bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein MRI Contrast Agents as an Effective Approach for Precision Molecular Imaging
Authors: Li Dongjun , Kirberger Michael , Qiao Jingjuan , Gui Zongxiang , Xue Shenghui , Pu Fan , Jiang Jie , Xu Yiting , Tan Shanshan , Salarian Mani , Ibhagui Oluwatosin , Hekmatyar Khan , Yang Jenny J.
Published: January 2024

Cancer and other acute and chronic diseases are results of perturbations of common molecular determinants in key biological and signaling processes. Imaging is critical for characterizing dynamic changes in tumors and metastases, the tumor microenvironment, tumor-stroma interactions, and drug targets, at multiscale levels. Magnetic resonance imaging (MRI) has emerged to be a primary imaging modality for both clinical and preclinical applications due to its advantages over other modalities, including sensitivity to soft tissues, nondepth limitations, and the use of nonionizing radiation. However, extending the application of MRI to achieve both qualitative and quantitative precise molecular imaging with the capability to quantify molecular biomarkers for early detection, staging, and monitoring therapeutic treatment requires the capacity to overcome several major challenges including the trade-off between metal-binding affinity and relaxivity, which is an issue frequently associated with small chelator contrast agents. In this review, we will introduce the criteria of ideal contrast agents for precision molecular imaging and discuss the relaxivity of current contrast agents with defined first shell coordination water molecules. We will then report our advances in creating a new class of protein-targeted MRI contrast agents (ProCAs) with contributions to relaxivity largely derived from the secondary sphere and correlation time. We will summarize our rationale, design strategy, and approaches to the development and optimization of our pioneering ProCAs with desired high relaxivity, metal stability, and molecular biomarker-targeting capability, for precision MRI. From first generation (ProCA1) to third generation (ProCA32), we have achieved dual high r1and r2values that are 6- to 10-fold higher than clinically approved contrast agents at magnetic fields of 1.5 T, and their relaxivity values at high field are also significantly higher, which enables high resolution during small animal imaging. Further engineering of multiple targeting moieties enables ProCA32 agents that have strong biomarker-binding affinity and specificity for an array of key molecular biomarkers associated with various chronic diseases, while maintaining relaxation and exceptional metal-binding and selectivity, serum stability, and resistance to transmetallation, which are critical in mitigating risks associated with metal toxicity. Our leading product ProCA32.collagen has enabled the first early detection of liver metastasis from multiple cancers at early stages by mapping the tumor environment and early stage of fibrosis from liver and lung in vivo, with strong translational potential to extend to precision MRI for preclinical and clinical applications for precision diagnosis and treatment.
Physiological 68Ga-PSMA-11 Uptake in Dural Venous Sinuses
Authors: Kulkarni Mukta , Joshi Prathamesh Vijay , Kumar Kritik
Published: January 2024

We describe hitherto unreported physiological low-grade 68Ga-PSMA-11 uptake in dural sinuses of patients who underwent 68Ga-PSMA-11 PET/CT for evaluation of prostate carcinoma. A strong positive correlation was found between SUVmax of tracer uptake in dural sinuses and SUVmax of blood pool activity in superior vena cava. Low-grade 68Ga-PSMA-11 uptake seen in dural sinuses is physiological and is most likely result of venous blood pool activity. Such uptake should not be interpreted as pathological. Knowledge of such physiological uptake is essential for optimal interpretation of PSMA PET/CT images and differentiating physiological versus pathological uptake.
Rare Findings of Gallbladder Metastasis From Cutaneous Melanoma on 18F-FDG PET/CT Imaging
Authors: Zhou Jing , Zhao Yigang
Published: January 2024

We present the imaging findings of a 77-year-old man with a history of malignant cutis melanoma that metastasized to the gallbladder. A restaging 18F-FDG PET/CT scan showed uneven thickening and elevated 18F-FDG uptake in the gallbladder wall. Subsequently, the patient underwent laparoscopic cholecystectomy, and histopathologic findings confirmed the diagnosis of metastatic melanoma of the gallbladder.
Technical Considerations in EEG Source Imaging
Authors: Brinkmann Benjamin H.
Published: January 2024

EEG source imaging is an established technique for identifying the origin of interictal and ictal epileptiform discharges in patients with epilepsy, and it is an important tool in neurophysiology research. Accurate and reliable EEG source imaging requires appropriate choices of how the head, skull, and scalp are modeled, and understanding of the different approaches to modeling is important to guide these choices. Similarly, numerous different approaches to modeling the electrical sources within the brain exist, and appropriate understanding of the strengths and limitations of each are essential to obtaining accurate, reliable, and interpretable solutions. This review aims to describe the essential theoretical basis for these head and source models while also discussing the practical implications of each in clinical or research applications.
Establishment of a novel minigenome system for the identification of drugs targeting Nipah virus replication
Authors: Ke Xianliang , Ye Chang , Liu Renyi , Liu Feng , Chen Quanjiao
Published: January 2024

