bluuebunny/crossref_metadata_2025_split huggingface dataset:
PPAR-γ is a promising therapeutic target for memory deficits induced by early alcohol exposure
Authors: Garcia-Baos Alba , Pastor Antoni , Gallego-Landin Ines , de la Torre Rafael , Sanz Ferran , Valverde Olga 
Published: January 2023

AbstractBackgroundPatients diagnosed with fetal alcohol spectrum disorder (FASD) show persistent cognitive disabilities, including memory deficits. However, the neurobiological substrates of these deficits remain unclear. Here, we studied the participation of the expanded endocannabinoid system (ECS), which is known to be affected by alcohol in other life periods, and it is involved in memory impairments of neurodevelopmental disorders.MethodsC57BL/6 female mice were exposed to a time-limited access to either water or alcohol to model prenatal and lactation alcohol exposure (PLAE). The expanded ECS was analyzed in the prefrontal cortex and the hippocampus of the offspring at post-partum day (PD) 25 and 70. Then, memory performance was tested after the repeated administration (from PD25 to PD34) of: i) URB597, to increase N-acylethanolamines (NAEs), and GW9662, a peroxisome proliferator-activated receptor gamma (PPAR-γ) antagonist; ii) pioglitazone, a PPAR-γ agonist. Finally, we used a viral approach to upregulate astrocytic PPAR-γ in the hippocampus to restore memory deficits.ResultsWe report that PLAE causes a hippocampal reduction of NAEs and PPAR-γ at PD25. Moreover, URB597 suppresses PLAE-induced memory deficits through PPAR-γ, since its effects are prevented by GW9662. Direct PPAR-γ activation, using pioglitazone, also ameliorates memory impairments. Lastly, we demonstrate that the upregulation of PPAR-γ in hippocampal astrocytes is sufficient to rescue PLAE-induced memory deficits.ConclusionOur data reveal a bidirectional link between memory deficits and expanded ECS alterations in the context of early alcohol exposure. Furthermore, we proved that PPAR-γ in hippocampal astrocytes represents a specific therapeutic target for memory deficits in FASD.
Cytotrophoblast cells are selectively permissive and favor Zika virus, but no other related flavivirus, invasion to the placental stroma
Authors: Viettri Mercedes , Caraballo Gerson , Sanchez Ma. Elena , Espejel-Nuñez Aurora , Betanzos Abigail , Ortiz-Navarrete Vianney , Estrada-Gutierrez Guadalupe , Nava Porfirio , Ludert Juan E. 
Published: January 2023

ABSTRACTBACKGROUNDZika virus (ZIKV) is highly teratogenic, in contrast with dengue virus (DENV) or the yellow fever virus vaccine (YFV-17D). The mechanisms employed by ZIKV to cross the placenta need to be elucidated.METHODSParallel infections with ZIKV, DENV and YFV-17D were compared in terms of efficiency, activation of mTOR pathways and cytokine secretion profile in human cytotrophoblastic HTR8 cells (CTB), and monocytic U937 cells, differentiated to M2 macrophages (M2-MØ).RESULTSIn CTB, ZIKV replication was significantly more efficient than DENV or YFV-17D. In M2-MØ, ZIKV replication continued to be more efficient, although differences between strains were reduced. Significantly greater activation of Phospho-S6r and Phospho-AKT/Ser473 fractions in CTB infected with ZIKV than with DENV or YFV-17D, was observed. CTB treated with the mTOR inhibitors rapamycin or AZD8055, showed a 20-fold-reduction in ZIKV yield, versus 5 and 3.5-fold for DENV and YFV-17D, respectively. Finally, we detected that ZIKV infection, but not DENV or YFV-17D, efficiently inhibited the interferon response of CTB cells.CONCLUSIONSThese results suggest that CTB cells are permissive and act favoring ZIKV entry into the placental stroma, over DENV and YFV-17D and that the mTOR complex is a switch that enhances the replication of ZIKV in CTB cells.
Cryo-EM structure of DNA polymerase θ helicase domain in complex with inhibitor novobiocin
Authors: Guo Hanbo , Wang YanXia , Mao Jun , Zhao Huimin , He Yuntong , Hu Yuandong , Li Jing , Liu Yujie , Guan Zheng , Guo Allen , Ni Xiaodan , Zhang Fengying , Heng Jie 
Published: January 2023

