bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Machine Learning Approach for Real-time Cortical State Estimation
Authors: Weiss David A , Borsa Adriano MF , Pala Aurélie , Sederberg Audrey J , Stanley Garrett B 
Published: June 2023

AbstractObjectiveCortical function is under constant modulation by internally-driven, latent variables that regulate excitability, collectively known as “cortical state”. Despite a vast literature in this area, the estimation of cortical state remains relatively ad hoc, and not amenable to real-time implementation. Here, we implement robust, data-driven, and fast algorithms that address several technical challenges for online cortical state estimation.ApproachWe use unsupervised Gaussian Mixture Models (GMMs) to identify discrete, emergent clusters in spontaneous local field potential (LFP) signals in cortex. We then extend our approach to a temporally-informed Hidden semi-Markov Model (HSMM) with Gaussian observations to better model and infer cortical state transitions. Finally, we implement our HSMM cortical state inference algorithms in a real-time system, evaluating their performance in emulation experiments.Main resultsUnsupervised clustering approaches reveal emergent state-like structure in spontaneous electrophysiological data that recapitulate arousal-related cortical states as indexed by behavioral indicators. HSMMs enable cortical state inferences in a real-time context by modeling the temporal dynamics of cortical state switching. Using HSMMs provides robustness to state estimates arising from noisy, sequential electrophysiological data.SignificanceTo our knowledge, this work represents the first implementation of a real-time software tool for continuously decoding cortical states with high temporal resolution (40 ms). The software tools that we provide can facilitate our understanding of how cortical states dynamically modulate cortical function on a moment-by-moment basis and provide a basis for state-aware brain machine interfaces across health and disease.
IFT cargo and motors associate sequentially with IFT trains to enter cilia
Authors: Mitra Aniruddha , Loseva Elizaveta , Peterman Erwin J.G. 
Published: June 2023

SummaryIntraflagellar transport (IFT) orchestrates entry of proteins into primary cilia. At the ciliary base, assembled IFT trains, driven by kinesin-2 motors, can transport cargo proteins into the cilium, across the crowded transition zone (TZ). How trains assemble at the base and how proteins associate with them is far from understood. Here, we use single-molecule imaging in the cilia ofC. eleganschemosensory neurons to directly visualize the entry of kinesin-2 motors kinesin-II and OSM-3, as well as anterograde cargo proteins IFT dynein and tubulin. Single-particle tracking shows that IFT components associate with trains sequentially, both in time and space. Super-resolution maps of IFT components in wild-type and mutant worms reveal ciliary ultrastructure and show that kinesin-II is essential for axonemal organization. Finally, imaging cilia lacking kinesin-II and/or TZ function uncovers the interplay of kinesin-II and OSM-3 in driving efficient transport of IFT trains across the TZ.
Multi_CycGT: a DL-based multimodal model for membrane permeability prediction of cyclic peptides
Authors: Cao Lujing , Xu Zhenyu , Shang Tianfeng , Zhang Chengyun , Wu Xinyi , Wu Yejian , Zhai Silong , Ma Liefeng , Duan Hongliang 
Published: June 2023

AbstractAs a highly versatile therapeutic modality, cyclic peptides have gained significant attention due to their exceptional binding affinity, minimal toxicity and capacity to target the surface of conventionally “undruggable” proteins. However, the development of cyclic peptides with therapeutic effects by targeting intracellular biological targets has been hindered by the issue of limited membrane permeability. In this paper, we have conducted an extensive benchmarking analysis of a proprietary dataset consisting of 6941 cyclic peptides, employing machine learning and deep learning models. In addition, we propose an innovative multimodal model called Multi_CycGT which combines a Graph Convolutional Network (GCN) and a Transformer to extract 1D and 2D features. These encoded features are then fused for the prediction of cyclic peptide permeability. The cross-validation experiments demonstrate that the proposed Multi_CycGT model achieved the highest level of accuracy on the test set, with an accuracy value of 0.8206 and an AUC value of 0.8650. This paper introduces a pioneering deep learning-based approach that demonstrates enhanced effectiveness in predicting the membrane permeability of cyclic peptides. It also represents the first attempt in this field. We hope that this work will help to accelerate the design of cyclic peptide active drugs in medicinal chemistry and chemical biology applications.
Spatiotemporal Control of Genomics and Epigenomics by Ultrasound
Authors: Wu Yiqian , Huang Ziliang , Liu Yahan , Yoon Chi Woo , Sun Kun , Situ Yinglin , Ho Phuong , Yuan Zhou , Zhu Linshan , Eyquem Justin , Zhao Yunde , Liu Thomas , Kwong Gabriel A , Chien Shu , Wang Yingxiao 
Published: June 2023