Nipah virus (NiV) is a deadly zoonotic pathogen with high potential to cause another pandemic. Owing to biosafety concerns, studies on living NiV must be performed in biosafety level 4 (BSL-4) laboratories, which greatly hinders the development of anti-NiV drugs. To overcome this issue, minigenome systems have been developed to study viral replication and screen for antiviral drugs. This study aimed to develop two minigenome systems (transient and stable expression) based on a helper cell line expressing the NiV P, N and L proteins required to initiate NiV RNA replication. Stable minigenome cells were resistant to ribavirin, remdesivir and favipiravir but sensitive to interferons. Cells of the transient replication system were sensitive to ribavirin and favipiravir and suitable for drug screening. Our study demonstrates a feasible and effective platform for studying NiV replication and shows great potential for high-throughput drug screening in a BSL-2 laboratory environment.
Genomic and functional insights into antibiotic resistance genes floR and strA linked with the SXT element of Vibrio cholerae non-O1/non-O139
Authors: Saha Mousumi , Pragasam Agila Kumari , Kumari Shashi , Verma Jyoti , Das Bhabatosh , Bhadra Rupak K.
Published: January 2024

The emergence and spread of antibiotic-resistant bacterial pathogens are a critical public health concern across the globe. Mobile genetic elements (MGEs) play an important role in the horizontal acquisition of antimicrobial resistance genes (ARGs) in bacteria. In this study, we have decoded the whole genome sequences of multidrug-resistant

Vibrio cholerae

clinical isolates carrying the ARG-linked SXT, an integrative and conjugative element, in their large chromosomes. As in others, the SXT element has been found integrated into the 5′-end of the prfC gene (which encodes peptide chain release factor 3 involved in translational regulation) on the large chromosome of

V. cholerae

non-O1/non-O139 strains. Further, we demonstrate the functionality of SXT-linked floR and strAB genes, which confer resistance to chloramphenicol and streptomycin, respectively. The floR gene-encoded protein FloR belongs to the major facilitator superfamily efflux transporter containing 12 transmembrane domains (TMDs). Deletion analysis confirmed that even a single TMD of FloR is critical for the export function of chloramphenicol. The floR gene has two putative promoters, P1 and P2. Sequential deletions reveal that P2 is responsible for the expression of the floR. Deletion analysis of the N- and/or C-terminal coding regions of strA established their importance for conferring resistance against streptomycin. Interestingly, qPCR analysis of the floR and strA genes indicated that both of the genes are constitutively expressed in

V. cholerae

cells. Further, whole genome-based global phylogeography confirmed the presence of the integrative and conjugative element SXT in non-O1/non-O139 strains despite being non-multidrug resistant by lacking antimicrobial resistance (AMR) gene cassettes, which needs monitoring.
DNA origami vaccine (DoriVac) nanoparticles improve both humoral and cellular immune responses to infectious diseases
Authors: Zeng Yang C. , Young Olivia J. , Si Longlong , Ku Min Wen , Isinelli Giorgia , Rajwar Anjali , Jiang Amanda , Wintersinger Chris M. , Graveline Amanda R. , Vernet Andyna , Sanchez Melinda , Ryu Ju Hee , Kwon Ick Chan , Goyal Girija , Ingber Donald E. , Shih William M.
Published: January 2024

Current SARS-CoV-2 vaccines have demonstrated robust induction of neutralizing antibodies and CD4+T cell activation, however CD8+responses are variable, and the duration of immunity and protection against variants are limited. Here we repurposed our DNA origami vaccine platform, DoriVac, for targeting infectious viruses, namely SARS-CoV-2, HIV, and Ebola. The DNA origami nanoparticle, conjugated with infectious-disease-specific HR2 peptides, which act as highly conserved antigens, and CpG adjuvant at precise nanoscale spacing, induced neutralizing antibodies, Th1 CD4+T cells, and CD8+T cells in naïve mice, with significant improvement over a bolus control. Pre-clinical studies using lymph-node-on-a-chip systems validated that DoriVac, when conjugated with antigenic peptides or proteins, induced promising cellular immune responses in human cells. These results suggest that DoriVac holds potential as a versatile, modular vaccine platform, capable of inducing both humoral and cellular immunities. The programmability of this platform underscores its potential utility in addressing future pandemics.
Histone acetyltransferase HAF2 associates with PDC to control H3K14ac and H3K23ac in ethylene response
Authors: Chen Chia-Yang , Shao Zhengyao , Wang Guihua , Zhao Bo , Hardtke Haley A. , Leong Josh , Zhou Tiffany , Zhang Y.Jessie , Qiao Hong
Published: January 2024

Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprogramming, in which EIN2-C-directed regulation of histone acetylation is the first key-step for chromatin to perceive ethylene signaling. However, the histone acetyltransferase in this process remains unknown. Here, we identified histone acetyltransferase HAF2, and mutations in HAF2 confer plants with ethylene insensitivity. Furthermore, we found that HAF2 interacts with EIN2-C in response to ethylene. Biochemical assays demonstrated that the bromodomain of HAF2 binds to H3K14ac and H3K23ac peptides with a distinct affinity for H3K14ac; the HAT domain possesses acetyltransferase catalytic activity for H3K14 and H3K23 acetylation, with a preference for H3K14. ChIP-seq results provide additional evidence supporting the role of HAF2 in regulating H3K14ac and H3K23ac levels in response to ethylene. Finally, our findings revealed that HAF2 co-functions with pyruvate dehydrogenase complex (PDC) to regulate H3K14ac and H3K23ac in response to ethylene in an EIN2 dependent manner. Overall, this research reveals that HAF2 as a histone acetyltransferase that forms a complex with EIN2-C and PDC, collectively governing histone acetylation of H3H14ac and H3K23ac, preferentially for H3K14 in response to ethylene.
Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription
Authors: Zhang Qian , Kim Wantae , Panina Svetlana , Mayfield Joshua E. , Portz Bede , Zhang Y. Jessie
Published: January 2024

