2023

Gene transfer agents (GTAs) are enigmatic elements that resemble small viruses and are known to be produced during nutritional stress by some bacteria and archaea. The production of GTAs is regulated by quorum sensing, under which a small fraction of the population acts as GTA producers, while the rest become GTA recipients. In contrast to canonical viruses, GTAs cannot propagate themselves because they package pieces of the producing cell’s genome. In alphaproteobacteria, GTAs are mostly vertically inherited and reside in their hosts’ genomes for hundreds of millions of years. While GTAs’ ability to transfer genetic material within a population and their long-term preservation suggests an increased fitness of GTA-producing microbes, the associated benefits and type of selection that maintains GTAs are poorly understood. By comparing rates of evolutionary change in GTA genes to the rates in gene families abundantly present across 293 alphaproteobacterial genomes, we detected 59 gene families that likely co-evolve with GTA genes. These gene families are predominantly involved in stress response, DNA repair, and biofilm formation. We hypothesize that biofilm formation enables the physical proximity of GTA-producing cells, limiting GTA-derived benefits only to a group of closely related cells. We further conjecture that population structure of biofilm-forming sub-populations ensures that the trait of GTA production is maintained despite the inevitable rise of “cheating” genotypes. Because release of GTA particles kills the producing cell, maintenance of GTAs is an exciting example of social evolution in a microbial population.

Importance

Gene transfer agents (GTAs) are viruses domesticated by some archaea and bacteria as vehicles for carrying pieces of the host genome. Produced under certain environmental conditions, GTA particles can deliver DNA to neighboring, closely related cells. Function of GTAs remains uncertain. While making GTAs is suicidal for a cell, GTA-encoding genes are widespread in genomes of alphaproteobacteria. Such GTA persistence implies functional benefits but raises question about how selection maintains this lethal trait. By showing that GTA genes co-evolve with genes involved in stress response, DNA repair, and biofilm formation, we provide support for the hypothesis that GTAs facilitate DNA exchange during the stress conditions and present a model for how GTAs persist in biofilm-forming bacterial populations despite being lethal.
Hybrid protein-ligand binding residue prediction with protein language models: Does the structure matter?
Authors: Gamouh Hamza , Novotný Marian , Hoksza David
Published: August 2023

Background

Predicting protein-ligand binding sites is crucial in studying protein interactions with applications in biotechnology and drug discovery. Two distinct paradigms have emerged for this purpose: sequence-based methods, which leverage protein sequence information, and structure-based methods, which rely on the three-dimensional (3D) structure of the protein. We propose to study a hybrid approach combining both paradigms’ strengths by integrating two recent deep learning architectures: protein language models (pLMs) from the sequence-based paradigm and Graph Neural Networks (GNNs) from the structure-based paradigm. Specifically, we construct a residue-level Graph Attention Network (GAT) model based on the protein’s 3D structure that uses pre-trained pLM embeddings as node features. This integration enables us to study the interplay between the sequential information encoded in the protein sequence and the spatial relationships within the protein structure on the model’s performance.

Results

By exploiting a benchmark dataset over a range of ligands and ligand types, we have shown that using the structure information consistently enhances the predictive power of baselines in absolute terms. Nevertheless, as more complex pLMs are employed to represent node features, the relative impact of the structure information represented by the GNN architecture diminishes.

Conclusions

The above observations suggest that, although using the experimental protein structure almost always improves the accuracy binding site prediction, complex pLMs still contain structural information that lead to good predictive performance even without using 3D structure.
Second Harmonic Generation Imaging Reveals Entanglement of Collagen Fibers in the Elephant Trunk Skin Dermis
Authors: Schulz Andrew K. , Plotczyk Magdalena , Sordilla Sophia , Boyle Madeline , Singal Krishma , Reidenberg Joy S. , Hu David L. , Higgins Claire A.
Published: August 2023

Form-function relationships often have tradeoffs: if a material is tough, it is often inflexible, and vice versa. This is particularly relevant for the elephant trunk, where the skin should be protective yet elastic. To investigate how this is achieved, we used classical histochemical staining and second harmonic generation microscopy to describe the morphology and composition of elephant trunk skin. We report structure at the macro and micro scales, from the thickness of the dermis to the interaction of 10μm thick collagen fibers. We analyzed several sites along the length of the trunk, to compare and contrast the dorsal-ventral and proximal-distal skin morphologies and compositions. We find the dorsal skin of the elephant trunk can have keratin armor layers over 2mm thick, which is nearly 100 times the thickness of the equivalent layer in human skin. We also found that the structural support layer (the dermis) of elephant trunk contains a distribution of collagen-I (COL1) fibers in both perpendicular and parallel arrangement. The bimodal distribution of collagen is seen across all portions of the trunk, and is dissimilar from that of human skin where one orientation dominates within a body site. We hypothesize that this distribution of COL1 in the elephant trunk allows both flexibility and load-bearing capabilities. Additionally, when viewing individual fiber interaction of 10μm thick collagen, we find the fiber crossings per unit volume are five times more common than in human skin, suggesting that the fibers are entangled. We surmise that these intriguing structures permit both flexibility and strength in the elephant trunk. The complex nature of the elephant skin may inspire the design of materials that can combine strength and flexibility.
Honey beeApis melliferaL. Responses to Oxidative Stress Induced by Pharmacological and Pesticide Compounds
Authors: Tahir Faizan , Goblirsch Michael , Adamczyk John , Karim Shahid , Alburaki Mohamed
Published: August 2023