AbstractCRISPR (clustered regularly interspaced short palindromic repeats) is a revolutionary technology for genome editing. Its derived technologies such as CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) further allow transcriptional and epigenetic modulations. Focused ultrasound (FUS) can penetrate deep in biological tissues and induce mild hyperthermia in a confined region to activate heat-sensitive genes. Here we engineer a set of CRISPR(a/i) tools containing heat-sensitive genetic modules controllable by FUS for the regulation of genome and epigenome in live cells and animals. We demonstrated the capabilities of FUS-inducible CRISPRa, CRISPRi, and CRISPR (FUS-CRISPR(a/i)) to upregulate, repress, and knockout exogenous and/or endogenous genes, respectively, in different cell types. We further targeted FUS-CRISPR to telomeres in tumor cells to induce telomere disruption, inhibiting tumor growth and enhancing tumor susceptibility to killing by chimeric antigen receptor (CAR)-T cells. FUS-CRISPR-mediated telomere disruption for tumor priming combined with CAR-T therapy demonstrated synergistic therapeutic effects in xenograft mouse models. The FUS-CRISPR(a/i) toolbox allows the remote, noninvasive, and spatiotemporal control of genomic and epigenomic reprogramming in vivo, with extended applications in cancer treatment.
The ALOG domain defines a new family of plant-specific Transcription Factors acting during Arabidopsis flower development
Authors: Rieu Philippe , Beretta Veronica , Caselli Francesca , Thévénon Emmanuel , Lucas Jérémy , Rizk Mahmoud , Franchini Emanuela , Caporali Elisabetta , Nanao Max , Kater Martin , Dumas Renaud , Zubieta Chloe , Parcy François , Gregis Veronica 
Published: June 2023

AbstractThe ALOGs (ArabidopsisLIGHT-DEPENDENT SHORT HYPOCOTYLS 1and OryzaG1) are Transcription Factors (TFs) from an evolutionarily conserved plant-specific family shown to play critical roles in meristem identity, inflorescence architecture and organ boundaries in diverse species from mosses to higher flowering plants. However, the DNA binding-specificity and molecular determinants of protein-DNA interactions of this family were uncharacterized. Usingin vitrogenome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from the liverwortMarchantia polymorphaand the flowering plants Arabidopsis, tomato and rice. In order to determine the amino acids responsible for DNA-binding specificity, we solved the 2.1Å structure of the ALOG DNA binding domain in complex with its cognate DNA. The ALOG DBD is an all-alpha helical domain with a structural zinc ribbon insertion and an N-terminal disordered NLS. The NLS sequence forms an integral part of the DNA binding domain and contributes to direct base read-out. To define the function of a group of redundant ALOG proteins in the model plant Arabidopsis thaliana, we generated a series ofalogmutants and uncovered their participation in a gene regulatory network involving the other floral regulators LEAFY, BLADE-ON-PETIOLE and PUCHI, all active in defining boundary regions between reproductive meristems and repressing bracts development. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in defining organ boundaries in Arabidopsis.Significance StatementTranscription Factors (TFs) are key proteins that bind specific regions in the genome and regulate the expression of associated genes. Not all organisms possess the same set of TFs and some, like the ALOGs, are specific to the plant kingdom. These TFs have been shown to play important roles from mosses to flowering plants. However, it was not known what DNA motif they recognize and how they bind DNA. Here we identify this motif, we show it is widely conserved in evolution and we understand how this new type of DNA binding domain works at the structural level. In addition, we also show that severalALOGgenes from Arabidopsis share a redundant function within the genetic network underlying correct floral meristem development.
Overcoming migratory exhaustion: Expression of Matrix metalloproteinase-8 (MMP-8) promotes tumor infiltration and anti-tumor activity of CAR-T cells
Authors: Bandey Irfan N. , Montalvo Melisa J. , Singh Harjeet , Varadarajan Navin 
Published: June 2023

