Nevin Manimala

Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2201208119. doi: 10.1073/pnas.2201208119. Epub 2022 Jul 18.

ABSTRACT

Completion of the Lassa virus (LASV) life cycle critically depends on the activities of the virally encoded, RNA-dependent RNA polymerase in replication and transcription of the viral RNA genome in the cytoplasm of infected cells. The contribution of cellular proteins to these processes remains unclear. Here, we applied proximity proteomics to define the interactome of LASV polymerase in cells under conditions that recreate LASV RNA synthesis. We engineered a LASV polymerase-biotin ligase (TurboID) fusion protein that retained polymerase activity and successfully biotinylated the proximal proteome, which allowed the identification of 42 high-confidence LASV polymerase interactors. We subsequently performed a small interfering RNA (siRNA) screen to identify those interactors that have functional roles in authentic LASV infection. As proof of principle, we characterized eukaryotic peptide chain release factor subunit 3a (eRF3a/GSPT1), which we found to be a proviral factor that physically associates with LASV polymerase. Targeted degradation of GSPT1 by a small-molecule drug candidate, CC-90009, resulted in strong inhibition of LASV infection in cultured cells. Our work demonstrates the feasibility of using proximity proteomics to illuminate and characterize yet-to-be-defined host-pathogen interactome, which can reveal new biology and uncover novel targets for the development of antivirals against highly pathogenic RNA viruses.

PMID:35858434 | DOI:10.1073/pnas.2201208119

Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2200732119. doi: 10.1073/pnas.2200732119. Epub 2022 Jul 19.

NO ABSTRACT

PMID:35858388 | DOI:10.1073/pnas.2200732119

Proc Natl Acad Sci U S A. 2022 Jul 19;119(29):e2114365119. doi: 10.1073/pnas.2114365119. Epub 2022 Jul 11.

ABSTRACT

Molecular analysis on the single-cell level represents a rapidly growing field in the life sciences. While bulk analysis from a pool of cells provides a general molecular profile, it is blind to heterogeneities between individual cells. This heterogeneity, however, is an inherent property of every cell population. Its analysis is fundamental to understanding the development, function, and role of specific cells of the same genotype that display different phenotypical properties. Single-cell mass spectrometry (MS) aims to provide broad molecular information for a significantly large number of cells to help decipher cellular heterogeneity using statistical analysis. Here, we present a sensitive approach to single-cell MS based on high-resolution MALDI-2-MS imaging in combination with MALDI-compatible staining and use of optical microscopy. Our approach allowed analyzing large amounts of unperturbed cells directly from the growth chamber. Confident coregistration of both modalities enabled a reliable compilation of single-cell mass spectra and a straightforward inclusion of optical as well as mass spectrometric features in the interpretation of data. The resulting multimodal datasets permit the use of various statistical methods like machine learning-driven classification and multivariate analysis based on molecular profile and establish a direct connection of MS data with microscopy information of individual cells. Displaying data in the form of histograms for individual signal intensities helps to investigate heterogeneous expression of specific lipids within the cell culture and to identify subpopulations intuitively. Ultimately, t-MALDI-2-MSI measurements at 2-µm pixel sizes deliver a glimpse of intracellular lipid distributions and reveal molecular profiles for subcellular domains.

PMID:35858333 | DOI:10.1073/pnas.2114365119

Chem Res Toxicol. 2022 Jul 20. doi: 10.1021/acs.chemrestox.2c00145. Online ahead of print.

ABSTRACT

Carcinogen and toxicant uptake by e-cigarette users have not been fully evaluated. In the study reported here, we recruited 30 e-cigarette users, 63 nonsmokers, and 33 cigarette smokers who gave monthly urine samples over a period of 4-6 months. Their product use status was confirmed by measurements of exhaled CO, urinary total nicotine equivalents, cyanoethyl mercapturic acid (CEMA), and total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol. Urinary biomarkers of exposure to the carcinogens acrolein (3-hydroxypropyl mercapturic acid, 3-HPMA), benzene (S-phenyl mercapturic acid, SPMA), acrylonitrile (CEMA), and a combination of crotonaldehyde, methyl vinyl ketone, and methacrolein (3-hydroxy-1-methylpropyl mercapturic acid, HMPMA) were quantified at each visit. Data from subject visits with CEMA > 27 pmol/mL were excluded from the statistical analysis of the results because of possible unreported exposures to volatile combustion products such as secondhand cigarette smoke or marijuana smoke exposure; this left 22 e-cigarette users with 4 or more monthly visits and all 63 nonsmokers. Geometric mean levels of 3-HPMA (1249 versus 679.3 pmol/mL urine) were significantly higher (P = 0.003) in e-cigarette users than in nonsmokers, whereas levels of SPMA, CEMA, and HMPMA did not differ between these two groups. All analytes were significantly higher in cigarette smokers than in either e-cigarette users or nonsmokers. The results of this unique multimonth longitudinal study demonstrate consistent significantly higher uptake of the carcinogen acrolein in e-cigarette users versus nonsmokers, presenting a warning signal regarding e-cigarette use.