The western honey bee,Apis melliferaL., is a eusocial insect that plays major roles in ecosystem balances and pollination of plants and food crops. Honey bees face multiple biotic and abiotic stressors, such as pathogens, diseases, chemical pesticides, and climate change, which all contribute to honey bee colony loss. This study investigated the impacts of multiple pharmacological and pesticide molecules on honey bee survival and gene regulation responses. In an 11-day cage experiment, sublethal doses of tunicamycin, thapsigargin, metformin, paraquat, hydrogen peroxide, and imidacloprid were administered to newly emerged sister bees. Daily treatment consumption and mortality were recorded, as well as the transcription expression of twelve major genes (AChE-2,Apisimin,Apidaecin,mrjp1,Sodq,cp450,SelT,SelK,Ire1,Xbp1,Derl-1,Hsc70), some of which are markers of oxidative and endoplasmic reticulum (ER) stresses in honey bees. At day 9 of the treatments, protein damage was quantified in caged bees. Kaplan-Meier model indicated significant (p< 0.001) toxicological effects of paraquat, H2O2and tunicamycin on bee survivorship compared to controls with better survivals for other molecules. Post-ingestive aversion responses were recorded only in the case of tunicamycin, hydrogen peroxide and imidacloprid. Nonetheless, significantly higher protein damage on day 9 was only identified in bees exposed to paraquat and imidacloprid. Some antioxidant genes significantly regulated vis-à-vis specific treatments. Our results reveal age-related regulation of other major genes with significant inter-gene positive correlations.
VISTA: An integrated framework for structural variant discovery
Authors: Sarwal Varuni , Lee Seungmo , Yang Jianzhi , Sankararaman Sriram , Chaisson Mark , Eskin Eleazar , Mangul Serghei
Published: August 2023

Structural variation (SV), refers to insertions, deletions, inversions, and duplications in human genomes. With advances in whole genome sequencing (WGS) technologies, a plethora of SV detection methods have been developed. However, dissecting SVs from WGS data remains a challenge, with the majority of SV detection methods prone to a high false-positive rate, and no existing method able to precisely detect a full range of SV’s present in a sample. Previous studies have shown that none of the existing SV callers can maintain high accuracy across various SV lengths and genomic coverages. Here, we report an integrated structural variant calling framework, VISTA (Variant Identification and Structural Variant Analysis) that leverages the results of individual callers using a novel and robust filtering and merging algorithm. In contrast to existing consensus-based tools which ignore the length and coverage, VISTA overcomes this limitation by executing various combinations of top-performing callers based on variant length and genomic coverage to generate SV events with high accuracy. We evaluated the performance of VISTA on using comprehensive gold-standard datasets across varying organisms and coverage. We benchmarked VISTA using the Genome-in-a-Bottle (GIAB) gold standard SV set, haplotype-resolved de novo assemblies from The Human Pangenome Reference Consortium (HPRC)1,2, along with an in-house PCR-validated mouse gold standard set. VISTA maintained the highest F1 score among top consensus-based tools measured using a comprehensive gold standard across both mouse and human genomes. VISTA also has an optimized mode, where the calls can be optimized for precision or recall. VISTA-optimized is able to attain 100% precision and the highest sensitivity among other variant callers. In conclusion, VISTA represents a significant advancement in structural variant calling, offering a robust and accurate framework that outperforms existing consensus-based tools and sets a new standard for SV detection in genomic research.
Reading of ingroup politicians’ smiles triggers smiling in the corner of one’s eyes
Authors: Fino Edita , Menegatti Michela , Avenanti Alessio , Rubini Monica
Published: August 2023

