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  1. Artikel ; Online: A model for organization and regulation of nuclear condensates by gene activity

    Halima H. Schede / Pradeep Natarajan / Arup K. Chakraborty / Krishna Shrinivas

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Band 15

    Abstract: Abstract Condensation by phase separation has recently emerged as a mechanism underlying many nuclear compartments essential for cellular functions. Nuclear condensates enrich nucleic acids and proteins, localize to specific genomic regions, and often ... ...

    Abstract Abstract Condensation by phase separation has recently emerged as a mechanism underlying many nuclear compartments essential for cellular functions. Nuclear condensates enrich nucleic acids and proteins, localize to specific genomic regions, and often promote gene expression. How diverse properties of nuclear condensates are shaped by gene organization and activity is poorly understood. Here, we develop a physics-based model to interrogate how spatially-varying transcription activity impacts condensate properties and dynamics. Our model predicts that spatial clustering of active genes can enable precise localization and de novo nucleation of condensates. Strong clustering and high activity results in aspherical condensate morphologies. Condensates can flow towards distant gene clusters and competition between multiple clusters lead to stretched morphologies and activity-dependent repositioning. Overall, our model predicts and recapitulates morphological and dynamical features of diverse nuclear condensates and offers a unified mechanistic framework to study the interplay between non-equilibrium processes, spatially-varying transcription, and multicomponent condensates in cell biology.
    Schlagwörter Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2023-07-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Chemoselective Ullmann Reaction of α‑Trisubstituted Thioamides

    Anwesha Bhattacharya / Annaram Thirupathi / Pradeep Natarajan / Saravanan Peruncheralathan

    ACS Omega, Vol 6, Iss 32, Pp 21169-

    Synthesis of Novel 2‑Iminobenzothiolanes

    2021  Band 21180

    Schlagwörter Chemistry ; QD1-999
    Sprache Englisch
    Erscheinungsdatum 2021-08-01T00:00:00Z
    Verlag American Chemical Society
    Dokumenttyp Artikel ; Online
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  3. Artikel ; Online: Trends in cholesterol testing during the COVID-19 pandemic

    Esra D. Gumuser / Sara Haidermota / Phoebe Finneran / Pradeep Natarajan / Michael C. Honigberg

    American Journal of Preventive Cardiology, Vol 6, Iss , Pp 100152- (2021)

    2021  

    Abstract: Objective: To characterize trends in cholesterol testing since the start of the COVID-19 pandemic. Methods: We extracted testing for total cholesterol performed in adults ≥40 years old within the Mass General Brigham healthcare system between March and ... ...

    Abstract Objective: To characterize trends in cholesterol testing since the start of the COVID-19 pandemic. Methods: We extracted testing for total cholesterol performed in adults ≥40 years old within the Mass General Brigham healthcare system between March and September 2020, as well those performed between March and September 2019 (reference period). Weekly cholesterol testing rates during the 2020 vs. 2019 study periods were compared using the paired samples t-test. Secondary analyses compared testing volumes and patient characteristics during the first vs. second half of the 2020 study period. Results: The study sample included 296,599 tests for total cholesterol performed in 220,215 individuals. The mean (SD) weekly cholesterol tests performed were 6,361 (682) in 2019 vs. 3,867 (2,373) in 2020 (P = 2.6 × 10−5), representing an overall decline of 39.2%. However, weekly testing rates in 2020 were not uniform. Greatest reductions coincided with the “first wave” of the pandemic (March-May 2020), with up to 92% reductions in testing observed. In the first 14 weeks of each study period (March to mid-June), weekly testing rates were 71.8% lower in 2020. Among individuals tested in 2020, those tested between March and mid-June had substantially lower total cholesterol compared with individuals tested after mid-June (174.2 vs. 181.5 mg/dL, P<2.2 × 10−16). Conclusions: In a large integrated healthcare system, cholesterol testing rates were 39% lower between March-September 2020 compared with the same time period in 2019. Mechanisms for safely facilitating cholesterol testing and management for high-risk patients will be important as COVID-19 re-surges across the U.S. until widespread vaccination and population immunity allow resumption of routine preventive care.
    Schlagwörter Cardiovascular disease ; Primary prevention ; Secondary prevention ; Risk factors ; Lipids and cholesterol ; Covid-19 ; Diseases of the circulatory (Cardiovascular) system ; RC666-701 ; Public aspects of medicine ; RA1-1270
    Thema/Rubrik (Code) 630
    Sprache Englisch
    Erscheinungsdatum 2021-06-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Genome-wide discovery for diabetes-dependent triglycerides-associated loci.

