bluuebunny/crossref_metadata_2025_split huggingface dataset:
Traditional Herbal Medicine Use Tripled the Risk of Multi-organ Dysfunction Syndrome in a Pediatric Intensive Care Unit in Ethiopia: A Prospective Cohort Study
Authors: Teshager Nahom Worku , Amare Ashenafi Tazebew , Tamirat Koku Sisay , Zeleke Mulualem Endeshaw , Taddese Asefa Adimasu 
Published: May 2023

AbstractObjectiveThis study aimed to investigate the incidence and predictors of MODS in a Pediatric Intensive Care Unit in Ethiopia, with a focus on the association between traditional herbal medicine (THM) use and the risk of MODS.MethodsThis was a single-center prospective cohort study conducted at a PICU in Ethiopia. The study enrolled eligible patients aged one month to 18 years admitted to the PICU during the study period. Recruitment was made at the time of admission to the PICU. Data on demographic characteristics, medical history, clinical and laboratory data, and outcome measures using standard case record forms, physical examination, and patient document reviews. The predictors of MODS were assessed using Cox proportional hazards models, with a focus on the association between traditional herbal medicine use and the risk of MODS.ResultsA total of 310 patients were included in the final analysis, with a median age of 48 months and a male-to-female ratio of 1.5:1. The proportion and incidence of MODS were 30.96% (95% CI:25.8, 36.6) and 7.71(95% CI: 6.10, 9.40) per 100-person-day observation respectively. Renal failure (17.74%), neurologic failure (15.16%), and heart failure (14.52%) were the leading organ failures identified. Nearly one-third of patients (32.9%) died in the PICU, of which 59.8% had MODS. The rate of mortality was higher in patients with MODS than in those without.The Cox proportional hazards model identified renal disease (AHR=6.32 (95%CI: 3.17,12.61)), intake of traditional herbal medication (AHR=2.45, 95% CI:1.29,4.65), modified Pediatric Index of Mortality 2 (mPIM 2) score (AHR=1.54 (95% CI: 1.38,1.71), and critical illness diagnoses (AHR=2.68 (95% CI: 1.77,4.07)) as predictors of MODS. Patients who used THM had a threefold increased risk of MODS (AHR) of 2.45 (95% CI: 1.29, 4.65).ConclusionThe incidence of MODS was high. Renal disease, THM use, mPIM 2 scores, and critical illness diagnoses were independent predictors of MODS. A threefold increase in the risk of MODS was seen in patients who used TMH. Healthcare providers should be aware of risks associated with THM, and educate caregivers about the potential harms of these products. Future studies with larger sample sizes and more comprehensive outcome measures are needed.
Diet-induced obesity dysregulates chromatin oxygen sensing regulating efferocytosis in macrophages
Authors: Takahashi Kentaro , Liu Jinghua , Jackson Jasmine R. , Thiruppathi Muthusamy , Benevolenskaya Elizaveta V. , Koh Timothy J. , Urao Norifumi 
Published: May 2023

AbstractMacrophages are plastic cell populations that normally adapt to their environment. Cellular adaptation to hypoxia occurs through transcription factors including hypoxia-inducible factors, and hypoxia-inducible transcriptions are further regulated by chromatin response through histone modification including histone methylation. However, the role of histone methylation in the hypoxia response of macrophages is not well understood. As obesity is associated with dysregulated macrophage functions, we investigated whether hypoxia response is cell-intrinsically dysregulated in macrophages in obesity.In mouse bone marrow-derived macrophages (BMDMs), immunoblotting revealed that 1% hypoxia rapidly increases the global levels of histone 3 methylations. We found that hypoxia-induction of histone 3-lysine 4 tri-methylation (H3K4me3) is specifically inhibited in BMDMs from mice fed a high-fat diet (HFD-BMDMs) compared to BMDMs from mice fed a normal diet (ND-BMDMs). Multi-omics approach with ChIP-seq and RNA-seq identified that glycolysis-related pathways and genes includingAldoaare upregulated after prolonged hypoxia along with upregulated H3K4me3 in ND-BMDMs. In contrast, no pathway is associated with hypoxia-upregulated H3K4me3 peaks in HFD-BMDMs and hypoxia-inducedAldoaexpression is decreased in HFD-BMDMs, suggesting both the extent and the genome location of H3K4me3 response to hypoxia is dysregulated in obesity. Consistently, lactate accumulation and induction of histone lactylation under hypoxia are reduced in HFD-BMDMs. Furthermore, HFD-BMDMs exhibited decreased dying cell clearance under hypoxia due to the reduced capacity of anaerobic glycolysis. Competitive bone marrow transplantation of hematopoietic stem cells (HSCs) shows that HFD-induced long-term memory reflects the impaired dying cell clearance in differentiated BMDMs, which is rescued by inhibiting oxidative stress in HSCs.In summary, chromatin response to hypoxia associated with H3K4me3 enrichment governs transcriptions for anaerobic glycolysis and dying cell clearance under hypoxia. Obesity dysregulates the extent and the genome location of H3K4me3 enrichment, glycolysis, and dying cell clearance of BMDMs under hypoxia, which is initiated in HSPCs via oxidative stress.
CRGEM: Cellular Reprogramming using mechanism-driven Gene Expression Modulation
Authors: Mahadik Avani , Nitin  , Jose Justin , Singh Vivek 
Published: May 2023