Capturing political support from spontaneous smile reactions detected in others’ faces can be used to gauge electorate preference. But will a smile elicited in the corner of one’s eye while reading of a favored politician smiling indicate positive disposition and political support for target candidates? From an embodied simulation perspective, we tested whether reading of an ingroup or outgroup politician smiling would trigger morphologically different smiles in faces of readers. In a reading task in the laboratory, participants were presented with subject-verb phrases describing left and right-wing politicians smiling or frowning while their facial muscular reactions were measured via electromyography (EMG) recording from the zygomaticus major (ZM, lip puller muscle), orbicularis oculi (OO, eye corner muscle) and the corrugator supercili (CS, wrinkler of the eyebrows). We expected and found that participants responded with a smile detected at the lip puller (ZM) and eye corner (OO) facial muscles when exposed to portrayals of smiling politicians of same political orientation, and reported more positive emotions towards these latter. When reading about outgroup politicians smiling, there was a weaker activation of the lip corner (ZM) muscle and no activation of the eye corner (OO) muscle, while emotions reported towards outgroup politicians were significantly more negative. Also, a more enhanced frown response (CS) was found for ingroup compared to outgroup politicians’ frown expressions. Present findings suggest that a politician’s smile may go a long way to influence electorates through both non-verbal and verbal pathways. They add another layer to our understanding of how language and social information shape embodied effects in a highly nuanced manner.
GetPrimers: a generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems
Authors: Miao Zepu , Wang Haiting , Tu Xinyu , Huang Zhengshen , Huang Shujing , Zhang Xinxin , Wang Fan , Huang Zhishen , Li Huihui , Jiao Yue , Gao Song , Zhou Zhipeng , Shan Chun-Min , Li Jing , Yue Jia-Xing
Published: August 2023

Genetic targeting (e.g., gene knockout and tagging) based on polymerase chain reaction (PCR) is a simple yet powerful approach for studying gene functions. Although originally developed in classic budding and fission yeast models, the same principle applies to other eukaryotic systems with efficient homologous recombination. One-step-PCR-based genetic targeting is conventionally used but the sizes of the homologous arms that it generates for recombination-mediated genetic targeting are usually limited. Alternatively, gene targeting can also be performed via fusion PCR, which can create homologous arms that are orders of magnitude larger, therefore substantially increases the efficiency of recombination-mediated genetic targeting. Here we present GetPrimers (https://www.evomicslab.org/app/getprimers/), a generalized computational framework and web tool to assist automatic targeting and verification primer design for both one-step-PCR-based and fusion-PCR-based genetic targeting experiments. Moreover, GetPrimers by design runs for any given genetic background of any species with full genome scalability. Therefore, GetPrimers is capable of empowering high-throughput functional genomics assays at multi-population and multi-species levels. Comprehensive experimental validations have been performed for targeting and verification primers designed by GetPrimers across multiple organism systems and experimental setups. We anticipate GetPrimers to become a highly useful and popular tool to facilitate easy and standardized gene modification across multiple systems.

Take Aways

Developed GetPrimers for generalized primer design of PCR-based genetic targeting.

GetPrimers shines with its high versatility and genome-wide scalability.

GetPrimers was validated across multiple organisms and experimental setups.
Mapping Natural Product Biosynthetic Hotspots: Prioritizing Conservation for Medicinal Resources
Authors: Fahmi Muhamad , Takanashi Kojiro , Kakei Yusuke , Kubota Yasuhiro , Kanemoto Keiichiro
Published: August 2023

Background

Natural products (NPs) are vital for promoting human health. Given the increasing threats of biodiversity loss and ecosystem degradation, understanding the geographical hotspots of NPs is essential to strategically prioritize areas for conservation, ensuring the sustained availability of these invaluable medicinal resources.

Methods

We constructed a global diversity map for 1,434 woody angiosperm species, each represented by existing genomic or transcriptomic data. We curated a list of 166 enzymes essential for the biosynthesis and structural diversity of NPs, and identified geographical hotspots of NPs by averaging enzyme presence across the grids. We also examined the distribution pattern of each enzyme. To gain deeper insights into NP distribution patterns, we performed a comparative analysis of enzyme groups responsible for the biosynthesis of two pharmacologically significant compounds with distinct biosynthetic pathways, shikonin derivatives and benzylisoquinoline alkaloids.

Findings

Our study reveals a correlation between NP hotspots and biodiversity hotspots, with a subset of markers displaying unique, region-specific patterns. Comparative analysis of enzymes for shikonin derivatives and benzylisoquinoline alkaloids biosynthetic pathways shows similar pattern, with the former demonstrating a unique and region-specific distribution.

Interpretation

Our findings emphasize the importance of preserving biodiversity hotspots for sustaining NP-based medicinal resources. Additionally, the specific distribution of certain enzyme markers, such as those related to shikonin derivatives, suggests that some NPs may necessitate targeted conservation strategies. This study provides a foundational roadmap for identifying the geographical hotspots of NPs and developing targeted conservation strategies.

