Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 306
Filter
Add more filters

Country/Region as subject
Publication year range
1.
Mol Cell ; 82(9): 1708-1723.e10, 2022 05 05.
Article in English | MEDLINE | ID: mdl-35320755

ABSTRACT

7SK is a conserved noncoding RNA that regulates transcription by sequestering the transcription factor P-TEFb. 7SK function entails complex changes in RNA structure, but characterizing RNA dynamics in cells remains an unsolved challenge. We developed a single-molecule chemical probing strategy, DANCE-MaP (deconvolution and annotation of ribonucleic conformational ensembles), that defines per-nucleotide reactivity, direct base pairing interactions, tertiary interactions, and thermodynamic populations for each state in RNA structural ensembles from a single experiment. DANCE-MaP reveals that 7SK RNA encodes a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium shifts in response to cell growth and stress and can be targeted to modulate expression of P-TEFbresponsive genes. Our study reveals that RNA structural dynamics underlie 7SK function as an integrator of diverse cellular signals to control transcription and establishes the power of DANCE-MaP to define RNA dynamics in cells.


Subject(s)
Positive Transcriptional Elongation Factor B , RNA-Binding Proteins , Binding Sites/genetics , HeLa Cells , Humans , Positive Transcriptional Elongation Factor B/genetics , RNA, Small Nuclear/genetics , RNA, Untranslated , RNA-Binding Proteins/genetics
2.
Mol Cell ; 80(6): 1078-1091.e6, 2020 12 17.
Article in English | MEDLINE | ID: mdl-33290746

ABSTRACT

We report that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with viral RNA. N-protein condenses with specific RNA genomic elements under physiological buffer conditions and condensation is enhanced at human body temperatures (33°C and 37°C) and reduced at room temperature (22°C). RNA sequence and structure in specific genomic regions regulate N-protein condensation while other genomic regions promote condensate dissolution, potentially preventing aggregation of the large genome. At low concentrations, N-protein preferentially crosslinks to specific regions characterized by single-stranded RNA flanked by structured elements and these features specify the location, number, and strength of N-protein binding sites (valency). Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is RNA sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules, and therefore presents a screenable process for identifying antiviral compounds effective against SARS-CoV-2.


Subject(s)
COVID-19/metabolism , Coronavirus Nucleocapsid Proteins/metabolism , Genome, Viral , Nucleocapsid/metabolism , RNA, Viral/metabolism , SARS-CoV-2/metabolism , Animals , Antiviral Agents/pharmacology , COVID-19/genetics , Chlorocebus aethiops , Coronavirus Nucleocapsid Proteins/genetics , Drug Evaluation, Preclinical , HEK293 Cells , Humans , Nucleocapsid/genetics , Phosphoproteins/genetics , Phosphoproteins/metabolism , SARS-CoV-2/genetics , Vero Cells , COVID-19 Drug Treatment
3.
Nature ; 596(7872): 444-448, 2021 08.
Article in English | MEDLINE | ID: mdl-34349262

ABSTRACT

MFSD2A is a sodium-dependent lysophosphatidylcholine symporter that is responsible for the uptake of docosahexaenoic acid into the brain1,2, which is crucial for the development and performance of the brain3. Mutations that affect MFSD2A cause microcephaly syndromes4,5. The ability of MFSD2A to transport lipid is also a key mechanism that underlies its function as an inhibitor of transcytosis to regulate the blood-brain barrier6,7. Thus, MFSD2A represents an attractive target for modulating the permeability of the blood-brain barrier for drug delivery. Here we report the cryo-electron microscopy structure of mouse MFSD2A. Our structure defines the architecture of this important transporter, reveals its unique extracellular domain and uncovers its substrate-binding cavity. The structure-together with our functional studies and molecular dynamics simulations-identifies a conserved sodium-binding site, reveals a potential lipid entry pathway and helps to rationalize MFSD2A mutations that underlie microcephaly syndromes. These results shed light on the critical lipid transport function of MFSD2A and provide a framework to aid in the design of specific modulators for therapeutic purposes.