    Margaret Sunitha Selvaraj / Kaavya Paruchuri / Sara Haidermota / Rachel Bernardo / Stephen S Rich / Gina M Peloso / Pradeep Natarajan

    PLoS ONE, Vol 17, Iss 10, p e

    2022  Band 0275934

    Abstract: Purpose We aimed to discover loci associated with triglyceride (TG) levels in the context of type 2 diabetes (T2D). We conducted a genome-wide association study (GWAS) in 424,120 genotyped participants of the UK Biobank (UKB) with T2D status and TG ... ...

    Abstract Purpose We aimed to discover loci associated with triglyceride (TG) levels in the context of type 2 diabetes (T2D). We conducted a genome-wide association study (GWAS) in 424,120 genotyped participants of the UK Biobank (UKB) with T2D status and TG levels. Methods We stratified the cohort based on T2D status and conducted association analyses of TG levels for genetic variants with minor allele count (MAC) at least 20 in each stratum. Effect differences of genetic variants by T2D status were determined by Cochran's Q-test and we validated the significantly associated variants in the Mass General Brigham Biobank (MGBB). Results Among 21,176 T2D and 402,944 non-T2D samples from UKB, stratified GWAS identified 19 and 315 genomic risk loci significantly associated with TG levels, respectively. Only chr6p21.32 exhibited genome-wide significant heterogeneity (I2 = 98.4%; pheterogeneity = 2.1x10-15), with log(TG) effect estimates of -0.066 (95%CI: -0.082, -0.050) and 0.002 (95%CI: -0.002, 0.006) for T2D and non-T2D, respectively. The lead variant rs9274619:A (allele frequency 0.095) is located 2Kb upstream of the HLA-DQB1 gene, between HLA-DQB1 and HLA-DQA2 genes. We replicated this finding among 25,137 participants (6,951 T2D cases) of MGBB (pheterogeneity = 9.5x10-3). Phenome-wide interaction association analyses showed that the lead variant was strongly associated with a concomitant diagnosis of type 1 diabetes (T1D) as well as diabetes-associated complications. Conclusion In conclusion, we identified an intergenic variant near HLA-DQB1/DQA2 significantly associates with decreased triglycerides only among those with T2D and highlights an immune overlap with T1D.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 616
    Sprache Englisch
    Erscheinungsdatum 2022-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
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  5. Artikel ; Online: Discovery of potential lumazine synthase antagonists for pathogens involved in bacterial meningitis

    Manne Munikumar / Pradeep Natarajan / Umamaheswari Amineni / K.V. Radha Krishna

    Informatics in Medicine Unlocked, Vol 15, Iss , Pp - (2019)

    In silico study

    2019  

    Abstract: Bacterial meningitis, an infection of the membranes (meninges) and cerebrospinal fluid (CSF) surrounding the brain and spinal cord, is a major cause of death and disability worldwide. Streptococcus pneumonia, Neisseria meningitidis, Haemophilus ... ...