AbstractIntroductionRegenerative medicine promises a cure for currently incurable diseases and pathological conditions. Its central idea is to leverage healthy cells to regenerate diseased cells, tissues or organs through the process of cellular reprogramming. The most common method to achieve this is by modulating the activity of specific transcription factors. However, the large number of protein-coding genes and transcription factors in humans and their complex interactions poses a challenge in identifying the most suitable ones for modulation. Here, we propose a computational workflow that facilitates the prediction of such transcription factors for achieving desired cellular reprogramming, along with highlighting their mechanistic basis in terms of the gene regulatory network of the target cell type.MethodsIn this paper, we propose a synergistic workflow that leverages existing computational tools: TransSynW, PAGA and SIGNET, a software – Cytoscape and two databases – TRRUST and UniProt. It uses single-cell transcriptome data of the starting and target cell types as inputs. We demonstrate this workflow by predicting suitable transcriptional modulations for reprogramming of human foreskin fibroblasts to oculomotor neurons.ResultsUsing the workflow, we hypothesized the core drivers for specific cellular reprogramming along with their functional understanding for experimental applications. The workflow predicted the transcription factors for modulation and provided insight into their differential expression dynamics and influence on the predicted gene regulatory network of the target cells.ConclusionOur computational workflow helps extract meaningful predictive and mechanistic insights from high-dimensional biological data, which otherwise is difficult to accomplish from individual tools alone. We believe this workflow can help researchers generate mechanistically founded hypotheses for achieving desired cellular reprogramming as a step towards regenerative medicine.HighlightsCombine computational tools as workflows to gain predictive and mechanistic insightsThe workflow predicts suitable transcription factors for targeted cellular reprogrammingGain insight into the influence of transcriptional modulation on gene regulatory networkThe workflow generates mechanistically founded hypotheses for transcriptional modulationRationalized experimental design for targeted cellular reprogramming for regenerative therapies
Conformational landscape of the transcription factor ATF4 is dominated by disordered-mediated inter-domain coupling
Authors: Patel Urval , Siang Steven , Potoyan Davit , Roche Julien 
Published: May 2023

ABSTRACTTransient intramolecular interactions between transactivation domain and DNA binding domain of transcription factors are known to play important functional roles, including modulation of DNA binding affinity and specificity. Similar type of inter-domain interactions has recently been reported for the transcription factor ATF4/CREB-2, a key regulator of the Integral Stress Response. In the case of ATF4, transient coupling between the transactivation and basic-leucine zipper (bZip) domains regulates the degree of phosphorylation of the disordered transactivation domain achievable by the casein kinase CK2. Despite the crucial importance of these inter-domain interactions, their structural and molecular basis remain ill-determined. In the present study, we use a combination of experimental and computational techniques to determine the precise nature of the long-range contacts established between the transactivation and bZip domains of ATF4 prior to its association with protein partners and DNA. Solution NMR spectroscopy experiments reveal that the isolated bZip domain of ATF4 is predominantly disordered and display evidence of conformational dynamics over a wide range of timescales. These experimental findings are supported by multi-microsecond timescale all-atom molecular simulations that unveil the molecular basis of the long-range interactions between the transactivation and bZip domains of ATF4. We found that inter-domain coupling is primarily driven by disorder-mediated interactions between a leucine-rich region of the transactivation domain and the leucine-zipper region of the bZip domain. This study uncovers the role played by structural disorder in facilitating the formation of long-range intramolecular interactions that shape the conformational ensemble of ATF4 in a critical manner.
Zoledronate reduces loading-induced microdamage in cortical ulna of ovariectomized rats
Authors: Ning Bohao , Londono Irène , Laporte Catherine , Villemure Isabelle 
Published: May 2023