Subject(s)
Blood-Brain Barrier/metabolism , Lipid Metabolism , Symporters/chemistry , Symporters/metabolism , Animals , Binding Sites , Biological Transport , HEK293 Cells , Humans , Mice , Models, Molecular , Molecular Dynamics Simulation , Mutation , Protein Domains , Sodium/metabolism , Symporters/genetics , Symporters/ultrastructure
4.
RNA ; 29(5): 691-704, 2023 05.
Article in English | MEDLINE | ID: mdl-36792358

ABSTRACT

Although not canonically polyadenylated, the long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) is stabilized by a highly conserved 76-nt triple helix structure on its 3' end. The entire MALAT1 transcript is over 8000 nt long in humans. The strongest structural conservation signal in MALAT1 (as measured by covariation of base pairs) is in the triple helix structure. Primary sequence analysis of covariation alone does not reveal the degree of structural conservation of the entire full-length transcript, however. Furthermore, RNA structure is often context dependent; RNA binding proteins that are differentially expressed in different cell types may alter structure. We investigate here the in-cell and cell-free structures of the full-length human and green monkey (Chlorocebus sabaeus) MALAT1 transcripts in multiple tissue-derived cell lines using SHAPE chemical probing. Our data reveal levels of uniform structural conservation in different cell lines, in cells and cell-free, and even between species, despite significant differences in primary sequence. The uniformity of the structural conservation across the entire transcript suggests that, despite seeing covariation signals only in the triple helix junction of the lncRNA, the rest of the transcript's structure is remarkably conserved, at least in primates and across multiple cell types and conditions.


Subject(s)
RNA, Long Noncoding , Animals , Humans , Chlorocebus aethiops , RNA, Long Noncoding/metabolism , Base Pairing , Cell Line , RNA Stability , Cell Proliferation , Cell Line, Tumor
5.
Antimicrob Agents Chemother ; : e0168423, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38656138

ABSTRACT

Novel antimicrobials are needed to treat rising nontuberculous mycobacteria (NTM) infections. Using standard broth microdilution methods, 68 NTM isolates were tested against gepotidacin, a new, first-in-class, oral triazaacenaphthylene bacterial topoisomerase inhibitor. MICs varied (0.25 to >64 µg/mL) with the lowest being M. fortuitum complex (0.25-8 µg/mL), M. mucogenicum complex (1-2 µg/mL), M. kansasii (0.25-8 µg/mL), and M. marinum (4-16 µg/mL). Testing greater numbers of some species is suggested to better understand gepotidacin activity against NTM.

6.
Genome Res ; 31(4): 529-537, 2021 04.
Article in English | MEDLINE | ID: mdl-33536225

ABSTRACT

Low-pass sequencing (sequencing a genome to an average depth less than 1× coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5× and 1×) and array genotyping (using the Illumina Global Screening Array [GSA]) on 120 DNA samples derived from African- and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave-one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome-wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼0.5× and higher compared to the Illumina GSA.


Subject(s)
Genome-Wide Association Study , Genotype , High-Throughput Nucleotide Sequencing , Genome, Human , Genome-Wide Association Study/methods , Genome-Wide Association Study/standards , Haplotypes , Humans , Risk Factors
7.
Hepatology ; 78(4): 1133-1148, 2023 10 01.
Article in English | MEDLINE | ID: mdl-37039560

ABSTRACT

BACKGROUND AND AIMS: The liver is remarkably regenerative and can completely recover even when 80% of its mass is surgically removed. Identification of secreted factors that regulate liver growth would help us understand how organ size and regeneration are controlled but also provide candidate targets to promote regeneration or impair cancer growth. APPROACH AND RESULTS: To enrich for secreted factors that regulate growth control, we induced massive liver overgrowth with either YAP or MYC . Differentially expressed secreted factors were identified in these livers using transcriptomic analysis. To rank candidates by functionality, we performed in vivo CRISPR screening using the Fah knockout model of tyrosinemia. We identified secreted phosphoprotein-2 (SPP2) as a secreted factor that negatively regulates regeneration. Spp2 -deficient mice showed increased survival after acetaminophen poisoning and reduced fibrosis after repeated carbon tetrachloride injections. We examined the impact of SPP2 on bone morphogenetic protein signaling in liver cells and found that SPP2 antagonized bone morphogenetic protein signaling in vitro and in vivo. We also identified cell-surface receptors that interact with SPP2 using a proximity biotinylation assay coupled with mass spectrometry. We showed that SPP2's interactions with integrin family members are in part responsible for some of the regeneration phenotypes. CONCLUSIONS: Using an in vivo CRISPR screening system, we identified SPP2 as a secreted factor that negatively regulates liver regeneration. This study provides ways to identify, validate, and characterize secreted factors in vivo.