The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. Recent insights highlight the pivotal role of CTD in driving condensate formation on gene loci. Yet, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear. Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulatory proteins, forms distinct condensates from unphosphorylated CTD. Function studies demonstrate CTD variants with diverse condensation properties in vitro exhibit difference in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths lead to alternative splicing outcomes impacting cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.
BCG activation of trained immunity is associated with induction of cross reactive COVID-19 antibodies in a BCG vaccinated population
Authors: Iqbal Najeeha Talat , Ahmed Kumail , Sattar Tehniat , Aziz Fatima , Hussain Rabia
Published: January 2024

Background

During the current COVID-19 pandemic, the rate of morbidity and mortality was considerably lower in BCG vaccinated countries like Pakistan. BCG has been shown to provide cross protection to both disseminated TB as well as non related viral infections in BCG vaccinated children which is consistent with COVID-19 morbidity in the younger age group. Recently, this cross protection was attributed to trained immunity (TI) associated with BCG recall responses in the innate arm of the immune system. Little is known about the longevity of BCG Trained Immunity (TI) beyond early childhood.

Objective

To assess the BCG-induced recall responses in healthy individuals by cytokines secreted from the TI network and its potential role in providing cross-protection against COVID-19 and other viral infections.

Study Design

In this cross-sectional study, healthy young adults and adolescents (n=20) were recruited from 16–40 years of age, with no prior history of TB treatment, autoimmune, or chronic inflammatory condition.

Methods

BCG-induced cytokine responses were assessed using prototypic markers for cells of the TI network {macrophages [M1 (TNFα, IFNγ), M2 (IL10)], NK (IL2), Gamma delta (γδ) T (IL17, IL4)} and SARS CoV2 IgG antibodies against RBD using short-term (12 hrs.) cultures assay.

Results

Significant differences were observed in the magnitude of recall responses to BCG with macrophage cytokines showing the highest mean levels of TNFα (9148 pg/ml) followed by IL10 (488 pg/ml) and IFNγ (355 pg/ml). The ratio of unstimulated vs.BCG-stimulated cytokines was 132 fold higher for TNFα, 40 fold for IL10, and 27 fold for IFNγ. Furthermore, SARS-CoV-2 antibodies were also detected in unstimulated plasma which showed cross reactivity with BCG.

Conclusion

The presence of cross reactive antibodies to SARS-CoV-2 and the relative ratio of pro-and anti-inflammatory cytokines secreted by activated TI cellular network may play a pivotal role in protection in the early stages of infection as observed during the COVID-19 pandemic in the younger age groups resulting in lower morbidity and mortality.
Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms
Authors: Behera Sairam , Catreux Severine , Rossi Massimiliano , Truong Sean , Huang Zhuoyi , Ruehle Michael , Visvanath Arun , Parnaby Gavin , Roddey Cooper , Onuchic Vitor , Cameron Daniel L , English Adam , Mehtalia Shyamal , Han James , Mehio Rami , Sedlazeck Fritz J
Published: January 2024

Research and medical genomics require comprehensive and scalable solutions to drive the discovery of novel disease targets, evolutionary drivers, and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size (e.g., SNV/SV) or location (e.g., repeats). Here we present DRAGEN that utilizes novel methods based on multigenomes, hardware acceleration, and machine learning based variant detection to provide novel insights into individual genomes with ∼30min computation time (from raw reads to variant detection). DRAGEN outperforms all other state-of-the-art methods in speed and accuracy across all variant types (SNV, indel, STR, SV, CNV) and further incorporates specialized methods to obtain key insights in medically relevant genes (e.g., HLA, SMN, GBA). We showcase DRAGEN across 3,202 genomes and demonstrate its scalability, accuracy, and innovations to further advance the integration of comprehensive genomics for research and medical applications.
A revised single-cell transcriptomic atlas ofXenopusembryo reveals new differentiation dynamics
Authors: Petrova Kseniya , Tretiakov Maksym , Kotov Aleksandr , Monsoro-Burq Anne H. , Peshkin Leonid
Published: January 2024