Funding

Japan Society for the Promotion of Science through the Grant-in-Aid for Scientific Research (A) 20H00651.
Stress granule dysfunction via chromophore-associated light inactivation
Authors: Koizumi Takumi , Fujimoto Ai , Kawaguchi Haruka , Kurosaki Tsumugi , Kitamura Akira
Published: August 2023

Stress granules (SGs) are cytoplasmic condensates composed of various proteins and RNAs that protect translation-associated machinery from harmful conditions during stress. However, the method of spatio-temporal inactivation of condensates such as SGs in live cells to study cellular phenotypes is still in the process of being demonstrated. Here, we show that the inactivation of SG by chromophore-associated light inactivation (CALI) using a genetically encoded red fluorescence protein (SuperNova-Red) as a photosensitizer leads to differences in cell viability during recovery from hyperosmotic stress. CALI delayed the disassembly kinetics of SGs during recovery from hyperosmotic stress. Consequently, CALI could inactivate the SGs, and the cellular fate due to SGs could be analyzed. Furthermore, CALI is an effective spatiotemporal knockdown method for intracellular condensates/aggregates and would contribute to the elucidation of importance of such condensates/aggregates.
Ikzf1 association with Foxp3 for Foxp3-dependent gene repression in Treg cells: induction of autoimmunity and tumor immunity by disrupting the association
Authors: Ichiyama Kenji , Long Jia , Kobayashi Yusuke , Horita Yuji , Kinoshita Takeshi , Nakamura Yamami , Kominami Chizuko , Georgopoulos Katia , Sakaguchi Shimon
Published: August 2023

The transcription factor Foxp3 specifically expressed in regulatory T (Treg) cells controls Treg function by repressing some genes and activating others. We have shown here that the transcription factor Ikzf1 associates with Foxp3 via its exon 5 (called IkE5) and that conditional deletion ofIkE5up-regulated the genes, includingIfng, normally repressed by Foxp3 upon TCR stimulation.IkE5-deletion in Treg cells indeed incurred IFN-γ overproduction, which destabilized Foxp3 expression and impaired suppressive function, consequently producing fatal systemic autoimmune diseases and evoking strong anti-tumor immunity. In addition, pomalidomide, which degrades IKZF1 and IKZF3, induced IFN-γ overproduction in human Treg cells. Mechanistically, the Foxp3/Ikzf1/Ikzf3 complex exerted gene-repressing function by competing with epigenetic co-activators, such as p300 and NFAT1, for binding to the target gene loci via chromatin remodeling. Collectively, the association of Ikzf1 with Foxp3 is essential for repressive function of Foxp3, and can be targeted to control autoimmunity and tumor immunity.
Characterization and Genome Sequencing of a Novel Lytic Bacteriophage Infecting Hospital-Associated Carbapenem-ResistantKlebsiella pneumoniaeStrain from Dhaka, Bangladesh
Authors: Khan Fahad , Salman Bhuiyan Mohammad Sami , Tabassum Syeda Naushin , Abrar Hossain Md. Sakib , Rahman Aura , Sadique Abdus , Jaber Abdullah All , Shams Fariza , Bhandare Sudhakar , Hossain Maqsud
Published: August 2023

Background

Multidrug-resistant bacterial pathogens pose a grave threat to global health, withKlebsiella pneumoniaebeing a particular concern due to its hypervariable extracellular matrix capsule and frequent development of extended-spectrum β-lactamases and other antibiotic defenses. TreatingK. pneumoniae-induced infections with antibiotics is becoming increasingly challenging, necessitating the development of new approaches to address this problem. Phages have emerged as a promising alternative to antibiotics due to their high host specificity, abundance in nature, and evolvability. However, their host specificity makes it difficult to target highly diverse bacterial species using phage therapy.

Methods

In this study, aK. pneumoniaebacteriophage was characterized using double-agar overlay (DLA), host range testing, and Oxford Nanopore Technologies (ONT) MinION long-read sequencer for whole genome sequencing.

Results

The phage was isolated from a hospital sewage drain and showed activity against multi-drug resistantK. pneumoniae, and showed extensive activity againststrains from Dhaka, Bangladesh. Sequence analysis confirmed that the phage belonged to the familySiphoviridae, subfamily UnclassifiedWebervirus.