Subject(s)
Liver Regeneration , Neoplasms , Mice , Animals , Liver/metabolism , Hepatocytes/metabolism , Signal Transduction
8.
Acc Chem Res ; 56(7): 763-775, 2023 04 04.
Article in English | MEDLINE | ID: mdl-36917683

ABSTRACT

RNA molecules convey biological information both in their linear sequence and in their base-paired secondary and tertiary structures. Chemical probing experiments, which involve treating an RNA with a reagent that modifies conformationally dynamic nucleotides, have broadly enabled examination of short- and long-range RNA structure in diverse contexts, including in living cells. For decades, chemical probing experiments have been interpreted in a per-nucleotide way, such that the reactivity measured at each nucleotide reports the average structure at a position over all RNA molecules within a sample. However, there are numerous important cases where per-nucleotide chemical probing falls short, including for RNAs that are bound by proteins, RNAs that form complex higher order structures, and RNAs that sample multiple conformations.Recent experimental and computational innovations have started a revolution in RNA structure analysis by transforming chemical probing into a massively parallel, single-molecule experiment. Enabled by a specialized reverse transcription strategy called mutational profiling (MaP), multiple chemical modification events can be measured within individual RNA molecules. Nucleotides that communicate structurally through direct base pairing or large-scale folding-unfolding transitions will react with chemical probes in a correlated manner, thereby revealing structural complexity hidden to conventional approaches. These single-molecule correlated chemical probing (smCCP) experiments can be interpreted to directly identify nucleotides that base pair (the PAIR-MaP strategy) and to reveal long-range, through-space structural communication (RING-MaP). Correlated probing can also define the thermodynamic populations of complex RNA ensembles (DANCE-MaP). Complex RNA-protein networks can be interrogated by cross-linking proteins to RNA and measuring correlations between cross-linked positions (RNP-MaP).smCCP thus visualizes RNA secondary and higher-order structure with unprecedented accuracy, defining novel structures, RNA-protein interaction networks, time-resolved dynamics, and allosteric structural switches. These strategies are not mutually exclusive; in favorable cases, multiple levels of RNA structure ─ base pairing, through-space structural communication, and equilibrium ensembles ─ can be resolved concurrently. The physical experimentation required for smCCP is profoundly simple, and experiments are readily performed in cells on RNAs of any size, including large noncoding RNAs and mRNAs. Single-molecule correlated chemical probing is paving the way for a new generation of biophysical studies on RNA in living systems.


Subject(s)
Nucleotides , RNA , Nucleic Acid Conformation , RNA/chemistry , Base Pairing , RNA, Messenger , Proteins/genetics
9.
Sex Transm Dis ; 51(5): 348-351, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38346404

ABSTRACT

BACKGROUND: Promptly recognizing mpox can facilitate earlier diagnosis and appropriate treatment. How accurately clinicians can diagnose mpox based on clinical data and before receiving molecular test results is not known. METHODS: Leveraging public health and clinical data collected in Seattle-King County's Sexual Health Clinic (SHC) from July 29, 2022, to September 30, 2022, we analyzed the proportion of patients who received presumptive versus results-based tecovirimat when clinicians had a high, intermediate, or low suspicion for mpox after clinical evaluation. We calculated the sensitivity, specificity, and positive (PPV) and negative predictive value (NPV) of this approach against criterion standard mpox polymerase chain reaction (PCR) results. RESULTS: Of 321 patients evaluated for mpox in the SHC, median age was 34.5 years and 88% were cisgender men. Overall, 121 of 319 (38%) tested positive by mpox PCR. Clinicians had high suspicion for mpox in 122 patients and offered empiric tecovirimat to 92 (88%), of whom 85 (92%) tested PCR positive. Of 13 intermediate suspicion patients offered presumptive therapy, all accepted but none tested positive by PCR. The sensitivity, specificity, PPV, and NPV of high/intermediate clinical suspicion for mpox were 99%, 90%, 86%, and 99%, respectively. A higher proportion of people with HIV were diagnosed with mpox (57% vs. 36%, P = 0.01, χ2 test), and sensitivity and PPV of high/intermediate clinical suspicion in this subgroup were 100% and 86%, respectively. CONCLUSIONS: Clinical providers working in a high-volume, public SHC were able to both accurately identify and rule out mpox based on clinical examination before receiving PCR test results.