This paper introduces an updated single-cell atlas for pivotal developmental stages inXenopus, encompassing gastrulation, neurulation, and early tailbud. Notably surpassing its predecessor, the new atlas enhances gene mapping, read counts, and gene/cell type nomenclature. Leveraging the latest Xenopus tropicalis genome version, alongside advanced alignment pipelines and machine learning for cell type assignment, this release maintains consistency with previous cell type annotations while rectifying nomenclature issues. Employing an unbiased approach for cell type assignment proves especially apt for embryonic contexts, given the considerable number of non-terminally differentiated cell types. An alternative cell type attribution here adopts a fuzzy, non-deterministic stance, capturing the transient nature of early embryo progenitor cells by presenting an ensemble of types in superposition. The value of the new resource is emphasized through numerous examples, with a focus on previously unexplored germ cell populations where we uncover novel transcription onset features. Offering interactive exploration via a user-friendly web portal and facilitating complete data downloads, this atlas serves as a comprehensive and accessible reference.
Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infection
Authors: Burman Nathaniel , Belukhina Svetlana , Depardieu Florence , Wilkinson Royce A. , Skutel Mikhail , Santiago-Frangos Andrew , Graham Ava B. , Livenskyi Alexei , Chechenina Anna , Morozova Natalia , Zahl Trevor , Henriques William S. , Buyukyoruk Murat , Rouillon Christophe , Shyrokova Lena , Kurata Tatsuaki , Hauryliuk Vasili , Severinov Konstantin , Groseille Justine , Thierry Agnès , Koszul Romain , Tesson Florian , Bernheim Aude , Bikard David , Wiedenheft Blake , Isaev Artem
Published: January 2024

Viruses compete with each other for limited cellular resources, and some viruses deliver defense mechanisms that protect the host from competing genetic parasites. PARIS is a defense system, often encoded in viral genomes, that is composed of a 53 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB). Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex. We use cryo-EM to determine the structure of this complex which explains how six molecules of AriA assemble into a propeller-shaped scaffold that coordinates three subunits of AriB. ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving the host tRNALys. Phage T5 subverts PARIS immunity through expression of a tRNALysvariant that prevents PARIS-mediated cleavage, and thereby restores viral infection. Collectively, these data explain how AriA functions as an ATP-dependent sensor that detects viral proteins and activates the AriB toxin. PARIS is one of an emerging set of immune systems that form macromolecular complexes for the recognition of foreign proteins, rather than foreign nucleic acids.
STING Licensing of Type I Dendritic Cells Potentiates Antitumor Immunity
Authors: Wang Jian , Li Suxin , Wang Maggie , Wang Xu , Chen Shuqing , Sun Zhichen , Ren Xiubao , Huang Gang , Sumer Baran D. , Yan Nan , Fu Yang-Xin , Gao Jinming
Published: January 2024

Stimulator of interferon genes (STING) is an immune adaptor protein that senses cyclic GMP-AMP (cGAMP) in response to self or microbial cytosolic DNA as a danger signal. STING is ubiquitously expressed in diverse cell populations including cancer cells with distinct cellular functions such as activation of type I interferons, autophagy induction, or triggering apoptosis. It is not well understood whether and which subsets of immune cells, stromal cells, or cancer cells are particularly important for STING-mediated antitumor immunity. Here using a polymeric STING-activating nanoparticle (PolySTING) with a “shock-and-lock” dual activation mechanism, we show type 1 conventional dendritic cell (cDC1) is essential for STING-mediated rejection of multiple established and metastatic murine tumors. STING status in the host but not in the cancer cells (Tmem173-/-) is important for antitumor efficacy. Specific depletion of cDC1 (Batf3-/-) or STING deficiency in cDC1 (XCR1creSTINGfl/fl) abolished PolySTING efficacy, whereas depletion of other myeloid cells had little effect. Adoptive transfer of wildtype cDC1 inBatf3-/-mice restored antitumor efficacy while transfer of cDC1 with STING or IRF3 deficiency failed to rescue. PolySTING induced a specific chemokine signature in wildtype but notBatf3-/-mice. Multiplexed immunohistochemistry analysis of STING-activating cDC1s in resected tumors correlates with patient survival while also showing increased expressions after neoadjuvant pembrolizumab therapy in non-small cell lung cancer patients. Therefore, we have defined that a subset of myeloid cells is essential for STING-mediated antitumor immunity with associated biomarkers for prognosis.

One Sentence Summary

A “shock-and-lock” nanoparticle agonist induces direct STING signaling in type 1 conventional dendritic cells to drive antitumor immunity with defined biomarkers
MapTurns: mapping the structure, H-bonding and contexts of beta turns in proteins
Authors: Newell Nicholas E.
Published: January 2024

Motivation

Beta turns are the most common type of secondary structure in proteins after alpha helices and beta sheets and play many key structural and functional roles. Turn backbone (BB) geometry has been classified at multiple levels of precision, but the current picture of side chain (SC) structure and interaction in turns is incomplete, because the distribution of SC conformations associated with each sequence motif has commonly been represented only by a static image of a single, typical structure for each turn BB geometry, and only motifs which specify single amino acids have been systematically investigated. Furthermore, no general evaluation has been made of the SC interactions between turns and the structures in their BB neighborhoods. Finally, the visualization and comparison of the wide range of turn conformations has been hampered by the almost exclusive characterization of turn structure in BB dihedral-angle (Ramachandran) space.