Conclusion

The findings of this study highlight the potential of sewage samples as a rich source of bacteriophages against medically important pathogens. Further studies on the biological characteristics of thisK. pneumoniaebacteriophage could yield valuable insights into the development of a potential therapeutic agent forK. pneumoniaespecific infections. It is worth noting that although the viruses were only found in sewage from places with increasing reports ofK. pneumoniaeinfections, such as public hospitals, they hold promise for addressing the growing problem of multidrug-resistant bacterial pathogens.
Mitochondrial complex I as a diagnostic and therapeutic target in a mouse model of tauopathy
Authors: Wong Jia Hui , Vincent Anselm S. , Khanapur Shivashankar , Rong Tang Jun , Ramasamy Boominathan , Hartimath Siddesh , Cheng Peter , Tsukada Hideo , Robins Edward G , Goggi Julian L , Barron Anna M.
Published: August 2023

Dysfunction of the energy producing organelle of the cell, mitochondria, plays a pivotal role in Alzheimer’s disease (AD). We have recently used a novel positron emission tomographic (PET) imaging tracer targeting mitochondrial complex I (MC-I) to visualize mitochondrial abnormalities in the brains of living tau transgenic (TauTg) mice. MC-I mediates the first and limiting step in oxidative phosphorylation, the primary source of neuronal energy production. Here we used MC-I-PET to test if inhibition of mutant tau expression through transgene suppression with doxycycline could reverse mitochondrial defects in a mouse model of tauopathy and evaluate the efficacy of a MC-I-targeted candidate therapeutic, Mdivi-1. We found that late-stage suppression of mutant tau did not rescue mitochondrial deficits measuredin vivoby MC-I-PET, despite reduced burden of tauopathy and neuroinflammation. These findings demonstrate that mitochondrial dysfunction may continue even if tauopathy is halted, particularly if initiated at late-stage disease. Further, we demonstrate the potential application of MC-I-PET for monitoring therapeutic efficacy, surprisingly finding detrimental effects of the mitochondrial-targeted candidate therapeutic, Mdivi-1, in TauTg mice. These findings directly contrast with the beneficial effects of Mdivi-1 observed in other models of neurodegeneration. Together, our findings highlight the need for clinical endpoints measuring mitochondrial damage in addition to markers of tauopathy in the assessment of disease prognosis and efficacy of candidate therapeutics and demonstrates the potential application of MC-I-PET to meet this need.
Structural basis of allosteric modulation of metabotropic glutamate receptor activation and desensitization
Authors: Strauss Alexa , Gonzalez-Hernandez Alberto J. , Lee Joon , Abreu Nohely , Selvakumar Purushotham , Salas-Estrada Leslie , Kristt Melanie , Marx Dagan C. , Gilliland Kristen , Melancon Bruce J. , Filizola Marta , Meyerson Joel , Levitz Joshua
Published: August 2023

The metabotropic glutamate receptors (mGluRs) are neuromodulatory family C G protein coupled receptors which assemble as dimers and allosterically couple extracellular ligand binding domains (LBDs) to transmembrane domains (TMDs) to drive intracellular signaling. Pharmacologically, mGluRs can be targeted either at the LBDs by glutamate and synthetic orthosteric compounds or at the TMDs by allosteric modulators. Despite the potential of allosteric TMD-targeting compounds as therapeutics, an understanding of the functional and structural basis of their effects on mGluRs is limited. Here we use a battery of approaches to dissect the distinct functional and structural effects of orthosteric versus allosteric ligands. We find using electrophysiological and live cell imaging assays that both agonists and positive allosteric modulators (PAMs) can drive activation and desensitization of mGluRs. The effects of PAMs are pleiotropic, including both the ability to boost the maximal response to orthosteric agonists and to serve independently as desensitization-biased agonists across mGluR subtypes. Conformational sensors reveal PAM-driven inter-subunit re-arrangements at both the LBD and TMD. Motivated by this, we determine cryo-electron microscopy structures of mGluR3 in the presence of either an agonist or antagonist alone or in combination with a PAM. These structures reveal PAM-driven re-shaping of intra- and inter-subunit conformations and provide evidence for a rolling TMD dimer interface activation pathway that controls G protein and beta-arrestin coupling.

Highlights

-Agonists and PAMs drive mGluR activation, desensitization, and endocytosis

-PAMs are desensitization-biased and synergistic with agonists

-Four combinatorial ligand conditions reveal an ensemble of full-length mGluR structures with novel interfaces

-Activation and desensitization involve rolling TMD interfaces which are re-shaped by PAM
Neutron crystallographic refinement withREFMAC5 of theCCP4 suite
Authors: Catapano Lucrezia , Long Fei , Yamashita Keitaro , Nicholls Robert A. , Steiner Roberto A. , Murshudov Garib N.
Published: August 2023

Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand recognition processes, and protein-protein interactions. However, their direct visualisation by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localisation of the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher), that is not often attainable. Differently, neutron diffraction methods enable the visualisation of most H atoms, typically in the form of deuterium (D) atoms at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought.REFMAC5 of the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of theCCP4 Monomer Library, the source of prior chemical information used in refinement. One new feature for neutron data analysis inREFMAC5 is the refinement of the protium/deuterium (1H/D) fraction. This parameter describes the relative1H/D contribution to neutron scattering for H atoms. The newly developedREFMAC5algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) by using either (i) neutron data-only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement withREFMAC5afforded models characterised byR-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy especially for structures at medium-low resolution.