PMID:35858275 | DOI:10.1021/acs.chemrestox.2c00145

J Speech Lang Hear Res. 2022 Jul 19:1-12. doi: 10.1044/2022_JSLHR-20-00722. Online ahead of print.

ABSTRACT

PURPOSE: Core lexicon measures have received growing attention in research. They are intended to provide clinicians with a clinician-friendly means to quantify word retrieval ability in discourse based on normal expectations of discourse production for specific discourse elicitation tasks. To date, different criteria have been used to develop core lexicon measures by groups of researchers. The need for statistical guidance in pursuit of the psychologically robust measure has been recognized.

AIMS: This study was to investigate the best criterion for accurate measurement. Specifically, we focused on two criteria (frequency vs. percentage) that have previously been used for the development of core lexicon measures.

METHOD: Core lexicon measures consisting of five different checklists by word class (verbs, nouns, adjectives, adverbs, and function words) and developed by the two criteria were applied to language samples produced by 470 cognitively healthy adults. Performance in word retrieval ability at the discourse level was modeled as a latent variable based on the observed proportions of the production of core lexicon items in two different sets of core lexicon measures using structural equation modeling.

RESULTS: Results indicated that both criterion for core lexicon measures capture word retrieval ability in discourse. Greater residual variances were found in the core lexicon measure established by the percentage criterion compared to the one established by the frequency criterion. This indicates that the measure based on the percentage criterion is more affected by measurement errors.

CONCLUSIONS: The findings provide evidence that the frequency criterion is better to use for the development of core lexicon measures for core nouns, verbs, adjectives, and adverbs, but not for function words. However, our findings are limited to core lexicon measures based on language samples elicited by wordless picture books. This may not be easily applied to other core lexicon measures that use different discourse elicitation tasks due to the difference in quality and quantity of language samples. Ideally, the same approach should be replicated to evaluate the appropriateness of respective criteria in the development of core lexicon measures.

SUPPLEMENTAL MATERIAL: https://doi.org/10.23641/asha.20304144.

PMID:35858271 | DOI:10.1044/2022_JSLHR-20-00722

Am J Speech Lang Pathol. 2022 Jul 12;31(4):1845-1853. doi: 10.1044/2022_AJSLP-21-00385. Epub 2022 Jul 7.

ABSTRACT

PURPOSE: The tongue plays a key role in bolus propulsion during swallowing, with reduced lingual pressure generation representing a risk factor for impaired swallowing safety and efficiency. We compared lingual pressure generation capacity in people with Parkinson disease (PwPD), people with amyotrophic lateral sclerosis (PwALS), and healthy older adults. We hypothesized that both patient cohorts would demonstrate reduced maximum anterior isometric pressure (MAIP) and regular effort saliva swallow (RESS) pressures compared with healthy controls, with the greatest reductions expected in the ALS cohort.

METHOD: We enrolled 20 PwPD, 18 PwALS, and 20 healthy adults over 60 years of age. The Iowa Oral Performance Instrument was used to measure MAIP, RESS, and lingual functional reserve (LFR, i.e., MAIP – RESS). Descriptive statistics were calculated; between-groups differences were explored using univariate analyses of variance and post hoc Sidak tests with alpha set at .05.

RESULTS: Mean MAIPs for the PD, ALS, and heathy cohorts were 54.7, 33.5, and 47.4 kPa, respectively. Significantly lower MAIP was found in PwALS compared with PwPD and healthy controls. RESS values did not differ significantly across groups. LFR was significantly higher in PwPD versus PwALS and healthy controls.

CONCLUSIONS: Lingual pressure generation capacity and functional reserve were reduced in PwALS, but not in PwPD, beyond changes seen with healthy aging. Both patient cohorts displayed preserved lingual pressure during saliva swallows. Future studies exploring longitudinal changes in tongue pressure generation on isometric and saliva swallowing tasks will be needed to confirm whether tongue pressure measures serve as noninvasive clinical biomarkers of swallowing impairment.

PMID:35858265 | DOI:10.1044/2022_AJSLP-21-00385

J Speech Lang Hear Res. 2022 Jul 18;65(7):2594-2607. doi: 10.1044/2022_JSLHR-22-00141. Epub 2022 Jul 5.

ABSTRACT

PURPOSE: The purpose of this meta-analysis was to assess the frequency of sex, race, and ethnicity reporting and proportional representation in funded, noncancerous voice clinical trials to determine the state of compliance with National Institutes of Health (NIH) guidelines for inclusivity in clinical research.

METHOD: Clinical trials registered with the NIH/U.S. National Library of Medicine between January 1988 and September 2021 were analyzed. Primary reports of the trials were obtained from clinicaltrials.gov and PubMed. Outcomes included the proportion of trials reporting sex, race, and ethnicity and the proportion of participants by sex, race, and ethnicity in the trials. Descriptive statistics and chi-square tests were used to analyze the data with 95% confidence intervals (CIs) reported.