Subject(s)
Mpox (monkeypox) , Sexual Health , Male , Humans , Adult , Ambulatory Care Facilities , Benzamides
10.
Sex Transm Dis ; 51(4): e11-e13, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38301640

ABSTRACT

ABSTRACT: We conducted a retrospective cohort study of preexposure prophylaxis patients at the municipal Sexual Health Clinic in Seattle-King County, Washington from 2019 to 2021 to determine whether monthly check-in text messages impacted 4- and 6-month pre-exposure prophylaxis retention. Monthly check-ins did not appear to improve retention above and beyond open-ended texting and appointment reminders.


Subject(s)
HIV Infections , Pre-Exposure Prophylaxis , Sexual Health , Text Messaging , Humans , Male , Retrospective Studies , Homosexuality, Male , HIV Infections/prevention & control
11.
Sex Transm Dis ; 51(8): 521-526, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38860677

ABSTRACT

BACKGROUND: Home-based sampling could create accessible testing opportunities for men who have sex with men (MSM) who use pre-exposure prophylaxis (PrEP). Blood collection is required for the most reliable laboratory results for HIV and syphilis testing. An innovative blood collection method (Tasso+) creates a vacuum and semi-automatically collects larger volumes of blood from the upper arm. This study aimed to assess acceptability and feasibility of this device among PrEP-using MSM and the performance of blood collection. METHODS: Between August 2022 and January 2023, 47 MSM were recruited during their routine PrEP consultations at a Dutch Centre for Sexual Health. Participants tested the method directly after consultation, and an online questionnaire determined acceptability and feasibility. Blood and residual serum volumes were measured after sampling and after HIV and syphilis testing. RESULTS: Of the participants, 87% had a positive attitude toward use of the device, and 77% would use it again for self-sampling at home. Participants rated the use of the blood collection device as easy (96%). On average, 536 µL whole blood (244 µL serum) was collected. All samples were tested for HIV and syphilis, and most samples had sufficient blood for routine HIV (91%) and syphilis testing (89%). Most samples (85%) had 220 µL residual blood, sufficient for further testing (e.g., confirmation). CONCLUSIONS: Blood self-sampling with a method that creates a vacuum from the upper arm is highly acceptable by users and performs well in blood collection for multiple tests. This method has promising potential for use in home-based sexual health care for PrEP-using MSM.


Subject(s)
HIV Infections , Homosexuality, Male , Pre-Exposure Prophylaxis , Syphilis , Humans , Male , Netherlands , HIV Infections/prevention & control , HIV Infections/diagnosis , Syphilis/diagnosis , Syphilis/prevention & control , Adult , Blood Specimen Collection/instrumentation , Patient Acceptance of Health Care/statistics & numerical data , Middle Aged , Feasibility Studies , Self Care , Surveys and Questionnaires , Sexual and Gender Minorities , Young Adult , HIV Testing
12.
Sex Transm Dis ; 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38864518

ABSTRACT

BACKGROUND: Sexual health clinics were frontline providers in the 2022 US mpox public health response, though data on clinic-based mpox vaccine scale-up, diagnoses, and treatment are limited. We describe the role of a public health sexual health clinic (SHC) in King County's mpox response, between 5/23/22-10/31/22. METHODS: In July 2022, the SHC implemented a dedicated vaccine clinic and presumptive tecovirimat treatment (prior to laboratory confirmation) with on-site dispensation. We describe SHC's vaccine scale-up and contribution to clinical care by calculating the weekly number of vaccines administered by SHC and the total number of patients diagnosed and treated for mpox within SHC, and comparing to countywide data. We calculated time from symptom onset to testing and time from testing to treatment, and assessed temporal changes in these metrics using linear regression. RESULTS: The SHC provided ≥1 vaccine doses to 7,442 individuals (10,295 doses), administering 42% of the 24,409 vaccine doses provided countywide, with the greatest contribution in the first week of August (n = 1,562, 58% of countywide vaccinations that week). Of 598 patients evaluated for mpox and tested, 178 (30%) tested positive (37% of countywide cases), and 152 (85% of SHC patients with mpox) received tecovirimat (46% of treatment countywide). Median time from symptom onset to testing decreased from 12 to 6 days (p = 0.045); time from testing to treatment decreased from 4.5 days to 0 days (p < 0.001). CONCLUSION: The SHC was central to mpox vaccination and treatment scale-up, particularly in the first months of the 2022 epidemic.