AbstractDNA double-strand breaks (DSBs) are highly toxic lesions that occur during the cellular metabolic process. DNA Polymerase theta (Polθ) is an error-prone polymerase that has been implicated in the repair of chromosome breaks, recovery of broken replication forks, and translesion synthesis. The inhibition of Polθ activity has been implicated in killing HR-deficient tumor cellsin vitroandin vivo. We present the first biochemical evidence that the antibiotics novobiocin (NVB) noncompetitively inhibit ATP hydrolysis by the ATPase domain of the Polθ helicase domain (Polθ-HLD). We report the Cryo-EM structure of apo dimeric Polθ helicase domain (Polθ-HLD), and the first inhibitor occupied Polθ-HLD structure. Our structure identifies a non-canonical novobiocin binding pocket, distinct from the canonical site that partially overlaps with the ATP in the ATPase domain. Comparison with the homolog helicase Hel308-DNA duplex complex suggests that the novobiocin competitively binds to a triangle hub on the DNA translocation pathway and blocks the ssDNA binding and translocation. Furthermore, the first dimeric structure of Polθ-HLD also provides a structural framework for revealing the microhomology-mediated end-joining mechanism. Our results demonstrate that the inhibitor-occupied structure combined with rational, structure-based drug design will undoubtedly accelerate the discovery of potent inhibitors with better efficacy and target selectivity to human Polθ.
Lipopolysaccharide integrity primes bacterial sensitivity to a cell wall-degrading intermicrobial toxin
Authors: Trotta Kristine L , Hayes Beth M , Schneider Johannes P , Wang Jing , Todor Horia , Grimes Patrick Rockefeller , Zhao Ziyi , Hatleberg William L , Silvis Melanie R , Kim Rachel , Koo Byoung Mo , Basler Marek , Chou Seemay 
Published: January 2023

ABSTRACTGram-negative bacteria can antagonize neighboring microbes using a type VI secretion system (T6SS) to deliver toxins that target different essential cellular features. Despite the conserved nature of these targets, T6SS potency can vary across recipient species. To understand the molecular basis of intrinsic T6SS susceptibility, we screened for essentialEscherichia coligenes that affect its survival when antagonized by a cell wall-degrading T6SS toxin fromPseudomonas aeruginosa, Tae1. We revealed genes associated with both the cell wall and a separate layer of the cell envelope, surface lipopolysaccharide, that modulate Tae1 toxicityin vivo. Disruption of lipopolysaccharide synthesis providedEscherichia coli (Eco)with novel resistance to Tae1, despite significant cell wall degradation. These data suggest that Tae1 toxicity is determined not only by direct substrate damage, but also by indirect cell envelope homeostasis activities. We also found that Tae1-resistantEcoexhibited reduced cell wall synthesis and overall slowed growth, suggesting that reactive cell envelope maintenance pathways could promote, not prevent, self-lysis. Together, our study highlights the consequences of co-regulating essential pathways on recipient fitness during interbacterial competition, and how antibacterial toxins leverage cellular vulnerabilities that are both direct and indirect to their specific targetsin vivo.
4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs
Authors: Pu Lianrong , Shamir Ron 
Published: January 2023

AbstractMicrobial communities usually harbor a mix of bacteria, archaea, plasmids, viruses, and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or two minor classes from bacteria and archaea in metagenome assemblies, but none can classify all of the four classes simultaneously. Moreover, existing classifiers have low precision on minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1-2 orders of magnitude faster than the other classifiers. The 4CAC software is available athttps://github.com/Shamir-Lab/4CAC.
Keratinocytes coordinate inflammatory responses and regulate development of secondary lymphedema
Authors: Park Hyeung Ju , Kataru Raghu P. , Shin Jinyeon , García Nores Gabriela D. , Encarnacion Elizabeth M. , Klang Mark G. , Riedel Elyn , Coriddi Michelle , Dayan Joseph H. , Mehrara Babak J. 
Published: January 2023

