bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stretchable, nano-crumpled MXene multilayers impart long-term antibacterial surface properties
Authors: Nagpal Neha , Tokmedash Mohammad Asadi , Chen Po-Yen , VanEpps J. Scott , Min Jouha 
Published: January 2023

ABSTRACTInfections are a significant risk to patients who receive medical implants, and can often lead to implant failure, tissue necrosis, and even amputation. So far, although various surface modification approaches have been proposed for prevention and treatment of microbial biofilms on indwelling medical devices, most are too expensive/complicated to fabricate, unscalable, or limited in durability for clinical use. Here we present a new bottom-up design for fabricating scalable and durable nano-pattered coatings with dynamic topography for long-term antibacterial effects. We show that MXene layer-by-layer (LbL) self-assembled coatings -- with finely tunable crumple structures with nanometer resolution and excellent mechanical durability -- can be successfully fabricated on stretchable poly(dimethylsiloxane) (PDMS). The crumpled MXene coating with sharp-edged peaks shows potent antibacterial effects againstStaphylococcus aureusandEscherichia coli. In addition, we find that on-demand dynamic deformation of the crumpled coating can remove ≥99% of adhered bacterial cells for both species, resulting in a clean surface with restored functionality. This approach offers improved practicality, scalability, and antibacterial durability over previous methods, and its flexibility may lend itself to many types of biomaterials and implantable devices.
A reliable and efficient adaptive Bayesian method to assess static lower limb position sense
Authors: Wood Jonathan M , Morton Susanne M , Kim Hyosub E 
Published: January 2023

AbstractBackgroundLower limb proprioception is critical for maintaining stability during gait and may impact how individuals modify their movements in response to changes in the environment and body state, a process termed “sensorimotor adaptation”. However, the connection between lower limb proprioception and sensorimotor adaptation during human gait has not been established. We suspect this gap is due in part to the lack of reliable, efficient methods to assess global lower limb proprioception in an ecologically valid context.New MethodWe assessed static lower limb proprioception using an alternative forced choice task, administered twice to determine test-retest reliability. Participants stood on a dual-belt treadmill which passively moved one limb to stimulus locations selected by a Bayesian adaptive algorithm. At the stimulus locations, participants judged relative foot positions and the algorithm estimated the point of subjective equality (PSE) and the uncertainty of lower limb proprioception.ResultsUsing the Bland-Altman method, combined with Bayesian statistics, we found that both the PSE and uncertainty estimates had good reliability.Comparison with Existing Method(s)Current methods assessing static lower limb proprioception do so within a single joint, in non-weight bearing positions, and rely heavily on memory. One exception assessed static lower limb proprioception in standing but did not measure reliability and contained confounds impacting participants’ judgments, which we experimentally controlled here.ConclusionsThis efficient and reliable method assessing lower limb proprioception will aid future mechanistic understanding of locomotor adaptation and serve as a useful tool for basic and clinical researchers studying balance and falls.
Prediction of SARS-CoV-2 spike protein mutations using Sequence-to-Sequence and Transformer models
Authors: Ahmadi Hamed , Nikoofard Vahid , Nikoofard Hossein , Abdolvahab Rouhollah , Nikoofard Narges , Esmaeilzadeh Mahdi 
Published: January 2023

AbstractIn the study of viral epidemics, having information about the structural evolution of the virus can be very helpful in controlling the disease and making vaccines. Various deep learning and natural language processing techniques (NLP) can be used to analyze genetic structure of viruses, namely to predict their mutations. In this paper, by using Sequence-to-Sequence (Seq2Seq) model with Long Short-Term Memory (LSTM) cell and Transformer model with the attention mechanism, we investigate the spike protein mutations of SARS-CoV-2 virus. We make time-series datasets of the spike protein sequences of this virus and generate upcoming spike protein sequences. We also determine the mutations of the generated spike protein sequences, by comparing these sequences with the Wuhan spike protein sequence. We train the models to make predictions in December 2021, February 2022, and October 2022. Furthermore, we find that some of our generated spike protein sequences have been reported in December 2021 and February 2022, which belong to Delta and Omicron variants. The results obtained in the present study could be useful for prediction of future mutations of SARS-CoV-2 and other viruses.
Distant sequence regions of JBP1 contribute to J-DNA binding
Authors: de Vries Ida , Ammerlaan Danique , Heidebrecht Tatjana , Celie Patrick H. N. , Geerke Daan P. , Joosten Robbie P. , Perrakis Anastassis 
Published: January 2023