Results

This work introduces MapTurns, a web server for motif maps, which employ a turn-local Euclidean-space coordinate system and a global turn alignment to comprehensively map the distributions of BB and SC structure and H-bonding associated with sequence motifs in beta turns and their local BB contexts. Maps characterize many new SC motifs, provide detailed rationalizations of sequence preferences, and support mutational analysis and the general study of SC interactions, and they should prove useful in applications such as protein design.

Availability and Implementation

MapTurns is available atwww.betaturn.comalong with a broad, map-based survey of SC motifs in beta turns. HTML/Javascript code for a sample map is available at:https://github.com/nenewell/MapTurns/tree/main.

Supplementary Information

Supplementary File 1: Methods.
Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168
Authors: Ai Huasong , Tong Zebin , Deng Zhiheng , Shi Qiang , Tao Shixian , Liang Jiawei , Sun Maoshen , Wu Xiangwei , Zheng Qingyun , Liang Lujun , Li Jia-Bin , Gao Shuai , Tian Changlin , Liu Lei , Pan Man
Published: January 2024

Abstracts

The DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, plays a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent Lys13 and Lys15 sites at the H2A N-terminal tail. However, understanding how RNF168 coordinates with its cognate E2 enzyme UbcH5c to ubiquitinate H2AK13/15 site-specifically has long been hampered by the lack of high-resolution structures of RNF168 and UbcH5c∼Ub in complex with nucleosomes. Here, we developed mechanism-based chemical trapping strategies and determined the cryo-EM structures of the RNF168/UbcH5c–Ub/NCP complex captured in transient H2AK13/15 monoubiquitination and adjacent dual-monoubiquitination reactions. Our structural analysis revealed that RNF168 stably binds to the nucleosomal H2A–H2B acidic patch through a basic helix with multiple interactions, which positions the UbcH5c active centre directly over the H2A N-terminus, providing a “helix-anchoring” mode for monomeric E3 ligase RNF168 on nucleosome in contrast to the “compass-binding” mode of dimeric E3 ligases. Furthermore, our chemically synthesized ubiquitinated histones have enabled the elucidation of the efficiency of Ub installation and the interplay between the initial and subsequent Ub modifications on the adjacent H2A K13 and K15 sites. Overall, our work not only provides structural snapshots of H2A K13/K15 site-specific monoubiquitination and adjacent dual-monoubiquitination, but also offers a near-atomic resolution structural framework for understanding how pathogenic mutations or physiological modifications affect the molecular function of RNF168 in H2A K13/15 ubiquitination.
Macromolecular crowding by hyaluronan: implications for binding reactions in the pericellular matrix and at the cell surface
Authors: Fernig David G.
Published: January 2024

In common with many glycosaminoglycan binding growth factors, the interactions of fibroblast growth factor-2 (FGF-2) with heparin/heparan sulfate regulate its biological activity. Consequently, much effort has been expended in characterising growth factor-glycoaminoglycan interactions. Many experiments are performedin vitroin dilute solution. However, the cell surface is an extremely crowded environment. We have, therefore, examined the parameters of FGF-2 binding to a heparin-derived tetradecasaccharide in the presence of two different crowding agents, dextran, a commonly used crowding agent, as well as hyaluronan (HA), which is normally present at the cell surface. The heparin tetradecassaccaride was immobilised through its reducing end onto a biosensor surface and the crowding agents were used in solution. The results show that the observed on-rate rate of association (kon) decreased over two-fold with increasing concentrations of both crowding agents. The slope of initial rate of association similarly decreased, indicating that as the solution became more crowded the diffusion of FGF-2 becomes increasingly limited. One thousand kDa HA was shown to be the most effective crowding agent, as diffusion became limited at concentrations above 0.5 mg/ml, compared to 1 mg/ml and 10 mg/ml for 100kDa HA and dextran, respectively. Such concentrations of hyaluronan are readily found extracellularly. The results, therefore, suggest that the effect of crowding at the cell surface and in the extracellular matrix may play an important role in governing the interactions of at least FGF-2 with its heparan sulfate co-receptor.
Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior
Authors: Chen Patrick B. , Chen Rachel , LaPierre Nathan , Chen Zeyuan , Mefford Joel , Marcus Emilie , Heffel Matthew G. , Soto Daniela C. , Ernst Jason , Luo Chongyuan , Flint Jonathan
Published: January 2024

Knowing the genes involved in quantitative traits provides a critical entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. Here we address a key step towards that goal by deploying a test that directly queries whether a gene mediates the effect of a quantitative trait locus (QTL). To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six QTLs, and identified six genes. Four genes,Lsamp, Ptprd, Nptx2andSh3gl,have known roles in synapse function; the fifth gene,Psip1,is a transcriptional co-activator not previously implicated in behavior; the sixth is a long non-coding RNA4933413L06Rikwith no known function. Single nucleus transcriptomic and epigenetic analyses implicated excitatory neurons as likely mediating the genetic effects. Surprisingly, variation in transcriptome and epigenetic modalities between inbred strains occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results open a bottleneck in using genetic mapping of QTLs to find novel biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.
Synaptic Proteomes of Cortical Interneuron Classes Revealed by Antibody Directed Proximity Labeling
Authors: Battison Alexandria S. , Liddle Jennifer C. , Sumsky Stefan L. , O’Connell Christopher B. , Balsbaugh Jeremy L. , LoTurco Joseph J.
Published: January 2024

Subtypes of inhibitory interneurons play diverse roles within neural circuits in cerebral cortex. Defining the molecular underpinnings of interneuron functions within cortical circuits will require identification of interneuron synaptic proteomes. In this study, we first combined genetically directed expression of tdTomato-synaptophysin with antibody-directed proximity labeling and tandem mass spectrometry to identify synaptic proteomes of three major interneuron classes in mouse cortex: parvalbumin (PV), somatostatin (SS), and vasoactive intestinal peptide (VIP).