AbstractDespite the encouraging success of chimeric antigen receptor (CAR) T-cell therapy in treating hematological malignancies, the translation of adoptive cell therapies to solid tumors remains a challenge. Several studies have attributed the inability of tumor-infiltrating T cells to traffic to solid tumors, primarily to the presence of the extracellular matrix (ECM) and immunosuppressive environment of solid tumors. The ability of the transferred T cells to infiltrate the tumor is an essential prerequisite for anti-tumor activity. We show here that upon activation and expansion, T cells quickly lose their migratory capacity, leading to migratory exhaustion. At the molecular level, migratory exhaustion could be attributed to the downregulation of matrix metalloproteinase 8 (MMP8). To overcome this, we hypothesized that T cells genetically modified to secrete the mature form of matrix metalloproteinase 8 (mMMP8) would facilitate migration across matrix barriersin vitroandin vivo. We demonstrated that CAR T cells that co-express mMMP8 demonstrate robust migration across Matrigel and can kill tumor cells embedded in Matrigelin vitro. We tested the efficacy of these mMMP8 engineered cells in both leukemic and ovarian cancer cell models embedded in Matrigel in xenograft mouse models. Our results illustrate that unlike parental CAR T cells that have minimal anti-tumor efficacy in these models, CAR T cells that secrete mMMP8 promote T-cell infiltration, leading to the eradication of the tumors and survival. We anticipate that the co-expression of mMMP8 can be broadly utilized to improve the infiltration and efficacy of CAR T cells targeting many different antigens.
Macromolecular Crowding Promotes Reentrant Liquid-Liquid Phase Separation of Human Serum Transferrin and Prevents Surface-Induced Fibrillation
Authors: Patel Chinmaya Kumar , Rani Chanchal , Kumar Rajesh , Mukherjee Tushar Kanti 
Published: June 2023

AbstractProtein aggregation and inactivation upon surface immobilization are major limiting factors for analytical applications in biotechnology related fields. Protein immobilization on solid surfaces often requires multi-step surface passivation which is time consuming and inefficient. Herein, we have discovered that biomolecular condensates of biologically active human serum transferrin (Tf) can effectively prevent surface-induced fibrillation and preserve the native-like conformation of phase separated Tf over a period of 30-days. It has been observed that macromolecular crowding promotes homotypic liquid-liquid phase separation (LLPS) of Tf through enthalpically driven multivalent hydrophobic interactions possibly via the involvement of its low complexity domain (residue 3–20) containing hydrophobic amino acids. The present LLPS of Tf is a rare example of salt-mediated reentrant phase separation in a broad range of salt concentrations (0–3 M) solely via the involvement of hydrophobic interactions. Notably, no liquid-to-solid-like phase transition has been observed over a period of 30-days, suggesting the intact conformational integrity of phase separated Tf as revealed from single droplet Raman, circular dichroism, and Fourier transform infrared spectroscopy measurements. More importantly, we discovered that the phase separated condensates of Tf completely inhibit the surface-induced fibrillation of Tf, illustrating the protective role of these liquid-like condensates against denaturation and aggregation of biomolecules. The cell mimicking aqueous compartments of biomolecular condensates with a substantial amount of interfacial water preserve the structure and functionality of biomolecules. Our present study highlights an important functional aspect of biologically active protein condensates and may have wide-ranging implications in cell physiology and biotechnological applications.
Enrichment of hard sweeps on the X chromosome compared to autosomes in sixDrosophilaspecies
Authors: Harris Mariana , Kim Bernard , Garud Nandita 
Published: June 2023