ABSTRACTBase-J (β-D-Glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J Binding Protein 1 (JBP1), that has a thymidine hydroxylase domain (THD) and a J-DNA binding domain (JDBD). How the THD synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for Molecular Dynamics (MD) simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.
PIC recruitment by synthetic reader-actuators to polycomb-silenced genes blocks triple-negative breast cancer invasion
Authors: Williams Natecia L. , Hong Lauren , Jaffe Maya , Shields Cara E. , Haynes Karmella A. 
Published: January 2023

ABSTRACTScientists have used small molecule inhibitors and genetic knockdown of gene-silencing polycomb repressive complexes (PRC1/2) to determine if restoring the expression of tumor suppressor genes can block proliferation and invasion of cancer cells. A major limitation of this approach is that inhibitors can not restore key transcriptional activators that are mutated in many cancers, such as p53 and members of the BRAF SWI/SNF complex. Furthermore, small molecule inhibitors can alter the activity of, rather than inhibit, the polycomb enzyme EZH2. While chromatin has been shown to play a major role in gene regulation in cancer, poor clinical results for polycomb chromatin-targeting therapies for diseases like triple-negative breast cancer (TNBC) could discourage further development of this emerging avenue for treatment. To overcome the limitations of inhibiting polycomb to study epigenetic regulation, we developed an engineered chromatin protein to manipulate transcription. The synthetic reader-actuator (SRA) is a fusion protein that directly binds a target chromatin modification and regulates gene expression. Here, we report the activity of an SRA built from polycomb chromodomain and VP64 modules that bind H3K27me3 and subunits of the Mediator complex, respectively. In SRA-expressing BT-549 cells, we identified 122 upregulated differentially expressed genes (UpDEGs, ≥ 2-fold activation, adjustedp< 0.05). On-target epigenetic regulation was determined by identifying UpDEGs at H3K27me3-enriched, closed chromatin. SRA activity induced activation of genes involved in cell death, cell cycle arrest, and the inhibition of migration and invasion. SRA-expressing BT-549 cells showed reduced spheroid size in Matrigel over time, loss of invasion, and activation of apoptosis. These results show that Mediator-recruiting regulators broadly targeted to silenced chromatin activate silenced tumor suppressor genes and stimulate anti-cancer phenotypes. Therefore further development of gene-activating epigenetic therapies might benefit TNBC patients.
Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq
Authors: Geiger-Schuller Kathryn , Eraslan Basak , Kuksenko Olena , Dey Kushal K. , Jagadeesh Karthik A. , Thakore Pratiksha I. , Karayel Ozge , Yung Andrea R. , Rajagopalan Anugraha , Meireles Ana M , Yang Karren Dai , Amir-Zilberstein Liat , Delorey Toni , Phillips Devan , Raychowdhury Raktima , Moussion Christine , Price Alkes L. , Hacohen Nir , Doench John G. , Uhler Caroline , Rozenblatt-Rosen Orit , Regev Aviv 
Published: January 2023