AbstractAs a daily physiological mechanism in bone, microdamage accumulation dissipates energy and helps to prevent fractures. However, excessive damage accumulation might bring adverse effects to bone mechanical properties, which is especially problematic among the osteoporotic and osteopenic patients treated by bisphosphonates. Some pre-clinical studies in the literature applied forelimb loading models to produce well-controlled microdamage in cortical bone. Ovariectomized animals were also extensively studied to assimilate human conditions of estrogen-related bone loss. In the present study, we combined both experimental models to investigate microdamage accumulation in the context of osteopenia and zoledronate treatment. Three-month-old normal and ovariectomized rats treated by saline or zoledronate underwent controlled compressive loading on their right forelimb to createin vivomicrodamage, which was then quantified by barium sulfate contrast-enhanced micro-CT imaging. Weeklyin vivomicro-CT scans were taken to evaluate bone (re)modeling and to capture microstructural changes over time. After sacrifice, three-point-bending tests were performed to assess bone mechanical properties. Results show that the zoledronate treatment can reduce cortical microdamage accumulation in ovariectomized rats, which might be explained by the enhancement of several bone structural properties such as ultimate force, yield force, cortical bone area and volume. The rats showed increased bone formation volume and surface after the generation of microdamage, especially for the normal and the ovariectomized groups. Woven bone formation was also observed in loaded ulnae, which was most significant in ovariectomized rats. Although all the rats showed strong correlations between periosteal bone formation and microdamage accumulation, the correlation levels were lower for the zoledronate-treated groups, potentially because of their lower levels of microdamage. The present study provides insights to further investigations of pharmaceutical treatments for osteoporosis and osteopenia. The same experimental concept can be applied in future studies on microdamage and drug testing.
Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in ParalogousPlasmodiumAcyl-CoA Binding Proteins
Authors: Dani Rahul , Pawloski Westley , Chaurasiya Dhruv Kumar , Srilatha Nonavinakere Seetharam , Agarwal Sonal , Fushman David , Naganathan Athi N. 
Published: May 2023

ABSTRACTParalogous proteins confer enhanced fitness to organismsviacomplex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we resolve the underlying mechanism of promiscuous bindingversuspartial sub-functionalization in paralogs by studying structurally-identical Acyl-CoA Binding Proteins (ACBPs) fromPlasmodium falciparumthat serve as promising drug targets due to their high expression during the protozoan proliferative phase. Combining spectroscopic measurements, solution NMR, SPR and simulations on two of the paralogs, A16 and A749, we show that minor sequence differences shape nearly every local and global conformational feature. A749 displays a broader and heterogeneous native ensemble, weaker thermodynamic coupling and cooperativity, enhanced fluctuations, and a larger binding-pocket volume, compared to A16. Site-specific tryptophan probes signal a graded reduction in the sampling of substates in theholoform, which is particularly more apparent in A749, hinting at conformational-selection-like mechanism of binding. The paralogs exhibit a spectrum of binding affinities to different acyl-CoAs with A749, the more promiscuous and hence the likely ancestor, binding 1000-fold stronger to Lauroyl-CoA under physiological conditions. We thus demonstrate how minor sequence changes modulate the extent of long-range interactions and dynamics, effectively contributing to the molecular evolution of contrasting functional repertoires in paralogs.
Persistent hepatitis B virus and HIV coinfections in dually humanized mice engrafted with human liver and immune system
Authors: Hogan Glenn , Winer Benjamin Y. , Ahodantin James , Sellau Julie , Huang Tiffany , Douam Florian , Funaki Masaya , Chiriboga Luis , Su Lishan , Ploss Alexander 
Published: May 2023