    Abstract Bacterial meningitis, an infection of the membranes (meninges) and cerebrospinal fluid (CSF) surrounding the brain and spinal cord, is a major cause of death and disability worldwide. Streptococcus pneumonia, Neisseria meningitidis, Haemophilus influenzae type b and Staphylococcus aureus are the predominant pathogens of bacterial meningitis. In our previous study, we have identified lumazine synthase as a common drug target in pathogens of bacterial meningitis. The three dimensional (3D) structure of lumazine synthase complex with 5-nitro-6-ribityl-amino-2,4(1 h, 3 h)-pyrimidinedione (INI) was generated based on PDBID: 1RVV as a template using Modeller 9v12. Multiple docking strategies including rigid receptor docking (RRD), QPLD and IFD were performed for lumazine synthase with 29 existing inhibitors, and screened for 13050 ligands, respectively. Three stages of RRD (HTVS, SP, XP) were carried out using Glide v5.9 resulted in 134 leads. The 134 leads were compared to 29 inhibitors; eight best leads were obtained, which were further utilized for QPLD-MM-GBSA analysis. Eight compounds had a least docking score, lower binding free energy, and better binding orientation towards lumazine synthase. Furthermore, to analyse the stability of the lumazine synthase, the lead1 complex was subjected to 50 ns MD simulations and found to be stable. The results from multiple docking analysis and MD simulations affirmed that lead1 may be a promising inhibitor for efficient inhibition of lumazine synthase activity in common pathogens of bacterial meningitis. Keywords: Bacterial meningitis, Lumazine synthase, Rigid receptor docking, QM-Polarized ligand docking, Induced fit docking, Molecular dynamics simulations
    Schlagwörter Computer applications to medicine. Medical informatics ; R858-859.7
    Thema/Rubrik (Code) 540
    Sprache Englisch
    Erscheinungsdatum 2019-01-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Association of premature menopause with incident pulmonary hypertension

    Michael C Honigberg / Aniruddh P Patel / Tim Lahm / Malissa J Wood / Jennifer E Ho / Puja Kohli / Pradeep Natarajan

    PLoS ONE, Vol 16, Iss 3, p e

    A cohort study.

    2021  Band 0247398

    Abstract: Background Several forms of pulmonary hypertension (PH) disproportionately affect women. Animal and human studies suggest that estradiol exerts mixed effects on the pulmonary vasculature. Whether premature menopause represents a risk factor for PH is ... ...

    Abstract Background Several forms of pulmonary hypertension (PH) disproportionately affect women. Animal and human studies suggest that estradiol exerts mixed effects on the pulmonary vasculature. Whether premature menopause represents a risk factor for PH is unknown. Methods and findings In this cohort study, women in the UK Biobank aged 40-69 years who were postmenopausal and had complete data available on reproductive history were included. Premature menopause, defined as menopause occurring before age 40 years. Postmenopausal women without premature menopause served as the reference group. The primary outcome was incident PH, ascertained by appearance of a qualifying ICD code in the participant's UK Biobank study record. Of 136,715 postmenopausal women included, 5,201 (3.8%) had premature menopause. Participants were followed up for a median of 11.1 (interquartile range 10.5-11.8) years. The primary outcome occurred in 38 women (0.73%) with premature menopause and 409 (0.31%) without. After adjustment for age, race, ever-smoking, body-mass index, systolic blood pressure, antihypertensive medication use, non-high-density lipoprotein cholesterol, cholesterol-lowering medication use, C-reactive protein, prevalent type 2 diabetes, obstructive sleep apnea, heart failure, mitral regurgitation, aortic stenosis, venous thromboembolism, forced vital capacity (FVC), the forced expiratory volume in 1 second-to-FVC ratio, use of menopausal hormone therapy, and hysterectomy status, premature menopause was independently associated with PH (hazard ratio 2.13, 95% CI 1.31-3.23, P<0.001). In analyses of alternate menopausal age thresholds, risk of PH appeared to increase progressively with younger age at menopause (Ptrend <0.001), with 4.8-fold risk in women with menopause before age 30 years (95% CI 1.82-12.74, P = 0.002). Use of menopausal hormone therapy did not modify the association of premature menopause with PH. Conclusions Premature menopause may represent an independent risk factor for PH in women. Further ...
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 610
    Sprache Englisch
    Erscheinungsdatum 2021-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Genetics of smoking and risk of clonal hematopoiesis