AbstractEpidermal changes are histological hallmarks of secondary lymphedema, but it is unknown if keratinocytes contribute to its pathophysiology. Using clinical lymphedema specimens and mouse models, we show that keratinocytes play a primary role in lymphedema development by producing T-helper 2 (Th2) -inducing cytokines. Specifically, we find that keratinocyte proliferation and expression of protease-activated receptor 2 (PAR2) are early responses following lymphatic injury and regulate the expression of Th2-inducing cytokines, migration of Langerhans cells, and skin infiltration of Th2-differentiated T cells. Furthermore, inhibition of PAR2 activation with a small molecule inhibitor or the proliferation inhibitor teriflunomide (TF) prevents activation of keratinocytes stimulated with lymphedema fluid. Finally, topical TF is highly effective for decreasing swelling, fibrosis, and inflammation in a preclinical mouse model. Our findings suggest that lymphedema is a chronic inflammatory skin disease, and topically targeting keratinocyte activation may be a clinically effective therapy for this condition.
Anoctamin 10/TMEM16K mediates convergent extension and tubulogenesis during notochord formation in the early chordateCiona intestinalis
Authors: Liang Zonglai , Dondorp Daniel Christiaan , Chatzigeorgiou Marios 
Published: January 2023

AbstractDuring embryonic development, cells are organized into complex tissues and organs. A highly conserved organ shape across metazoans is the epithelial tube. Tube morphogenesis is a complex multistep process where the molecular mechanisms underlying the diversity of cell behaviors such as convergent extension, cell elongation, and lumen formation are still intensely studied. Here, using genome editing and quantitative imaging in the early chordateCiona intestinaliswe show that Ano10/Tmem16k, a member of the evolutionarily ancient family of transmembrane proteins called Anoctamin/TMEM16 is required for convergent extension, lumen expansion and connection during notochord morphogenesis. In addition, we find that loss of Cii.Ano10/Tmem16k hampers cell behavior and cytoskeletal organization during tubulogenesis. In vivo Ca2+imaging revealed that genetic ablation of Cii.Ano10/Tmem16k hinders the ability of notochord cells to regulate bioelectrical signaling. Finally, we use electrophysiological recordings and a scramblase assay in tissue culture to demonstrate that Cii.Ano10/Tmem16k likely acts as an ion channel but not as a phospholipid scramblase. More generally, this work provides insights into the pre-vertebrate functions of Anoctamins and raises the possibility that Anoctamin/Tmem16 family members have an evolutionarily conserved role in tube morphogenesis.
Fine scale sampling reveals spatial heterogeneity of rhizosphere microbiome in youngBrachypodiumplants
Authors: Acharya Shwetha M. , Yee Mon Oo , Diamond Spencer , Andeer Peter F. , Baig Nameera F. , Aladesanmi Omolara T. , Northen Trent R. , Banfield Jillian F. , Chakraborty Romy 
Published: January 2023

AbstractFor a deeper and comprehensive understanding of the diversity, composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary across distinct parts of the root giving rise to spatially distinct microbial niches. To address this, we analyzed microbial community from two spatially distinct zones of the primary root (the tip vs. the base) inBrachypodium distachyon, grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a stronger rhizosphere effect in the root base vs. bulk soil compared to the root tips vs. bulk soil, resulting in an enrichment of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, few OTUs belonging to less characterized lineages such as Verrucomicrobia and Acidobacteria. While the microbial community distributions are similar across growth containers, the EcoFAB displayed higher replicate reproducibility. Genome-resolved and bulk metagenomics revealed that genes associated with transcriptional regulation, transport of nutrients and catabolic enzymes indicating active metabolism, biofilm formation and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to the root tips, implying the presence of easily available, labile carbon and nutrients in the rhizosphere relative to bulk soil. Such insights into the relationships between root structure, exudation and microbial communities are critical for developing understanding of plant-microbe interactions.
Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction
Authors: Monshizadeh Mahsa , Ye Yuzhen 
Published: January 2023