ABSTRACTE3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the balance of DC1, DC2, migratory DC and macrophage states and a gradient of DC maturation. Family members grouped into co-functional modules that were enriched for physical interactions and impacted specific programs through substrate transcription factors. E3s and their adaptors co-regulated the same processes, but partnered with different substrate recognition adaptors to impact distinct aspects of the DC life cycle. Genetic interactions were more prevalent within than between modules, and a deep learning model, comβVAE, predicts the outcome of new combinations by leveraging modularity. The E3 regulatory network was associated with heritable variation and aberrant gene expression in immune cells in human inflammatory diseases. Our study provides a general approach to dissect gene function.
A fluid biomarker reveals loss of TDP-43 splicing repression in pre-symptomatic ALS
Authors: Irwin Katherine E. , Jasin Pei , Braunstein Kerstin E. , Sinha Irika , Bowden Kyra D. , Moghekar Abhay , Oh Esther S. , Raitcheva Denitza , Bartlett Dan , Berry James D. , Traynor Bryan , Ling Jonathan P. , Wong Philip C. 
Published: January 2023

AbstractLoss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well-documented in postmortem tissues of amyotrophic lateral sclerosis (ALS), yet whether this abnormality occurs during early-stage disease remains unresolved. Cryptic exon inclusion reflects functional loss of TDP-43, and thus detection of cryptic exon-encoded peptides in cerebrospinal fluid (CSF) could reveal the earliest stages of TDP-43 dysregulation in patients. Here, we use a newly characterized monoclonal antibody specific to a TDP-43-dependent cryptic epitope (encoded by the cryptic exon found inHDGFL2) to show that loss of TDP-43 splicing repression occurs inC9ORF72-associated ALS, including pre-symptomatic mutation carriers. In contrast to neurofilament light and heavy chain proteins, cryptic HDGFL2 accumulates in CSF at higher levels during early stages of disease. Our findings indicate that loss of TDP-43 splicing repression occurs early in disease progression, even pre-symptomatically, and that detection of HDGFL2’s cryptic neoepitope may serve as a prognostic test for ALS which should facilitate patient recruitment and measurement of target engagement in clinical trials.
Site-specific Covalent Labeling of DNA Substrates by an RNA Transglycosylase
Authors: Tota Ember M. , Devaraj Neal K. 
Published: January 2023

AbstractBacterial tRNA guanine transglycosylases (TGTs) catalyze the exchange of guanine for the 7-deazaguanine queuine precursor, prequeuosine1 (preQ1). While the native nucleic acid substrate for bacterial TGTs is the anticodon loop of queuine-cognate tRNAs, the minimum recognition sequence for the enzyme is a structured hairpin containing the target G nucleobase in a “UGU” loop motif. Previous work has established an RNA modification system, RNA-TAG, in which E. coli TGT exchanges the target G on an RNA of interest for chemically modified preQ1 substrates linked to a small molecule reporter such as biotin or a fluorophore. While extending the substrate scope of RNA transglycosylases to include DNA would enable numerous applications, it has been previously reported that TGT is incapable of modifying native DNA. Here we demonstrate that TGT can in fact recognize and label specific DNA substrates. Through iterative testing of rationally mutated DNA hairpin sequences, we determined the minimal sequence requirements for transglycosylation of unmodified DNA by E. coli TGT. Controlling steric constraint in the DNA hairpin dramatically affects labeling efficiency, and, when optimized, can lead to near quantitative site-specific modification. We demonstrate the utility of our newly developed DNA-TAG system by rapidly synthesizing probes for fluorescent Northern blotting of spliceosomal U6 RNA and RNA FISH visualization of the long noncoding RNA, MALAT1. The ease and convenience of the DNA-TAG system will provide researchers with a tool for accessing a wide variety of affordable modified DNA substrates.
“Development and Implementation of Novel Chatbot-based Genomic Research Consent”
Authors: Smith Erica D. , Savage Sarah K. , Andrew E. Hallie , Martin Gloria Mas , Kahn-Kirby Amanda H. , LoTempio Jonathan , Délot Emmanuèle , Cohen Andrea J. , Pitsava Georgia , Berger Seth , Fusaro Vincent A. , Vilain Eric 
Published: January 2023