After stringent filtering we identified 581 proteins: 228 identified in all cell classes and 353 in one or two of three classes. The PV class had the largest number of uniquely identified proteins (141), followed by VIP (30) and SST (20). Consistent with previously reported electrophysiological evidence, PV presynaptic proteomes were enriched for NMDA receptor subunits and scaffolding proteins. We used antibodies against synaptotagmin 2 (Syt2), a presynaptic protein present at PV synapses, to confirm NMDAR localization, and to find that the mu-opioid receptor agonist buprenorphine rapidly caused reorganization of the PV presynaptic proteome. Overall, our results reveal proteomes of PV, SST, and VIP interneurons in cortex that likely underlie distinct and dynamic interneuron synaptic properties.
A PACAP-activated network for secretion requires coordination of Ca2+influx and Ca2+mobilization
Authors: Chen Xiaohuan , Bell Nicole A. , Coffman Breanna L. , Rabino Agustin A. , Garcia-Mata Rafael , Kammermeier Paul J. , Yule David I. , Axelrod Daniel , Smrcka Alan V. , Giovannucci David R. , Anantharam Arun
Published: January 2024

Chromaffin cells of the adrenal medulla transduce sympathetic nerve activity into stress hormone secretion. The two neurotransmitters principally responsible for coupling cell stimulation to secretion are acetylcholine and pituitary adenylate activating polypeptide (PACAP). In contrast to acetylcholine, PACAP evokes a persistent secretory response from chromaffin cells. However, the mechanisms by which PACAP acts are poorly understood. Here, it is shown that PACAP induces sustained increases in cytosolic Ca2+which are disrupted when Ca2+influx through L-type channels is blocked or internal Ca2+stores are depleted. PACAP liberates stored Ca2+via inositol trisphosphate receptors (IP3Rs) on the endoplasmic reticulum (ER), thereby functionally coupling Ca2+mobilization to Ca2+influx and supporting Ca2+-induced Ca2+-release. These Ca2+influx and mobilization pathways are unified by an absolute dependence on phospholipase C epsilon (PLCε) activity. Thus, the persistent secretory response that is a defining feature of PACAP activity,in situ, is regulated by a signaling network that promotes sustained elevations in intracellular Ca2+through multiple pathways.
Standardized Parts for Activation of Small GTPase Signaling in Living Cells
Authors: He Yuchen , Faulkner Benjamin M. , Roberti Meaghan A. , Bassford Dana K. , Stains Cliff I.
Published: January 2024

Small GTPases comprise a superfamily of over 167 proteins in the human genome and are critical regulators of a variety of pathways including cell migration and proliferation. Despite the importance of these proteins in cell signaling, a standardized approach for controlling small GTPase activation within living cells is lacking. Herein, we report a split-protein-based approach to directly activate small GTPase signaling in living cells. Importantly, our fragmentation site can be applied across the small GTPase superfamily. We highlight the utility of these standardized parts by demonstrating the ability to directly modulate the activity of four different small GTPases with user-defined inputs, providing a plug and play system for direct activation of small GTPases in living cells.
Reinforcement Expectation in the Honey Bee (Apis mellifera): Can Downshifts in Reinforcement Show Conditioned Inhibition?
Authors: Mahoney Shawn , Hosler Jay , Smith Brian H
Published: January 2024

When animals learn the association of a Conditioned Stimulus with an Unconditioned Stimulus, later presentation of the CS invokes a representation of the US. When the expected US fails to occur, theoretical accounts predict that conditioned inhibition can accrue to any other stimuli that are associated with this change in the US. Empirical work with mammals has confirmed the existence of conditioned inhibition. But the way it is manifested, the conditions that produce it, and determining whether it is the opposite of excitatory conditioning, are important considerations. Invertebrates can make valuable contributions to this literature because of the well-established conditioning protocols and access to the central nervous system for studying neural underpinnings of behavior. Nevertheless, while conditioned inhibition has been reported, it has yet to be thoroughly investigated in invertebrates. Here we evaluate the role of the unconditioned stimulus (US) in producing conditioned inhibition by using Proboscis Extension Response conditioning of the honey bee (Apis mellifera). Specifically, using variations of a ‘feature-negative’ experimental design, we employ downshifts in US intensity relative to US intensity used during initial excitatory conditioning, to show that an odorant in an odor-odor mixture can become a conditioned inhibitor. We argue that some alternative interpretations to conditioned inhibition are unlikely. However, we show variation across individuals in how strongly they show Conditioned Inhibition, with some individuals possibly revealing a different means of learning about changes in reinforcement. We discuss how resolution of these differences is needed to fully understand whether and how Conditioned Inhibition is manifested in the honey bee, and whether it can be extended to investigate how it is encoded in the CNS. It is also important for extension to other insect models. In particular, work like this will be important as more is revealed of the complexity of the insect brain from connectome projects.
Fas2EB112: A Tale of Two Chromosomes
Authors: Finegan Tara M. , Cammarota Christian , Andrade Oscar Mendoza , Garoutte Audrey M. , Bergstralh Dan T.
Published: January 2024