Synopsis

The macromolecular refinement packageREFMAC5 of theCCP4 suite has been extended with the incorporation of algorithms for neutron crystallography.
A spatially constrained independent component analysis jointly informed by structural and functional network connectivity
Authors: Fouladivanda Mahshid , Iraji Armin , Wu Lei , van Erp Theodorus G.M. , Belger Aysenil , Hawamdeh Faris , Pearlson Godfrey D. , Calhoun Vince D.
Published: August 2023

There are a growing number of neuroimaging studies motivating joint structural and functional brain connectivity. Brain connectivity of different modalities provides insight into brain functional organization by leveraging complementary information, especially for brain disorders such as schizophrenia. In this paper, we propose a multi-modal independent component analysis (ICA) model that utilizes information from both structural and functional brain connectivity guided by spatial maps to estimate intrinsic connectivity networks (ICNs). Structural connectivity is estimated through whole-brain tractography on diffusion-weighted MRI (dMRI), while functional connectivity is derived from resting-state functional MRI (rs-fMRI). The proposed structural-functional connectivity and spatially constrained ICA (sfCICA) model estimates ICNs at the subject level using a multi-objective optimization framework. We evaluated our model using synthetic and real datasets (including dMRI and rs-fMRI from 149 schizophrenia patients and 162 controls). Multi-modal ICNs revealed enhanced functional coupling between ICNs with higher structural connectivity, improved modularity, and network distinction, particularly in schizophrenia. Statistical analysis of group differences showed more significant differences in the proposed model compared to the unimodal model. In summary, the sfCICA model showed benefits from being jointly informed by structural and functional connectivity. These findings suggest advantages in simultaneously learning effectively and enhancing connectivity estimates using structural connectivity.
Goblet cell invasion promotes breaching of respiratory epithelia by an opportunistic human pathogen
Authors: Swart A. Leoni , Laventie Benoît-Joseph , Sütterlin Rosmarie , Junne Tina , Yu Xiao , Karagkiozi Evdoxia , Okujava Rusudan , Jenal Urs
Published: August 2023

While commensal bacteria generally respect natural barriers of the human body, pathogens are able to breach epithelia, invade deeper tissue layers and cause life-threatening infections.Pseudomonas aeruginosa, an opportunistic human pathogen, is a leading cause of severe hospital-acquired pneumonia, with mortality rates as high as 50% in mechanically ventilated patients1–3. Effective colonization and breaching of lung mucosa are hallmarks ofP. aeruginosapathogenesis4. Although virulence factors and behavioral strategies ofP. aeruginosahave been described5,6, it has remained unclear how this pathogen disseminates on functional mucosal surfaces, how it avoids mucociliary clearance and how it invades the tissue barrier. Using fully differentiated human lung epithelia, we demonstrate thatP. aeruginosaefficiently spreads on the apical tissue surface before it breaches epithelia by specifically invading mucus secreting goblet cells. Internalization leads to host cell death and expulsion and the formation of ruptures of the epithelial barrier. Rupture sites are rapidly colonized by extracellular bacteria through active chemotaxis, leading to increasing tissue damage and successful pathogen translocation to the unprotected basolateral side of the epithelium. We show that cell invasion is promoted by two Type-6 toxin secretion systems (T6SS), while Type-3 (T3SS) mediates cell death of infected goblet cells. T3SS mutants invade goblet cells normally, but internalized bacteria fail to trigger goblet cell expulsion and instead show unrestrained intracellular replication. While the effective shedding of infected host cells reveals potent tissue protection mechanisms, the discovery of an intracellular lifestyle ofP. aeruginosain human lung epithelia provides new entry points into investigating the intersection of antibiotic and immune mechanisms during lung infections. By demonstrating thatP. aeruginosauses a combination of specific virulence factors and collective behavior to invade goblet cells and breach the lung tissue barrier from within, these studies reveal novel mechanisms underlying lung infection dynamics under physiological conditions.
Degeneracy in negative feedback (NFBL) and incoherent feedforward (IFFL) loops: Adaptation and resonance
Authors: Ventura Alejandra C. , Rotstein Horacio G.
Published: August 2023