ABSTRACTObjectiveTo conduct a retrospective analysis comparing traditional human-based consenting to an automated chat-based consenting process.Materials and MethodsWe developed a new chat-based consent using our IRB-approved consent forms. We leveraged a previously developed platform (Gia®, or “Genetic Information Assistant”) to deliver the chat content to candidate participants. The content included information about the study, educational information, and a quiz to assess understanding. We analyzed 144 families referred to our study during a 6-month time period. A total of 37 families completed consent using the traditional process, while 35 families completed consent using Gia.ResultsEngagement rates were similar between both consenting methods. The median length of the consent conversation was shorter for Gia users compared to traditional (44 vs. 76 minutes). Additionally, the total time from referral to consent completion was faster with Gia (5 vs. 16 days). Within Gia, understanding was assessed with a 10-question quiz that most participants (96%) passed. Feedback about the chat consent indicated that 86% of participants had a positive experience.DiscussionUsing Gia resulted in time savings for both the participant and study staff. The chatbot enables studies to reach more potential candidates. We identified five key features related to human-centered design for developing a consent chat.ConclusionThis analysis suggests that it is feasible to use an automated chatbot to scale obtaining informed consent for a genomics research study. We further identify a number of advantages when using a chatbot.
Endogenous inflammatory mediators produced by injury activate TRPV1 and TRPA1 nociceptors to induce sexually dimorphic cold pain that is dependent on TRPM8 and GFRα3
Authors: Yang Chenyu , Yamaki Shanni , Jung Tyler , Kim Brian , Huyhn Ryan , McKemy David D. 
Published: January 2023

ABSTRACTThe detection of environmental temperatures is critical for survival, yet inappropriate responses to thermal stimuli can have a negative impact on overall health. The physiological effect of cold is distinct among somatosensory modalities in that it is soothing and analgesic, but also agonizing in the context of tissue damage. Inflammatory mediators produced during injury activate nociceptors to release neuropeptides, such as CGRP and substance P, inducing neurogenic inflammation which further exasperates pain. Many inflammatory mediators induce sensitization to heat and mechanical stimuli but, conversely, inhibit cold responsiveness, and the identity of molecules inducing cold pain peripherally is enigmatic, as are the cellular and molecular mechanisms altering cold sensitivity. Here, we asked if inflammatory mediators that induce neurogenic inflammation via the nociceptive ion channels TRPV1 and TRPA1 lead to cold pain in mice. Specifically, we tested cold sensitivity in mice after intraplantar injection of lysophosphatidic acid (LPA) or 4-hydroxy-2-nonenal (4HNE), finding each induces cold pain that is dependent on the cold-gated channel TRPM8. Inhibition of either CGRP, substance P, or toll-like receptor 4 (TLR4) signaling attenuates this phenotype, and each neuropeptide produces TRPM8-dependent cold pain directly. Further, the inhibition of CGRP or TLR4 signaling alleviates cold allodynia differentially by sex. Lastly, we find that cold pain induced by inflammatory mediators and neuropeptides requires the neurotrophin artemin and its receptor GFRα3. These results demonstrate that tissue damage alters cold sensitivity via neurogenic inflammation, likely leading to localized artemin release that induces cold pain via GFRα3 and TRPM8.Significance StatementThe cellular and molecular mechanisms that generate pain are complex with a diverse array of pain-producing molecules generated during injury that act to sensitize peripheral sensory neurons, thereby inducing pain. Here we identify a specific neuroinflammatory pathway involving the ion channel TRPM8 and the neurotrophin receptor GFRα3 that leads to cold pain, providing select targets for potential therapies for this pain modality.
The sound of restored soil: Measuring soil biodiversity in a forest restoration chronosequence with ecoacoustics
Authors: Robinson Jake M. , Breed Martin F. , Abrahams Carlos 
Published: January 2023