AbstractThe X chromosome, being hemizygous in males, is exposed one third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population ofDrosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across six commonly studiedDrosophilaspecies. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps, and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multipleDrosophilaspecies.
Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant
Authors: Zhao Lei , Zhou Wei , He Jun , Li De-Zhu , Li Hong-Tao 
Published: June 2023

AbstractSex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigated in animals and brown algae, less is known about evolutionary forces in dioecious angiosperms. In this study, we separately compared the expression of sex-biased genes between female and male floral buds and between female and male flowers at anthesis in dioeciousTrichosanthes pilosa(Cucurbitaceae). In floral buds, sex-biased gene expression was pervasive, and had significantly different roles in sexual dimorphism such as physiology. We observed higher rates of sequence evolution for male-biased genes in floral buds compared to female-biased and unbiased genes. Male-biased genes under positive selection were mainly associated with functions to abiotic stress and immune responses, suggesting that high evolutionary rates are driven by adaptive evolution. Additionally, relaxed purifying selection may contribute to accelerated evolution in male-biased genes generated by gene duplication. Our findings, for the first time in angiosperms, suggest evident rapid evolution of male-biased genes, advance our understanding of the patterns and forces driving the evolution of sexual dimorphism in dioecious plants.
Molecular physiological characterization of the dynamics of persister formation inStaphylococcus aureus
Authors: Liu Shiqi , Huang Yixuan , Jensen Sean , Laman Paul , Kramer Gertjan , Zaat Sebastian A. J. , Brul Stanley 
Published: June 2023

AbstractBacteria possess the ability to enter a growth arrested state known as persistence in order to survive antibiotic exposure. Clinically, persisters are regarded as the main causative agents for chronic and recurrent infectious diseases. To combat this antibiotic-tolerant population, a better understanding of the molecular physiology of persisters is required. In this study, we collected samples at different stages of the biphasic kill curve to reveal the dynamics of the cellular molecular changes that occur in the process of persister formation. After exposure to antibiotics with different modes of action, namely vancomycin and enrofloxacin, similar persister levels were obtained. Both shared and distinct stress responses were enriched for the respective persister populations. However, the dynamics of the presence of proteins linked to the persister phenotype throughout the biphasic kill curve and the molecular profiles in a stable persistent population did show large differences depending on the antibiotic used. This suggests that persisters at the molecular level are highly stress specific, emphasizing the importance of characterizing persisters generated under different stress conditions. Additionally, although generated persisters exhibited cross-tolerance toward tested antibiotics, combined therapies were demonstrated to be a promising approach to reduce persister levels. In conclusion, this investigation sheds light on the stress-specific nature of persisters, highlighting the necessity of tailored treatment approaches and the potential of combined therapy.ImportanceBy monitoring proteome and metabolites duringStaphylococcus aureuspersister formation under vancomycin and enrofloxacin exposure, we revealed the dynamic information of the molecular physiology of persister formation upon exposure to two different antibiotics with different modes of action. The data shows that cells that phenotypically are similarly classified as persisters, do have several molecular characteristics in common but, remarkably so, differ substantially in a significant number of other aspects of their molecular makeup. These contrasts provided valuable insights into persister eradication, which holds considerable clinical relevance.
Discovery, Characterization, and Bioactivity of the Achromonodins: Lasso Peptides Encoded byAchromobacter
Authors: Carson Drew V. , Zhang Yi , So Larry , Cheung-Lee Wai Ling , Cartagena Alexis Jaramillo , Darst Seth A. , Link A. James 
Published: June 2023