RESULTS: The search yielded 46 research studies. After inclusion and exclusion criteria were applied and attempts to locate studies were conducted, 11 total articles were ultimately evaluated. Descriptively, there were more female subjects, yet overall, no significant difference in sex distribution (χ² = 0.07, p = .75, 95% CI [-0.25, -0.19]). Race and ethnicity were only reported in two clinical trials. Black participants were underrepresented in one clinical trial (χ² = 4.93, p = .02, 95% CI [-0.11, -0.02]), whereas Hispanic participants were underrepresented in a second trial (χ² = 11.27, p < .00, 95% CI [-0.20, – 0.13]).

CONCLUSIONS: This preliminary analysis highlights the disparities in race and ethnicity recruitment and reporting in noncancerous voice clinical trials. There is a need for strategic recruitment strategies and improved reporting practices to adhere to the NIH inclusivity directives.

PMID:35858261 | DOI:10.1044/2022_JSLHR-22-00141

J Speech Lang Hear Res. 2022 Jul 18;65(7):2586-2593. doi: 10.1044/2022_JSLHR-21-00632. Epub 2022 Jul 5.

ABSTRACT

PURPOSE: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that affects bulbar functions including speech and voice. Voice onset time (VOT) was examined in speakers with ALS in early and late stages to explore the coordination of the articulatory and phonatory systems during speech production.

METHOD: VOT was measured in nonword /bap/ produced by speakers with early-stage ALS (n = 11), late-stage ALS (n = 6), and healthy controls (n = 13), and compared with speech performance decline (a marker of disease progression) in ALS.

RESULTS: Overall comparison of the VOT values among the three groups showed a significant difference, F(2,27) = 11.71, p < .01. Speakers in late-stage ALS displayed longer voicing lead (negative VOT) than both healthy speakers and speakers in early-stage ALS. VOT was also significantly negatively correlated with speech performance (i.e., Intelligible Speaking Rate), r(15) = .74, p < .01.

CONCLUSIONS: Speakers with more severe ALS showed greater occurrence of voicing lead and longer voicing lead. Findings show voicing precedes articulatory onset with disease progression in the production of bilabial stops, which suggests that the relative timing of coordination between the supralaryngeal structures and the phonatory system is affected in the late stage of ALS.

PMID:35858258 | DOI:10.1044/2022_JSLHR-21-00632

J Speech Lang Hear Res. 2022 Jul 18;65(7):2677-2690. doi: 10.1044/2022_JSLHR-21-00522. Epub 2022 Jul 6.

ABSTRACT

PURPOSE: Individual-randomized trials are the gold standard for testing the efficacy and effectiveness of drugs, devices, and behavioral interventions. Health care delivery, educational, and programmatic interventions are often complex, involving multiple levels of change and measurement precluding individual randomization for testing. Cluster-randomized trials and cluster-randomized stepped-wedge trials are alternatives where the intervention is allocated at the group level, such as a clinic or a school, and the outcomes are measured at the person level. These designs are introduced along with the statistical implications of similarities among individuals within the same cluster. We also illustrate the parameters that have the most impact on the likelihood of detecting intervention effects, which must be considered when planning these trials.

CONCLUSION: Cluster-randomized and stepped-wedge designs should be considered by researchers as experimental alternatives to individual-randomized trials when testing speech, language, and hearing care interventions in real-world settings.

PMID:35858257 | DOI:10.1044/2022_JSLHR-21-00522

Am J Physiol Endocrinol Metab. 2022 Jul 20. doi: 10.1152/ajpendo.00052.2022. Online ahead of print.

ABSTRACT

The objective of this study was to investigate the effect of dietary fatty acid (FA) composition on bile acid (BA) metabolism in a pig model of NAFLD, by using a multiomics approach combined with histology and serum biochemistry. Thirty 20-d-old Iberian pigs pair-housed in pens were randomly assigned to receive 1 of 3 hypercaloric diets for 10 weeks: 1) lard-enriched (LAR; n=5 pens), 2) olive oil-enriched (OLI, n=5), and 3) coconut oil-enriched (COC; n=5). Animals were euthanized on week 10 after blood sampling, and liver, colon and distal ileum (DI) were collected for histology, metabolomics, and transcriptomics. Data were analyzed by multivariate and univariate statistics. Compared with OLI and LAR, COC increased primary and secondary BAs in liver, plasma and colon. In addition, both COC and OLI reduced circulating fibroblast growth factor 19, increased hepatic necrosis, composite lesion score, and liver enzymes in serum, and upregulated genes involved in hepatocyte proliferation and DNA repair. The severity of liver disease in COC and OLI pigs was associated with increased levels of phosphatidylcholines, medium-chain triacylglycerides, trimethylamine-N-oxide, and long-chain acylcarnitines in the liver, and the expression of pro-fibrotic markers in DI, but not with changes in the composition or size of BA pool. In conclusion, our results indicate a role of dietary FAs in the regulation of BA metabolism and progression of NAFLD. Interventions that aim to modify the composition of dietary FAs, rather than to regulate BA metabolism or signaling, may be more effective in the treatment of NAFLD.

PMID:35858244 | DOI:10.1152/ajpendo.00052.2022