The cell-cell adhesion molecule Fasciclin II (Fas2) has long been studied for its evolutionarily-conserved role in axon guidance. It is also expressed in the follicular epithelium, where together with a similar protein, Neuroglian (Nrg), it helps to drive the reintegration of cells born out of the tissue plane. Remarkably, one Fas2 protein null allele,Fas2G0336, demonstrates a mild reintegration phenotype, whereas work with the classic null alleleFas2EB112showed more severe epithelial disorganization. These observations raise the question of which allele (if either) causes abona fideloss of Fas2 protein function. The problem is not only relevant to reintegration but fundamentally important to understanding what this protein does and how it works:Fas2EB112has been used in at least 37 research articles, andFas2G0336in at least three. An obvious solution is that one of the two chromosomes carries a modifier that either suppresses (Fas2G0336) or enhances (Fas2EB112) phenotypic severity. We find not only the latter to be the case, but identify the enhancing mutation asNrg14, also a classic null allele.
A Genome-Wide CRISPR Screen Identifies Sortilin as the Receptor Responsible for Galectin-1 Lysosomal Trafficking
Authors: Donnelly Justin , Kamber Roarke A. , Wisnovsky Simon , Roberts David S. , Peltan Egan L. , Bassik Michael C. , Bertozzi Carolyn R.
Published: January 2024

Galectins are a family of mammalian glycan-binding proteins that have been implicated as regulators of myriad cellular processes including cell migration, apoptosis, and immune modulation. Several members of this family, such as galectin-1, exhibit both cell-surface and intracellular functions. Interestingly, galectin-1 can be found in the endomembrane system, nucleus, or cytosol, as well as on the cell surface. The mechanisms by which galectin-1 traffics between cellular compartments, including its unconventional secretion and internalization processes, are poorly understood. Here, we determined the pathways by which exogenous galectin-1 enters cells and explored its capacity as a delivery vehicle for protein and siRNA therapeutics. We used a galectin-1-toxin conjugate, modelled on antibody-drug conjugates, as a selection tool in a genome-wide CRISPR screen. We discovered that galectin-1 interacts with the endosome-lysosome trafficking receptor sortilin in a glycan-dependent manner, which regulates galectin-1 trafficking to the lysosome. Further, we show that this pathway can be exploited for delivery of a functional siRNA. This study sheds light on the mechanisms by which galectin-1 is internalized by cells and suggests a new strategy for intracellular drug delivery via galectin-1 conjugation.
Multi-omic characterization of allele-specific regulatory variation in hybrid pigs
Authors: Quan Jianping , Yang Ming , Wang Xingwang , Cai Gengyuan , Ding Rongrong , Zhuang Zhanwei , Zhou Shenping , Tan Suxu , Ruan Donglin , Wu Jiajing , Zheng Enqin , Zhang Zebin , Liu Langqing , Meng Fanming , Wu Jie , Xu Cineng , Qiu Yibin , Wang Shiyuan , Lin Meng , Li Shaoyun , Ye Yong , Zhou Fuchen , Lin Danyang , Li Xuehua , Deng Shaoxiong , Zhang Yuling , Yao Zekai , Gao Xin , Yang Yingshan , Liu Yiyi , Zhan Yuexin , Liu Zhihong , Zhang Jiaming , Ma Fucai , Yang Jifei , Chen Qiaoer , Yang Jisheng , Ye Jian , Dong Linsong , Gu Ting , Huang Sixiu , Xu Zheng , Li Zicong , Yang Jie , Huang Wen , Wu Zhenfang
Published: January 2024

Genetic variation in the regulation of gene expression contributes substantially to phenotypic variation. Understanding how variation in DNA sequences and epigentic modifications leads to gene expression variation remains a challenging task. In hybrid animals where cellular environments are homogeneous, differences between the expression of paternal and maternal alleles must be due tocissequence or epigenic differences. Therefore, hybrid mapping is a powerful approach to efficiently identify and characterize genes under regulation through mechanisms incis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we performed a comprehensive multi-omic characterization of regulatory variation across brain, liver, muscle, and placenta in four developmental stages. We produced one of the largest multi-omic datasets to date in pigs, including 16 whole genome sequenced genomes, 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We developed a novel read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We showed that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identified 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. By integrating methylation, chromatin accessibility, and gene expression data, many of these allele specific expression can be explained by allele specific methylation and/or chromatin accessibility. This study provides one of the most comprehensive characterizations of regulatory variation across multiple tissues and developmental stages in pigs and offers new opportunity of genetic improvement for this important food animal species.
Normal and Aberrant Cell Cycles Characterized by a Continuous-Time Stochastic Boolean Model of Cell Cycle Regulation in Budding Yeast
Authors: Taoma Kittisak , Tyson John J. , Laomettachit Teeraphan , Kraikivski Pavel
Published: January 2024