Degeneracy in dynamic models refers to these situations where multiple combinations of parameter values produce identical patterns for the observable variable. We investigate this phenomenon in two qualitatively different adaptive circuit mechanisms: nonlinear feedback loop (NFBL) and incoherent feedback loop (IFFL). We use minimal models of these circuit types together with analytical calculations, regular perturbation analysis, dynamical systems tools and numerical simulations. In response to constant (or step-constant) inputs, NFBLs and IFFLs produce and overshoot allowing the observable variable to return to a value closer to baseline than the peak (adaptation). We identify the dynamic principles underlying the emergence of degeneracy in adaptive patterns both within and across circuit types in representative NFBL and IFFL models in terms of biologically plausible parameters. We identify the conditions under which degeneracy persists in response to oscillatory inputs with arbitrary frequencies, giving rise to resonance and phasonance degeneracy. This naturally extends to the response of adaptive systems to time-dependent inputs within a relatively large class. By using phase-plane analysis, we provide a mechanistic, dynamical systems-based interpretation of degeneracy. Our results have implication for the understanding of adaptive systems, for the relationship between adaptive and resonant/phasonant systems, for the understanding of complex biochemical circuits, for neuronal computation, and for the development of methods for circuit and dynamical systems reconstruction based on experimental or observational data.
Germline mutation rate predicts cancer mortality across 37 vertebrate species
Authors: Kapsetaki Stefania E. , Compton Zachary T. , Mellon Walker , Vincze Orsolya , Giraudeau Mathieu , Harrison Tara M. , Abegglen Lisa M. , Boddy Amy M. , Maley Carlo C. , Schiffman Joshua D.
Published: August 2023

The explanation for why some species are more susceptible to cancer than others remains an area of intense investigation. Cancer evolves in part through the accumulation of mutations and, therefore, we hypothesized that germline mutation rates would be associated with cancer prevalence and mortality across species. We collected previously published data on germline mutation rate and cancer mortality data for 37 vertebrate species. Germline mutation rate was positively correlated with cancer mortality (P= 0.008). Why animals with increased germline mutation rates die more from cancer remains an open question, however they may benefit from close monitoring for tumors due to hereditary cancer predisposition syndromes. Early diagnoses of cancer in these species may increase their chances of treatment and overall survival.
The interplay between focus of attention, respiratory phases, and the Heartbeat Evoked Potential
Authors: Zaccaro Andrea , della Penna Francesca , Mussini Elena , Parrotta Eleonora , Perrucci Mauro Gianni , Costantini Marcello , Ferri Francesca
Published: August 2023

The Heartbeat Evoked Potential (HEP) is an EEG fluctuation that reflects the cortical processing of cardiac signals. HEP amplitude increases during various tasks involving cardiac interoception. Recent research has also indicated that HEP amplitude and cardiac interoceptive accuracy are higher during exhalation compared to inhalation. This difference may be due to the suppression of heartbeat-related sensations during inhalation and the amplification of sensations during exhalation through attentional mechanisms. Despite significant advancements in HEP research, the interactions between the HEP, interoceptive attention, and respiration are still unclear. In this study, we developed a novel experimental paradigm to investigate the relationship between HEP amplitude and respiratory phases during tasks that involve attention to cardiac interoception, non-cardiac interoception (specifically, respiration), and exteroceptive stimuli. The tasks included the Heartbeat Counting Task and the Breath Counting Task as interoceptive tasks, as well as the Cardiac-Tone Counting Task and the Breath-Tone Counting Task as exteroceptive tasks. Results demonstrated significant increases in HEP amplitude during the Heartbeat Counting Task compared to the Cardiac-Tone Counting Task and the Breath Counting Task, mostly observed over fronto-central electrodes in a late time-window. Notably, the amplitude increases during the Heartbeat Counting Task were primarily driven by HEPs recorded during exhalation, while inhalation had minimal impact. These findings align with the predictive coding model of interoceptive perception, suggesting that HEP amplitude reflects a precision-weighting process of prediction errors related to cardiac sensations that is specifically influenced by attention directed toward the heart. Furthermore, our findings emphasize the crucial role of exhalation in this precision-weighting process. These results may have considerable implications for the development of respiratory interventions to fine-tune cardiac interoception.
Action space restructures visual working memory in prefrontal cortex
Authors: Jonikaitis Donatas , Zhu Shude
Published: August 2023