AbstractForest restoration requires monitoring to assess changes in above- and below-ground communities, which is challenging due to practical and resource limitations. With emerging sound recording technologies, ecological acoustic survey methods—also known as ‘ecoacoustics’—are increasingly available. These provide a rapid, effective, and non-intrusive means of monitoring biodiversity. Above-ground ecoacoustics is increasingly widespread, but soil ecoacoustics has yet to be utilised in restoration despite its demonstrable effectiveness at detecting meso- and macrofauna acoustic signals. This study applied ecoacoustic tools and indices (Acoustic Complexity Index, Normalised Difference Soundscape Index, and Bioacoustic Index) to measure above- and below-ground biodiversity in a forest restoration chronosequence. We hypothesised that higher acoustic complexity, diversity and high-frequency to low-frequency ratio would be detected in restored forest plots. We collectedn= 198 below-ground samples andn= 180 ambient and controlled samples from three recently degraded (within 10 years) and three restored (30-51 years ago) deciduous forest plots across three monthly visits. We used passive acoustic monitoring to record above-ground biological sounds and a below-ground sampling device and sound-attenuation chamber to record soil communities. We found that restored plot acoustic complexity and diversity were higher in the sound-attenuation chamber soil but notin situor above-ground samples. Moreover, we found that restored plots had a significantly greater high-frequency to low-frequency ratio for soil, but no such association for above-ground samples. Our results suggest that ecoacoustics has the potential to monitor below-ground biodiversity, adding to the restoration ecologist’s toolkit and supporting global ecosystem recovery.Implications for PracticeThis is the first known study to assess the sounds of soil biodiversity in a forest restoration context, paving the way for more comprehensive studies and practical applications to support global ecosystem recovery.Soil ecoacoustics has the potential to support restoration ecology/biodiversity assessments, providing a minimally intrusive, cost-effective and rapid surveying tool. The methods are also relatively simple to learn and apply.Ecoacoustics can contribute toward overcoming the profound challenge of quantifying the effectiveness (i.e., success) of forest restoration interventions in reinstating target species, functions and so-called ‘services’ and reducing disturbance.
Direct Tests of Cytochrome Function in the Electron Transport Chain of Malaria Parasites
Authors: Espino-Sanchez Tanya J. , Wienkers Henry , Marvin Rebecca G. , Nalder Shai-anne , García-Guerrero Aldo E. , VanNatta Peter E. , Jami-Alahmadi Yasaman , Blackwell Amanda Mixon , Whitby Frank G. , Wohlschlegel James A. , Kieber-Emmons Matthew T. , Hill Christopher P. , Sigala Paul A. 
Published: January 2023

ABSTRACTThe mitochondrial electron transport chain (ETC) ofPlasmodiummalaria parasites is a major antimalarial drug target, but critical cytochrome functions remain unstudied and enigmatic. Parasites express two distinct cytchomologs (candc-2) with unusually sparse sequence identity and uncertain fitness contributions.P. falciparumcytc-2 is the most divergent eukaryotic cytchomolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cytchomologs and the related cytc1for inducible knockdown. Translational repression of cytcand cytc1was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cytc-2 knockdown or knock-out had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cytcfor ETC function. Biochemical and structural studies revealed that both cytcandc-2 are hemylated by holocytochromecsynthase, but UV-vis absorbance and EPR spectra strongly suggest that cytc-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino-acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergentPlasmodiumcytochromecwith molecular adaptations that defy a conserved role in eukaryotic evolution.SIGNIFICANCE STATEMENTMitochondria are critical organelles in eukaryotic cells that drive oxidative metabolism. The mitochondrion ofPlasmodiummalaria parasites is a major drug target that has many differences from human cells and remains poorly studied. One key difference from humans is that malaria parasites express two cytochromecproteins that differ significantly from each other and play untested and uncertain roles in the mitochondrial electron transport chain (ETC). Our study revealed that one cytcis essential for ETC function and parasite viability while the second, more divergent protein has unusual structural and biochemical properties and is not required for growth of blood-stage parasites. This work elucidates key biochemical properties and evolutionary differences in the mitochondrial ETC of malaria parasites.