The cell cycle of budding yeast is governed by an intricate protein regulatory network whose dysregulation can lead to lethal mistakes or aberrant cell division cycles. In this work, we model this network in a Boolean framework for stochastic simulations. Our model is sufficiently detailed to account for the phenotypes of 41 mutant yeast strains (85% of the experimentally characterized strains that we simulated) and also to simulate an endoreplicating strain (multiple rounds of DNA synthesis without mitosis) and a strain that exhibits ‘Cdc14 endocycles’ (periodic transitions between metaphase and anaphase). Because our model successfully replicates the observed properties of both wild-type yeast cells and many mutant strains, it provides a reasonable, validated starting point for more comprehensive stochastic-Boolean models of cell cycle controls. Such models may provide a better understanding of cell cycle anomalies in budding yeast and ultimately in mammalian cells.
Microvilli regulate the release modes of alpha-tectorin to organize the domain-specific matrix architecture of the tectorial membrane
Authors: Niazi Ava , Kim Ju Ang , Kim Dong-Kyu , Lu Di , Sterin Igal , Park Joosang , Park Sungjin
Published: January 2024

The tectorial membrane (TM) is an apical extracellular matrix (ECM) in the cochlea essential for auditory transduction. The TM exhibits highly ordered domain-specific architecture. Alpha-tectorin/TECTA is a glycosylphosphatidylinositol (GPI)-anchored ECM protein essential for TM organization. Here, we identified that TECTA is released by distinct modes: proteolytic shedding by TMPRSS2 and GPI-anchor-dependent release from the microvillus tip. In the medial/limbal domain, proteolytically shed TECTA forms dense fibers. In the lateral/body domain produced by the supporting cells displaying dense microvilli, the proteolytic shedding restricts TECTA to the microvillus tip and compartmentalizes the collagen-binding site. The tip-localized TECTA, in turn, is released in a GPI-anchor-dependent manner to form collagen-crosslinking fibers, required for maintaining the spacing and parallel organization of collagen fibrils. Overall, we showed that distinct release modes of TECTA determine the domain-specific organization pattern, and the microvillus coordinates the release modes along its membrane to organize the higher-order ECM architecture.

Abstract Figure

Graphical Abstract
Toward a universal description of hadronic phase of QCD
Authors: Abhishek Aman , Sharma Sayantan
Published: January 2024

Mean-field model quantum field theories of hadrons were traditionally developed to describe cold and dense nuclear matter and are by now very well constrained from the recent neutron star merger observations. We show that when augmented with additional known hadrons and resonances but not included earlier, these mean-field models can be extended beyond its regime of applicability. Calculating some specific ratios of baryon number susceptibilities for finite temperature and moderate values of baryon densities within mean-field approximation, we show that these match consistently with the lattice QCD data available at lower densities, unlike the results obtained from a noninteracting hadron resonance gas model. We also estimate the curvature of the line of constant energy density, fixed at its corresponding value at the chiral crossover transition in QCD, in the temperature-density plane. The number density at low temperatures and high density is found to be about twice the nuclear saturation density. Moreover from this line we can indirectly constrain the critical endpoint of QCD to be beyond μB=596  MeV for temperature ∼125  MeV.

Published by the American Physical Society
2024
BMS-invariant free fermion models
Authors: Hao Peng-Xiang , Song Wei , Xiao Zehua , Xie Xianjin
Published: January 2024

We used the Cartan formalism to construct fermionic models that are compatible with Galilean or Carrollian symmetry and rigid scaling symmetry. The free Carrollian fermion model exhibits conformal Carrollian symmetry which is isomorphic to the asymptotic symmetries for flat spacetime in three dimensions, namely the BMS3 symmetry. We performed canonical quantization to this free Bondi-van der Burg-Metzner-Sachs (BMS) fermion model, discussed both the highest weight vacuum and the induced vacuum, calculated the correlation functions and the torus partition function. Finally, we constructed N=2 supersymmetric theories by combining the free fermion model and the free scalar model [].

Published by the American Physical Society
2024
Does state-led urbanization come at the cost of agriculture? Evidence from China
Authors: Liu Wenhua , He Zekai , Wang Qi
Published: January 2024

Purpose

This paper explores the relationship between state-led urbanization and primary industry development using the difference-in-differences (DiD) method.

Design/methodology/approach

The study uses the DiD method.

Findings

Exploiting county-city mergers during 2010–2018, the key strategy to expand the city outward and promote urbanization on the urban fringe by local government, the authors find that county-city mergers led to the growth of primary industry decline by 4.23%. The result can be explained by the loss of essential production factors, including land and labor used for farming. In addition, the negative effect is more pronounced for counties with more substantial manufacturing. The results indicate that urbanization in China relocates land and labor; however, it does not improve the efficiency of agricultural output.

Originality/value

This paper contributes to the understanding of urbanization and rural development from the perspective of the primary industry by showing production factor redistribution. Second, this study complements the literature on local government mergers.