AbstractThrough genome mining efforts, we discovered two lasso peptide biosynthetic gene clusters (BGCs) within two different species ofAchromobacter, a genus that contains pathogenic organisms that can infect patients with cystic fibrosis. Using gene-refactored BGCs inE. coli, we heterologously expressed two lasso peptides, which we named achromonodin-1 and achromonodin-2. Achromonodin-1 is naturally encoded by certain isolates from the sputum of patients with cystic fibrosis. We solve the NMR structure of achromonodin-1, demonstrating that it is a threaded lasso peptide with a large loop and short tail structure, reminiscent of previously characterized lasso peptides that inhibit RNA polymerase (RNAP). We then show that achromonodin-1 inhibits RNAPin vitroand has potent but narrow-spectrum activity towardsAchromobacter pulmonis, another isolate from the sputum of a cystic fibrosis patient. Our efforts expand the repertoire of antimicrobial lasso peptides and provide insights into howAchromobacterisolates from certain ecological niches may interact with each other.
ALS-related p97 R155H mutation disrupts lysophagy in iPSC-derived motor neurons
Authors: Klickstein Jacob A. , Johnson Michelle A. , Antonoudiou Pantelis , Maguire Jamie , Paulo Joao A. , Gygi Steve P. , Weihl Chris , Raman Malavika 
Published: June 2023

AbstractMutations in the AAA+ ATPase p97 (also known as valosin containing protein, VCP) cause multisystem proteinopathy 1 (MSP-1) which includes amyotrophic-lateral sclerosis (ALS); however, the pathogenic mechanisms that contribute to motor neuron loss in familial ALS caused by p97 mutations remain obscure. Here, we use two distinct induced pluripotent stem cell models differentiated into spinal motor neurons to investigate how p97 mutations perturb the motor neuron proteome. Using multiplexed quantitative proteomics in these cells, we find that motor neurons harboring the p97 R155H mutation have deficits in lysosome quality control and the selective autophagy of lysosomes (lysophagy). p97 R155H motor neurons are unable to efficiently clear damaged lysosomes and have reduced viability. Additionally, lysosomes in mutant motor neurons have increased pH compared to their wildtype counterparts. The endo-lysosomal damage repair (ELDR) complex is required for clearance of damaged lysosomes and involves UBXD1-p97 interaction which is disrupted in mutant motor neurons. Finally, we report that inhibition of the ATPase activity of p97 R155H using the ATP competitive inhibitor CB-5083 rescues lysophagy defects in mutant motor neurons. These results add to the increasing evidence that endo-lysosomal dysfunction is a key aspect of disease pathogenesis in p97-related disorders.
Functional interaction of torsinA and its activators in liver lipid metabolism
Authors: Hernandez-Ono Antonio , Zhao Yi Peng , Murray John W. , Östlund Cecilia , Lee Michael J. , Shi Angsi , Dauer William T. , Worman Howard J. , Ginsberg Henry N. , Shin Ji-Yeon 
Published: June 2023

AbstractTorsinA is an atypical ATPase that lacks intrinsic activity unless it is bound to its activators lamina-associated polypeptide 1 (LAP1) in the perinuclear space or luminal domain-like LAP1 (LULL1) throughout the endoplasmic reticulum. However, the interaction of torsinA with LAP1 and LULL1 has not yet been shown to modulate a defined physiological process in mammalsin vivo. We previously demonstrated that depletion of torsinA from mouse hepatocytes leads to reduced liver triglyceride secretion and marked steatosis, whereas depletion of LAP1 had more modest similar effects. We now show that depletion of LULL1 alone does not significantly decrease liver triglyceride secretion or cause steatosis. However, simultaneous depletion of both LAP1 and LULL1 from hepatocytes leads to defective triglyceride secretion and marked steatosis similar to that observed with depletion of torsinA. Our results demonstrate that torsinA and its activators dynamically regulate a physiological process in mammalsin vivo.