13.
Nucleic Acids Res ; 50(17): 9689-9704, 2022 09 23.
Article in English | MEDLINE | ID: mdl-36107773

ABSTRACT

SERPINA1 mRNAs encode the protease inhibitor α-1-antitrypsin and are regulated through post-transcriptional mechanisms. α-1-antitrypsin deficiency leads to chronic obstructive pulmonary disease (COPD) and liver cirrhosis, and specific variants in the 5'-untranslated region (5'-UTR) are associated with COPD. The NM_000295.4 transcript is well expressed and translated in lung and blood and features an extended 5'-UTR that does not contain a competing upstream open reading frame (uORF). We show that the 5'-UTR of NM_000295.4 folds into a well-defined multi-helix structural domain. We systematically destabilized mRNA structure across the NM_000295.4 5'-UTR, and measured changes in (SHAPE quantified) RNA structure and cap-dependent translation relative to a native-sequence reporter. Surprisingly, despite destabilizing local RNA structure, most mutations either had no effect on or decreased translation. Most structure-destabilizing mutations retained native, global 5'-UTR structure. However, those mutations that disrupted the helix that anchors the 5'-UTR domain yielded three groups of non-native structures. Two of these non-native structure groups refolded to create a stable helix near the translation initiation site that decreases translation. Thus, in contrast to the conventional model that RNA structure in 5'-UTRs primarily inhibits translation, complex folding of the NM_000295.4 5'-UTR creates a translation-optimized message by promoting accessibility at the translation initiation site.


Subject(s)
Protein Biosynthesis , Pulmonary Disease, Chronic Obstructive , alpha 1-Antitrypsin/genetics , 5' Untranslated Regions , Humans , Protease Inhibitors , Pulmonary Disease, Chronic Obstructive/genetics , RNA, Messenger/metabolism
14.
Zoo Biol ; 2024 May 02.
Article in English | MEDLINE | ID: mdl-38698564

ABSTRACT

Asian elephant (Elephas maximus) and African savanna elephant (Loxodonta africana) populations collectively managed by ex-situ facilities accredited by the Association of Zoos and Aquariums (AZA) face sustainability challenges. Among the priorities to strengthen animal wellbeing and population sustainability is male elephant management. We conducted a survey of AZA facilities currently housing male elephants to assess the status, challenges, and priorities in three areas of male elephant management: musth, socialization, and semen collection. Surveys were administered to elephant care teams at AZA-accredited institutions between November 2022 and February 2023, and we received responses from 34 institutions (91.9% of AZA-accredited facilities holding adult male elephants), housing 32 adult male Asians and 26 adult male Africans. Most facilities prioritized breeding and male socialization over musth management and semen collection (although most facilities acknowledged that all these efforts are important), citing leadership support and staffing as most important to achieve male management goals. Behaviors most commonly accompanying musth included reduced appetite, difficulty training or shifting, human-directed aggression, and interest in females. Musth timing was variable between males and facilities. Most males were well-socialized with females and/or other males, though elephant compatibility and facility design were limiting factors in managing socialization. Although 60.6% of facilities collected semen or were training for semen collection, very few male elephants could reliably provide viable semen samples, challenging assisted reproductive efforts that could bolster population sustainability in both species. Together, our results provide a better understanding of the state of male elephant management, offering specific areas deserving of research and development to enhance wellbeing and sustainability.

15.
J Lipid Res ; 64(2): 100328, 2023 02.
Article in English | MEDLINE | ID: mdl-36626966

ABSTRACT

HDL are dynamic transporters of diverse molecular cargo and play critical roles in lipid metabolism and inflammation. We have previously reported that HDL transport both host and nonhost small RNAs (sRNA) based on quantitative PCR and sRNA sequencing approaches; however, these methods require RNA isolation steps which have potential biases and may not isolate certain forms of RNA molecules from samples. HDL have also been reported to accept functional sRNAs from donor macrophages and deliver them to recipient endothelial cells; however, using PCR to trace HDL-sRNA intercellular communication has major limitations. The present study aims to overcome these technical barriers and further understand the pathways involved in HDL-mediated bidirectional flux of sRNAs between immune cells. To overcome these technical limitations, SYTO RNASelect, a lipid-penetrating RNA dye, was used to quantify a) overall HDL-sRNA content, b) bidirectional flux of sRNAs between HDL and immune cells, c) HDL-mediated intercellular communication between immune cells, and d) HDL-mediated RNA export changes in disease. Live cell imaging and loss-of-function assays indicate that the endo-lysosomal system plays a critical role in macrophage storage and export of HDL-sRNAs. These results identify HDL as a substantive mediator of intercellular communication between immune cells and demonstrate the importance of endocytosis for recipient cells of HDL-sRNAs. Utilizing a lipid-penetrating RNA-specific fluorescence dye, we were able to both quantify the absolute concentration of sRNAs transported by HDL and characterize HDL-mediated intercellular RNA transport between immune cells.