Visual working memory enables flexible behavior by decoupling sensory stimuli from behavioral actions. While previous studies have predominantly focused on the storage component of working memory, the role of future actions in shaping working memory remains unknown. To answer this question, we used two working memory tasks that allowed the dissociation of sensory and action components of working memory. We measured behavioral performance and neuronal activity in the macaque prefrontal cortex area, frontal eye fields. We show that the action space reshapes working memory, as evidenced by distinct patterns of memory tuning and attentional orienting between the two tasks. Notably, neuronal activity during the working memory period predicted future behavior and exhibited mixed selectivity in relation to the sensory space but linear selectivity relative to the action space. This linear selectivity was achieved through the rapid transformation from sensory to action space and was subsequently maintained as a stable cross-temporal population activity pattern. Combined, we provide direct physiological evidence of the action-oriented nature of frontal eye field neurons during memory tasks and demonstrate that the anticipation of behavioral outcomes plays a significant role in transforming and maintaining the contents of visual working memory.
Secretory protein Rv1987, a ‘probable chitinase’ fromMycobacterium tuberculosisis a novel chitin and cellulose binding protein lacking enzymatic function
Authors: Prakash Chiranth M. , Janakiraman Vani
Published: August 2023

Bacterial chitinases serve to hydrolyse chitin as food source or as defence mechanism. Given that chitin is not produced by mammals, it is intriguing thatMycobacterium tuberculosis, an exclusively human pathogen harbours Rv1987, a probable chitinase and secretes it. Interestingly genes annotated as chitinases are widely distributed amongMycobacterium tuberculosiscomplex species, clinical isolates and other human pathogensM. abscessusandM. ulcerans. However, Mycobacterial chitinases are not characterized and hence the functions remain unknown. In the present study, we show that Rv1987 is a chitin and cellulose binding protein lacking enzymatic activity in contrary to its current annotation. Further, we show Rv1987 has moon lighting functions inM. tuberculosispathobiology signifying roles of bacterial cellulose binding clusters in infections.
Mechanical force regulates ligand binding and function of PD-1
Authors: Li Kaitao , Cardenas-Lizana Paul , Kellner Anna V. , Yuan Zhou , Ahn Eunseon , Lyu Jintian , Li Zhenhai , Salaita Khalid , Ahmed Rafi , Zhu Cheng
Published: August 2023

Immune checkpoint blockade targeting PD-1 shows great success in cancer therapy. However, the mechanism of how ligand binding initiates PD-1 signaling remains unclear. As prognosis markers of multiple cancers, soluble PD-L1 is found in patient sera and can bind PD-1, but fails to suppress T cell function. This and our previous observations that T cells exert endogenous forces on PD-1– PD-L2 bonds prompt the hypothesis that mechanical force might be critical to PD-1 triggering, which is missing in the soluble ligand case due to the lack of mechanical support afforded by surface-anchored ligand. Here we show that PD-1 function is eliminated or reduced when mechanical support on ligand is removed or dampened, respectively. Force spectroscopic analysis reveals that PD-1 forms catch bonds with both PD-Ligands <7 pN where force prolongs bond lifetime, but slip bonds >8 pN where force accelerates dissociation. Steered molecular dynamics finds PD-1–PD-L2 complex very sensitive to force due to the two molecules’ “side-to-side” binding via β sheets. Pulling causes relative rotation and translation between the two molecules by stretching and aligning the complex along the force direction, yielding new atomic contacts not observed in the crystal structure. Compared to wild-type, PD-1 mutants targeting the force-induced new interactions maintain the same binding affinity but display lower rupture force, shorter bond lifetime, reduced tension, and most importantly, impaired capacity to suppress T cell activation. Our results uncover a mechanism for cells to probe the mechanical support of PD-1–PD-Ligand bonds using endogenous forces to regulate PD-1 triggering.
The Selenoproteome as a dynamic response mechanism to oxidative stress in methanogenic communities
Authors: Kleikamp Hugo , Palacios Paola A. , Papaharalabos George , Bentien Anders , Kofoed Michael V. W. , Nielsen Jeppe L.
Published: August 2023

Methanogenesis is a critical process in the carbon cycle that is applied industrially in anaerobic digestion and biogas production. While naturally occurring in diverse environments, methanogenesis requires anaerobic and reduced conditions though varying degrees of oxygen tolerance have been described. Micro-aeration is touted as the next step to increase methane production and improve hydrolysis in digestion processes; therefore, a deeper understanding of the methanogenic response to oxygen stress is needed. In order to explore the drivers of oxygen tolerance in methanogenesis, two parallel enrichments were performed in an environment without reducing agents and in a redox-controlled environment by adding redox mediator AQDS. The cellular response to oxidative conditions is mapped using proteomic analysis. The resulting community showed remarkable tolerance to high-redox environments and was unperturbed in its methane production. Next to expressing pathways to mitigate reactive oxygen species, the higher redox potential environment showed an increased presence of selenocysteine and selenium-associated pathways. By including sulfur-to-selenium mass shifts in a proteomic database search, we provide the first evidence of dynamic and large-scale incorporation of selenocysteine as a response to oxidative stress by methanogenic organisms and the presence of a dynamic selenoproteome.