ABSTRACTChronic hepatitis B (CHB), caused by hepatitis B virus (HBV), remains a major medical problem. HBV has a high propensity for progressing to chronicity and can result in severe liver disease, including fibrosis, cirrhosis and hepatocellular carcinoma. CHB patients frequently present with viral coinfection, including HIV and hepatitis delta virus. About 10% of chronic HIV carriers are also persistently infected with HBV which can result in more exacerbated liver disease. Mechanistic studies of HBV-induced immune responses and pathogenesis, which could be significantly influenced by HIV infection, have been hampered by the scarcity of immunocompetent animal models. Here, we demonstrate that humanized mice dually engrafted with components of a human immune system and a human liver supported HBV infection, which was partially controlled by human immune cells, as evidenced by lower levels of serum viremia and HBV replication intermediates in the liver. HBV infection resulted in priming and expansion of human HLA-restricted CD8+ T cells, which acquired an activated phenotype. Notably, our dually humanized mice support persistent coinfections with HBV and HIV which opens opportunities for analyzing immune dysregulation during HBV and HIV coinfection and preclinical testing of novel immunotherapeutics.
Pichia pastorisgrowth - coupled heme biosynthesis analysis using metabolic modelling
Authors: Pentjuss Agris , Bolmanis Emils , Suleiko Anastasija , Didrihsone Elina , Suleiko Arturs , Dubencovs Konstantins , Liepins Janis , Kazaks Andris , Vanags Juris 
Published: May 2023

ABSTRACTSoy legHemoglobin is one of the most important and key ingredients in plant-based meat substitutes that can imitate the colour and flavour of the meat. In order to improve the high-yield production of legHemoglobin protein and its main component - heme in the yeastPichia pastoris, glycerol and methanol cultivation conditions were studied. Additionally,in-silicometabolic modelling analysis of growth-coupled enzyme quantity, suggests metabolic gene up/down-regulation strategies for heme production. First, cultivations and metabolic modelling analysis ofP. pastoriswere performed on glycerol and methanol in different growth media. Glycerol cultivation uptake and production rates can be increased by 50 % according to metabolic modelling results, but methanol cultivation – is near the theoretical maximum. Growth-coupled metabolic optimisation results revealed the best feasible upregulation (33 reactions) (1.47 % of total reactions) and 67 downregulation/deletion (2.98 % of total) reaction suggestions. Finally, we describe reaction regulation suggestions with the highest potential to increase heme production yields.
Targeted inhibition of SCFSKP2confers anti-tumor activities resulting in a survival benefit in osteosarcoma
Authors: Wang Jichuan , Ferrena Alexander , Singh Swapnil , Zhang Ranxin , Viscarret Valentina , Al-Hardan Waleed , Aldahamsheh Osama , Borjihan Hasibagan , Singla Amit , Yaguare Simon , Tingling Janet , Zi Xiaolin , Lo Yungtai , Gorlick Richard , Schwartz Edward L. , Zhao Hongling , Yang Rui , Geller David S. , Zheng Deyou , Hoang Bang H. 
Published: May 2023

AbstractOsteosarcoma(OS) is a highly aggressive bone cancer for which treatment has remained essentially unchanged for decades. Although OS is characterized by extensive genomic heterogeneity and instability,RB1andTP53have been shown to be the most commonly inactivated tumor suppressors in OS. We previously generated a mouse model with a double knockout (DKO) ofRb1andTrp53within cells of the osteoblastic lineage, which largely recapitulates human OS with nearly complete penetrance. SKP2 is a repression target of pRb and serves as a substrate recruiting subunit of the SCFSKP2complex. In addition, SKP2 plays a central role in regulating the cell cycle by ubiquitinating and promoting the degradation of p27. We previously reported the DKOAA transgenic model, which harbored a knock-in mutation in p27 that impaired its binding to SKP2. Here, we generated a novelp53-Rb1-SKP2triple-knockout model (TKO) to examine SKP2 function and its potential as a therapeutic target in OS. First, we observed that OS tumorigenesis was significantly delayed in TKO mice and their overall survival was markedly improved. In addition, the loss ofSKP2also promoted an apoptotic microenvironment and reduced the stemness of DKO tumors. Furthermore, we found that small-molecule inhibitors of SKP2 exhibited anti-tumor activities in vivo and in OS organoids as well as synergistic effects when combined with a standard chemotherapeutic agent. Taken together, our results suggest that SKP2 inhibitors may reduce the stemness plasticity of OS and should be leveraged as next-generation adjuvants in this cancer.
Tectonic Complex Impedes Diffusion through the Ciliary Transition Zone to Ensure Proper Sorting of Membrane Proteins
Authors: Truong Hanh M. , Cruz-Colón Kevin O. , Martínez-Márquez Jorge Y. , Willer Jason R. , Travis Amanda M. , Biswas Sondip K. , Lo Woo-Kuen , Bolz Hanno J. , Pearring Jillian N. 
Published: May 2023