AbstractWe developed MicroKPNN, a prior-knowledge guided interpretable neural network for microbiomebased human host phenotype prediction. The prior-knowledge used in MicroKPNN includes the metabolic activities of different bacterial species, phylogenetic relationships, and bacterial community structure. Application of MicroKPNN to seven gut microbiome datasets (involving five different human diseases including inflammatory bowel disease, type 2 diabetes, liver cirrhosis, colorectal cancer, and obesity) shows that incorporation of the prior knowledge helped improve the microbiome-based host phenotype prediction. MicroKPNN outperformed fully-connected neural network based approaches in all seven cases, with the most improvement of accuracy in the prediction of type 2 diabetes. MicroKPNN outperformed a recently developed deep-learning based approach DeepMicro, which selects the best combination of autoencoder and machine learning approach to make predictions, in six out of the seven cases. More importantly, we showed that MicroKPNN provides a way for interpretation of the predictive models. Our results suggested that the metabolic potential of the bacterial species contributed more than the two other sources of prior knowledge. MicroKPNN is publicly available athttps://github.com/mgtools/MicroKPNN.
Impact of acquisition and modeling parameters on test-retest reproducibility of edited GABA+
Authors: Hupfeld Kathleen E. , Zöllner Helge J. , Hui Steve C. N. , Song Yulu , Murali-Manohar Saipavitra , Yedavalli Vivek , Oeltzschner Georg , Prisciandaro James J. , Edden Richard A. E. 
Published: January 2023

AbstractLiterature values for within-subject test-retest reproducibility of gamma-aminobutyric acid (GABA), measured with edited magnetic resonance spectroscopy (MRS), vary widely. Reasons for this variation remain unclear. Here we tested whether sequence complexity (two-experiment MEGA-PRESS versus four-experiment HERMES), editing pulse duration (14 versus 20 ms), scanner frequency drift (interleaved water referencing (IWR) turned ON versus OFF), and linear combination modeling variations (three different co-edited macromolecule models and 0.55 versus 0.4 ppm spline baseline knot spacing) affected the within-subject coefficient of variation of GABA + macromolecules (GABA+). We collected edited MRS data from the dorsal anterior cingulate cortex from 20 participants (30.8 ± 9.5 years; 10 males). Test and retest scans were separated by removing the participant from the scanner for 5-10 minutes. Each acquisition consisted of two MEGA-PRESS and two HERMES sequences with editing pulse durations of 14 and 20 ms (referred to here as: MEGA-14, MEGA-20, HERMES-14, and HERMES-20; all TE = 80 ms, 224 averages). Reproducibility did not consistently differ for MEGA-PRESS compared with HERMES or for 14 compared with 20 ms editing pulses. A composite model of the 0.9 and 3 ppm macromolecules (particularly for HERMES) and sparser (0.55 compared with 0.4 ppm) spline baseline knot spacing yielded generally better test-retest reproducibility for GABA+. Replicating our prior results, linear combination modeling in Osprey compared with simple peak fitting in Gannet resulted in substantially better test-retest reproducibility. These results highlight the importance of model selection for edited MRS studies of GABA+, particularly for clinical studies which focus on individual patient differences in GABA+ or changes following an intervention.
Conformational free-energy landscapes of a Na+/Ca2+exchanger explain its alternating-access mechanism and functional specificity
Authors: Marinelli Fabrizio , Faraldo-Gómez José D. 
Published: January 2023