    Michael G. Levin / Tetsushi Nakao / Seyedeh M. Zekavat / Satoshi Koyama / Alexander G. Bick / Abhishek Niroula / Benjamin Ebert / Scott M. Damrauer / Pradeep Natarajan

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Band 5

    Abstract: Abstract Clonal hematopoiesis of indeterminate potential (CHIP) and mosaic chromosomal alterations (mCAs) represent two forms of clonal hematopoiesis where clones bearing expanded somatic mutations have been linked to both oncologic and non-oncologic ... ...

    Abstract Abstract Clonal hematopoiesis of indeterminate potential (CHIP) and mosaic chromosomal alterations (mCAs) represent two forms of clonal hematopoiesis where clones bearing expanded somatic mutations have been linked to both oncologic and non-oncologic clinical outcomes including atherosclerosis and all-cause mortality. Epidemiologic studies have highlighted smoking as an important driver of somatic mutations across multiple tissues. However, establishing the causal role of smoking in clonal hematopoiesis has been limited by observational study designs, which may suffer from confounding and reverse-causality. We performed two complementary analyses to investigate the role of smoking in mCAs and CHIP. First, using an observational study design among UK Biobank participants, we confirmed strong associations between smoking and mCAs. Second, using two-sample Mendelian randomization, smoking was strongly associated with mCA but not with CHIP. Overall, these results support a causal association between smoking and mCAs and suggest smoking may variably shape the fitness of clones bearing somatic mutations.
    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2022-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: Heart rate variability with photoplethysmography in 8 million individuals

    Aravind Natarajan, PhD / Alexandros Pantelopoulos, PhD / Hulya Emir-Farinas, PhD / Pradeep Natarajan, MD

    The Lancet: Digital Health, Vol 2, Iss 12, Pp e650-e

    a cross-sectional study

    2020  Band 657

    Abstract: Summary: Background: Heart rate variability, or the variation in the time interval between consecutive heart beats, is a non-invasive dynamic metric of the autonomic nervous system and an independent risk factor for cardiovascular death. Consumer wrist- ... ...

    Abstract Summary: Background: Heart rate variability, or the variation in the time interval between consecutive heart beats, is a non-invasive dynamic metric of the autonomic nervous system and an independent risk factor for cardiovascular death. Consumer wrist-worn tracking devices using photoplethysmography, such as Fitbit, now provide the unique potential of continuously measuring surrogates of sympathetic and parasympathetic nervous system activity through the analysis of interbeat intervals. We aimed to leverage wrist-worn trackers to derive and describe diverse measures of cardiac autonomic function among Fitbit device users. Methods: In this cross-sectional study, we collected interbeat interval data that are sent to a central database from Fitbit devices during a randomly selected 24 h period. Age, sex, body-mass index, and steps per day in the 90 days preceding the measurement were extracted. Interbeat interval data were cleaned and heart rate variability features were computed. We analysed heart rate variability metrics across the time (measured via the root mean square of successive RR interval differences [RMSSD] and SD of the RR interval [SDRR]), frequency (measured by high-frequency and low-frequency power), and graphical (measured by Poincare plots) domains. We considered 5 min windows for the time and frequency domain metrics and 60 min measurements for graphical domain metrics. Data from participants were analysed to establish the correlation between heart rate variability metrics and age, sex, time of day, and physical activity. We also determined benchmarks for heart rate variability (HRV) metrics among the users. Findings: We included data from 8 203 261 Fitbit users, collected on Sept 1, 2018. HRV metrics decrease with age, and parasympathetic function declines faster than sympathetic function. We observe a strong diurnal variation in the heart rate variability. SDRR, low-frequency power, and Poincare S2 show a significant variation with sex, whereas such a difference is not seen with RMSSD, ...
    Schlagwörter Computer applications to medicine. Medical informatics ; R858-859.7
    Thema/Rubrik (Code) 590
    Sprache Englisch
    Erscheinungsdatum 2020-12-01T00:00:00Z
    Verlag Elsevier
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    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel: Coupled Structural and Kinetic Model of Lignin Fast Pyrolysis