Subject(s)
RNA, Small Untranslated , RNA, Small Untranslated/genetics , RNA, Small Untranslated/metabolism , Lipoproteins, HDL , Endothelial Cells/metabolism , Macrophages/metabolism , Cell Communication , Dendritic Cells/metabolism
16.
J Biol Chem ; 298(6): 101952, 2022 06.
Article in English | MEDLINE | ID: mdl-35447119

ABSTRACT

Extracellular small RNAs (sRNAs) are abundant in many biofluids, but little is known about their mechanisms of transport and stability in RNase-rich environments. We previously reported that high-density lipoproteins (HDLs) in mice were enriched with multiple classes of sRNAs derived from the endogenous transcriptome, but also from exogenous organisms. Here, we show that human HDL transports tRNA-derived sRNAs (tDRs) from host and nonhost species, the profiles of which were found to be altered in human atherosclerosis. We hypothesized that HDL binds to tDRs through apolipoprotein A-I (apoA-I) and that these interactions are conferred by RNA-specific features. We tested this using microscale thermophoresis and electrophoretic mobility shift assays and found that HDL binds to tDRs and other single-stranded sRNAs with strong affinity but did not bind to double-stranded RNA or DNA. Furthermore, we show that natural and synthetic RNA modifications influenced tDR binding to HDL. We demonstrate that reconstituted HDL bound to tDRs only in the presence of apoA-I, and purified apoA-I alone were able to bind sRNA. Conversely, phosphatidylcholine vesicles did not bind tDRs. In summary, we conclude that HDL binds to single-stranded sRNAs likely through nonionic interactions with apoA-I. These results highlight binding properties that likely enable extracellular RNA communication and provide a foundation for future studies to manipulate HDL-sRNA interactions for therapeutic approaches to prevent or treat disease.


Subject(s)
Lipoproteins, HDL , RNA, Small Untranslated , Animals , Apolipoprotein A-I/metabolism , Atherosclerosis , Humans , Lipoproteins, HDL/chemistry , Lipoproteins, HDL/metabolism , Mice , Phosphatidylcholines , RNA, Small Untranslated/chemistry
17.
J Neurophysiol ; 129(3): 591-608, 2023 03 01.
Article in English | MEDLINE | ID: mdl-36651913

ABSTRACT

Detection of sounds is a fundamental function of the auditory system. Although studies of auditory cortex have gained substantial insight into detection performance using behaving animals, previous subcortical studies have mostly taken place under anesthesia, in passively listening animals, or have not measured performance at threshold. These limitations preclude direct comparisons between neuronal responses and behavior. To address this, we simultaneously measured auditory detection performance and single-unit activity in the inferior colliculus (IC) and cochlear nucleus (CN) in macaques. The spontaneous activity and response variability of CN neurons were higher than those observed for IC neurons. Signal detection theoretic methods revealed that the magnitude of responses of IC neurons provided more reliable estimates of psychometric threshold and slope compared with the responses of single CN neurons. However, pooling small populations of CN neurons provided reliable estimates of psychometric threshold and slope, suggesting sufficient information in CN population activity. Trial-by-trial correlations between spike count and behavioral response emerged 50-75 ms after sound onset for most IC neurons, but for few neurons in the CN. These results highlight hierarchical differences between neurometric-psychometric correlations in CN and IC and have important implications for how subcortical information could be decoded.NEW & NOTEWORTHY The cerebral cortex is widely recognized to play a role in sensory processing and decision-making. Accounts of the neural basis of auditory perception and its dysfunction are based on this idea. However, significantly less attention has been paid to midbrain and brainstem structures in this regard. Here, we find that subcortical auditory neurons represent stimulus information sufficient for detection and predict behavioral choice on a trial-by-trial basis.