AbstractSecondary-active transporters catalyze the movement of myriad substances across all cellular membranes, typically against opposing concentration gradients, and without consuming any ATP. To do so, these proteins employ an intriguing structural mechanism evolved to be activated only upon recognition or release of the transported species. We examine this self-regulated mechanism using a homolog of the cardiac Na+/Ca2+exchanger as a model system. Using advanced computer simulations, we map out the complete functional cycle of this transporter, including unknown conformations that we validate against existing experimental data. Calculated free-energy landscapes reveal why this transporter functions as an antiporter rather than a symporter, why it specifically exchanges Na+and Ca2+, and why the stoichiometry of this exchange is exactly 3:1. We also rationalize why the protein does not exchange H+for either Ca2+or Na+, despite being able to bind H+and its high similarity with H+/Ca2+exchangers. Interestingly, the nature of this transporter is not explained by its primary structural states, known as inward- and outward-open conformations; instead, the defining factor is the feasibility of conformational intermediates between those states, wherein access pathways leading to the substrate binding sites become simultaneously occluded from both sides of the membrane. This analysis offers a physically-coherent, broadly transferable route to understand the emergence of function from structure among secondary-active membrane transporters.SignificanceThe class of membrane proteins known as secondary-active transporters mediate a wide range of critical cellular processes, including nutrient uptake, transmembrane signaling, and resistance to cytotoxic compounds, like human-made drugs. A detailed understanding of their molecular mechanisms is therefore of interest not only from a fundamental standpoint, but also because it will facilitate the design of inhibitors or stimulators that may be used as therapeutic agents. This study provides a conceptual mechanistic framework, grounded on statistical thermodynamics, that bridges the specific physiological function of these proteins and their molecular structure. While the study is focused on a particular subclass of transporters involved in cardiac physiology and cellular Ca2+homeostasis, we envisage our conclusions will be broadly applicable.
Direct observation of coordinated assembly of individual native centromeric nucleosomes
Authors: Popchock Andrew R. , Larson Joshua D. , Dubrulle Julien , Asbury Charles L. , Biggins Sue 
Published: January 2023

AbstractEukaryotic chromosome segregation requires the kinetochore, a megadalton-sized machine that forms on specialized centromeric chromatin containing CENP-A, a histone H3 variant. CENP-A deposition requires a chaperone protein HJURP that targets it to the centromere, but it has remained unclear whether HJURP has additional functions beyond CENP-A targeting and why high AT DNA content, which disfavors nucleosome assembly, is widely conserved at centromeres. To overcome the difficulties of studying nucleosome formation in vivo, we developed a microscopy assay that enables direct observation of de novo centromeric nucleosome recruitment and maintenance with single molecule resolution. Using this assay, we discover that CENP-A can arrive at centromeres without its dedicated centromere-specific chaperone HJURP, but stable incorporation depends on HJURP and additional DNA-binding proteins of the inner kinetochore. We also show that homopolymer AT runs in the yeast centromeres are essential for efficient CENP-A deposition. Together, our findings reveal requirements for stable nucleosome formation and provide a foundation for further studies of the assembly and dynamics of native kinetochore complexes.
SOS2 regulates the threshold of mutantEGFR-dependent oncogenesis
Authors: Theard Patricia L. , Linke Amanda J. , Sealover Nancy E. , Daley Brianna R. , Yang Johnny , Cox Katherine , Kortum Robert L 
Published: January 2023

AbstractSon of Sevenless 1 and 2 (SOS1 and SOS2) are RAS guanine nucleotide exchange factors (RasGEFs) that mediate physiologic and pathologic RTK-dependent RAS activation. Here, we show that SOS2 modulates the threshold of epidermal growth factor receptor (EGFR) signaling to regulate the efficacy of and resistance to the EGFR-TKI osimertinib in lung adenocarcinoma (LUAD).SOS2deletion sensitizedEGFR-mutated cells to perturbations in EGFR signaling caused by reduced serum and/or osimertinib treatment to inhibit PI3K/AKT pathway activation, oncogenic transformation, and survival. Bypass RTK reactivation of PI3K/AKT signaling represents a common resistance mechanism to EGFR-TKIs;SOS2KO reduced PI3K/AKT reactivation to limit osimertinib resistance. In a forced HGF/MET-driven bypass model,SOS2KO inhibited HGF-stimulated PI3K signaling to block HGF-driven osimertinib resistance. Using a long termin situresistance assay, a majority of osimertinib resistant cultures exhibited a hybrid epithelial/mesenchymal phenotype associated with reactivated RTK/AKT signaling. In contrast, RTK/AKT-dependent osimertinib resistance was markedly reduced bySOS2deletion; the fewSOS2KO cultures that became osimertinib resistant primarily underwent non-RTK dependent EMT. Since bypass RTK reactivation and/or tertiaryEGFRmutations represent the majority of osimertinib-resistant cancers, these data suggest that targeting SOS2 has the potential to eliminate the majority of osimertinib resistance.One sentence summarySOS2 modulates the threshold of EGFR-PI3K signaling to regulate the efficacy of and resistance to osimertinib.