ABSTRACTThe primary cilium is a signaling organelle with a unique membrane composition maintained by a diffusional barrier residing at the transition zone. Many transition zone proteins, such as the tectonic complex, are linked to preserving ciliary composition; however, whether these proteins regulate active transport or physically impede membrane diffusion remains unknown. To understand tectonic’s role, we generated a photoreceptor specificTctn1knockout mouse. Loss of Tctn1 resulted in an absence of the entire tectonic complex yet had minimal effects on transition zone structure. Interestingly, we found that protein composition of the photoreceptor cilium was disrupted as non-resident membrane proteins accumulated in the cilium over time, ultimately resulting in photoreceptor degeneration. We further show that membrane proteins moved faster through the transition zone illustrating that the tectonic complex acts as a physical barrier to slow diffusion of membrane proteins so they can be properly sorted by ciliary transport carriers.
Use of Epivolve phage display to generate a monoclonal antibody with opsonic activity directed against a subdominant epitope on extracellular loop 4 ofTreponema pallidumBamA (TP0326)
Authors: Ferguson Mary , Delgado Kristina N. , McBride Shannon , Orbe Isabel C. , La Vake Carson J. , Caimano Melissa J. , Mendez Qiana , Moraes Trevor F. , Schryvers Anthony B. , Moody M. Anthony , Radolf Justin D. , Weiner Michael , Hawley Kelly L. 
Published: May 2023

ABSTRACTSyphilis, a sexually transmitted infection caused by the spirocheteTreponema pallidum(Tp), is resurging globally. Opsonic antibodies (Abs) targeting surface-exposed epitopes of the spirochete’s outer membrane proteins (OMPs) are believed to promote macrophage-mediated clearance of the bacterium during infection and are presumed to be key to vaccine development.Tp’s repertoire of outer membrane proteins includes BamA (β-barrelassemblymachinery subunitA/TP0326), the central component of the molecular machine that inserts newly exported OMP precursors into the OM lipid bilayer. BamA is a bipartite protein consisting of an 18-stranded β-barrel with nine extracellular loops (ECLs) and five periplasmic POTRA (polypeptidetransport-associated) domains. Antisera directed against BamA ECL4 promote internalization ofTpby rabbit peritoneal macrophages. Herein, we employed a novel two-stage, phage display strategy, termed “Epivolve” (forepitopeevolution), to generate five site-directed murine monoclonal Abs (mAbs) targeting a centrally located peptide (S2) of BamA ECL4. Each of the five mAbs demonstrated reactivity by immunoblotting and ELISA to nanogram amounts of BamA ECL4 displayed by aPyrococcus furiosusthioredoxin (PfTrx) scaffold (PfTrxBamA/ECL4). One mAb containing a unique amino acid sequence in both light and heavy chains showed activity in an opsonophagocytosis assay employing murine bone marrow-derived macrophages. Mice and rabbits hyperimmunized withPfTrxBamA/ECL4produced opsonic antisera that strongly recognized the ECL presented in a heterologous scaffold and overlapping ECL4 peptides including S2. In contrast, Abs generated duringTpinfection of mice and rabbits poorly recognized the peptides, indicating that S2 contains a subdominant epitope. Epivolve, which circumvents the natural immune response, can be utilized for the generation of mAbs that target subdominant opsonic epitopes in ECLs ofTpOMPs.
Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte -Alternaria burnsiiNCIM 1409
Authors: Natarajan Shakunthala , Pucker Boas , Srivastava Smita 
Published: May 2023

AbstractCamptothecin is an important anticancer alkaloid produced by particular plant species. No suitable synthetic route has been established for camptothecin production yet, imposing a stress on plant-based production systems. Endophytes associated with these camptothecin-producing plants have been reported to also produce camptothecin and other high-value phytochemicals. A previous study identified a fungal endophyteAlternaria burnsiiNCIM 1409, isolated fromNothapodytes nimmoniana, to be a sustainable producer of camptothecin. Our study provides key insights on camptothecin biosynthesis in this recently discovered endophyte. The whole genome sequence ofAlternaria burnsiiNCIM 1409 was assembled and screened for biosynthetic gene clusters. Comparative studies with related fungi supported the identification of candidate genes involved in camptothecin synthesis and also helped to understand some aspects of the endophyte’s defense against the toxic effects of camptothecin. No evidence for horizontal gene transfer of the camptothecin biosynthetic genes from the host plant to the endophyte was detected suggesting an independent evolution of the camptothecin biosynthesis in this fungus.