Subject(s)
Auditory Cortex , Cochlear Nucleus , Inferior Colliculi , Animals , Inferior Colliculi/physiology , Auditory Perception/physiology , Auditory Cortex/physiology , Cochlear Nucleus/physiology , Neurons/physiology , Acoustic Stimulation , Auditory Pathways/physiology
18.
Ann Surg ; 278(2): e349-e359, 2023 08 01.
Article in English | MEDLINE | ID: mdl-36111847

ABSTRACT

OBJECTIVE: Our objective was to identify macrophage subpopulations and gene signatures associated with regenerative or fibrotic healing across different musculoskeletal injury types. BACKGROUND: Subpopulations of macrophages are hypothesized to fine tune the immune response after damage, promoting either normal regenerative, or aberrant fibrotic healing. METHODS: Mouse single-cell RNA sequencing data before and after injury were assembled from models of musculoskeletal injury, including regenerative and fibrotic mouse volumetric muscle loss (VML), regenerative digit tip amputation, and fibrotic heterotopic ossification. R packages Harmony , MacSpectrum , and Seurat were used for data integration, analysis, and visualizations. RESULTS: There was a substantial overlap between macrophages from the regenerative VML (2 mm injury) and regenerative bone models, as well as a separate overlap between the fibrotic VML (3 mm injury) and fibrotic bone (heterotopic ossification) models. We identified 2 fibrotic-like (FL 1 and FL 2) along with 3 regenerative-like (RL 1, RL 2, and RL 3) subpopulations of macrophages, each of which was transcriptionally distinct. We found that regenerative and fibrotic conditions had similar compositions of proinflammatory and anti-inflammatory macrophages, suggesting that macrophage polarization state did not correlate with healing outcomes. Receptor/ligand analysis of macrophage-to-mesenchymal progenitor cell crosstalk showed enhanced transforming growth factor ß in fibrotic conditions and enhanced platelet-derived growth factor signaling in regenerative conditions. CONCLUSION: Characterization of macrophage subtypes could be used to predict fibrotic responses following injury and provide a therapeutic target to tune the healing microenvironment towards more regenerative conditions.


Subject(s)
Muscle, Skeletal , Ossification, Heterotopic , Mice , Animals , Macrophages , Wound Healing/physiology , Platelet-Derived Growth Factor
19.
Opt Express ; 31(24): 40557-40572, 2023 Nov 20.
Article in English | MEDLINE | ID: mdl-38041353

ABSTRACT

Ocean reflectance inversion algorithms provide many products used in ecological and biogeochemical models. While a number of different inversion approaches exist, they all use only spectral remote-sensing reflectances (Rrs(λ)) as input to derive inherent optical properties (IOPs) in optically deep oceanic waters. However, information content in Rrs(λ) is limited, so spectral inversion algorithms may benefit from additional inputs. Here, we test the simplest possible case of ingesting optical data ('seeding') within an inversion scheme (the Generalized Inherent Optical Property algorithm framework default configuration (GIOP-DC)) with both simulated and satellite datasets of an independently known or estimated IOP, the particulate backscattering coefficient at 532 nm (bbp(532)). We find that the seeded-inversion absorption products are substantially different and more accurate than those generated by the standard implementation. On global scales, seasonal patterns in seeded-inversion absorption products vary by more than 50% compared to absorption from the GIOP-DC. This study proposes one framework in which to consider the next generation of ocean color inversion schemes by highlighting the possibility of adding information collected with an independent sensor.

20.
Chemistry ; 29(66): e202302664, 2023 Nov 24.
Article in English | MEDLINE | ID: mdl-37608784

ABSTRACT

Electroorganic synthesis is generally considered to be a green alternative to conventional redox reactions. Electrochemical reductions, however, are less advantageous in terms of sustainability, as sacrificial metal anodes are often employed. Divided cell operation avoids contact of the reduction products with the anode and allows for convenient solvent oxidation, enabling metal free greener electrochemical reductions. However, the ion exchange membranes required for divided cell operation on a commercial scale are not amenable to organic solvents, which hinders their applicability. Herein, we demonstrate that electrochemical reduction of oxidatively sensitive compounds can be carried out in an undivided cell without sacrificial metal anodes by controlling the mass transport to a small surface area electrode. The concept is showcased by an electrochemical method for the reductive cleavage of aryl disulfides. Fine tuning of the electrode surface area and current density has enabled the preparation of a wide variety of thiols without formation of any oxidation side products. This strategy is anticipated to encourage further research on greener, metal free electrochemical reductions.

SELECTION OF CITATIONS
SEARCH DETAIL