    Yanez, Abraham J / Linda J. Broadbelt / Pradeep Natarajan / Ross Mabon / Wenjun Li

    Energy & fuels. 2018 Feb. 15, v. 32, no. 2

    2018  

    Abstract: Lignocellulosic biomass is a promising feedstock for renewable fuels and chemical intermediates; in particular, lignin attracts attention for its favorable chemical composition. One obstacle to lignin utilization and valorization is the unknown chemical ... ...

    Abstract Lignocellulosic biomass is a promising feedstock for renewable fuels and chemical intermediates; in particular, lignin attracts attention for its favorable chemical composition. One obstacle to lignin utilization and valorization is the unknown chemical mechanism that gives rise to the complex product distributions observed upon deconstruction. Among possible deconstruction chemistries, fast pyrolysis is promising due to its short residence time, thus enabling high-volume production. However, the chemistry is inherently complex, thereby hampering the creation of detailed kinetic models describing pathways to specific low molecular products. To this end, we created a detailed kinetic model of lignin decomposition via pyrolysis comprised of 4313 reactions and 1615 species based on pathways suggested by pyrolysis of model compounds in the literature. Using a rule-based reaction network generation approach, a pathways-level reaction network is proposed to predict the evolution of macromolecular species and the formation of various low molecular weight products identified from experimental studies. This reaction network is coupled to a structural model of wheat straw lignin via a kinetic Monte Carlo framework to simulate lignin fast pyrolysis. The mass yields of and speciation within four commonly observed fractions, viz., light gases, an aqueous phase containing water and small oxygenates, char, and a highly complex aromatic fraction, are compared to an experimental report of a putatively similar biomass source. Additional capabilities of the model include the time-resolved prediction of volatilization profiles and the evolution of the molecular weight distribution, which may assist in efforts to valorize lignin to a higher degree than that achieved by current approaches.
    Schlagwörter biomass ; chemical composition ; feedstocks ; fuels ; gases ; kinetics ; lignin ; lignocellulose ; models ; molecular weight ; prediction ; pyrolysis ; renewable energy sources ; volatilization ; wheat straw
    Sprache Englisch
    Erscheinungsverlauf 2018-0215
    Umfang p. 1822-1830.
    Erscheinungsort American Chemical Society
    Dokumenttyp Artikel
    ZDB-ID 1483539-3
    ISSN 1520-5029 ; 0887-0624
    ISSN (online) 1520-5029
    ISSN 0887-0624
    DOI 10.1021/acs.energyfuels.7b03311
    Datenquelle NAL Katalog (AGRICOLA)

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  10. Artikel ; Online: INTERVENTIONS TO MITIGATE CARDIOVASCULAR DISEASE RISK AFTER ADVERSE PREGNANCY OUTCOMES

    Amanda R. Jowell / Amy A. Sarma / Martha Gulati Erin D. Michos / Arthur J. Vaught / Pradeep Natarajan / Camille E. Powe / Michael C. Honigberg

    American Journal of Preventive Cardiology, Vol 7, Iss , Pp 100266- (2021)

    A REVIEW

    2021  

    Schlagwörter Diseases of the circulatory (Cardiovascular) system ; RC666-701 ; Public aspects of medicine ; RA1-1270
    Sprache Englisch
    Erscheinungsdatum 2021-09-01T00:00:00Z
    Verlag Elsevier
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    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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