bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Ethanol Tolerance and Production in Pyruvate Dehydrogenase Mutant ofSaccharomyces cerevisiae
Authors: Yang Anna , Ranaivoarisoa Tahina O. , Bose Arpita 
Published: January 2023

AbstractEthanol, a naturally synthesized compound bySaccharomyces cerevisiaeyeast through alcoholic fermentation, has previously been studied as a renewable alternative to traditional fossil fuels. However, current challenges of engineeringS. cerevisiaestrains for ethanol production remain: low ethanol productivity, inefficient substrate catabolism, and a buildup of toxic products to inhibitory levels. In this study, we proposed a method of metabolic rewiring via the deletion of thepda1gene, which leads to pyruvate dehydrogenase (PDH) deficiency. The Δpda1mutant strain was created by CRISPR Cas-9 knockout using the constructed pCRCT-PDA1 plasmid. Subsequently, mutant candidates were screened by PCR and Sanger sequencing, confirming a 17 bp deletion in thepda1gene. The wild-type and mutant strains were analyzed for growth under aerobic and anaerobic conditions in glucose and glycerol, as well as ethanol production and tolerance. The Δpda1mutant displays a ~two-fold increase in anaerobic ethanol production and an aerobic growth defect with no observed increase in ethanol production. The mutant is also hyper-tolerant to ethanol, which allows a faster buildup of products in growth media with minimal reduction in growth. This newS. cerevisiaestrain deficient in PDH may provide a solution to the efficient and abundant synthesis of biofuels such as ethanol by redirecting metabolic flux and altering stress response.
Salience-based information integration: An overarching function of the “social brain”?
Authors: Lugrin Claire , Konovalov Arkady , Ruff Christian 
Published: January 2023

ABSTRACTBehavior in social contexts is routinely accompanied by neural activity in a brain network comprising the bilateral temporoparietal junction (TPJ), dorsomedial and dorsolateral prefrontal cortex (dmPFC and dlPFC), and precuneus. This network – often referred to as the “social brain network” (SBN) – is thought to have evolved in response to the information processing demands of life in social groups. However, its precise functional contributions to behavior are unclear, since many of its areas are also activated in non-social contexts requiring, for example, attentional orienting or context updating. Here we argue that these results may reflect a basic neural mechanism implemented by areas in this network that is commonly required in both social and non-social contexts: Integrating multiple sensory and memory inputs into salient configurations, such as social constellations or perceptual Gestalts. We tested this hypothesis using a numeracy paradigm that orthogonally varied the salience of sensory target configurations and the required motor responses. Even in this non-social task, several regions of the SBN (TPJ, dmPFC, and precuneus) showed higher activity when the goal required the brain to attend to more versus less salient perceptual configurations. This activation pattern was specific to configuration salience and did not reflect general task demand or switching to new contexts. Taken together, these results suggest that the integration of information into salient configurations may be a key function of SBN regions, thus offering a new perspective on the widespread recruitment of these areas across social and non-social contexts.
Reciprocal regulation of TLR4, TLR3 and Macrophage Scavenger Receptor 1 regulates nonopsonic phagocytosis of the fungal pathogenCryptococcus neoformans
Authors: Onyishi Chinaemerem U. , Desanti Guillaume E. , Wilkinson Alex L. , Fejer Gyorgy , Christophe Olivier D. , Bryant Clare E. , Mukhopadhyay Subhankar , Gordon Siamon , May Robin C. 
Published: January 2023

AbstractThe opportunistic fungal pathogenCryptococcus neoformanscauses lethal infections in immunocompromised patients. Macrophages are central to the host response to cryptococci; however, it is unclear howC. neoformansis recognized and phagocytosed by macrophages. Here we investigate the role of TLR4 in the nonopsonic phagocytosis ofC. neoformans. We find that loss of TLR4 function unexpectedly increases phagocytosis of nonopsonized cryptococci. The increased phagocytosis observed inTlr4-/-cells was dampened by pre-treatment of macrophages with either a TLR3 inhibitor or oxidised-LDL, a known ligand of scavenger receptors. The scavenger receptor, macrophage scavenger receptor 1 (MSR1) (also known as SR-A1 or CD204) was upregulated inTlr4-/-macrophages and there was a 75% decrease in phagocytosis of nonopsonized cryptococci byMsr1-/-macrophages. Furthermore, immunofluorescence imaging revealed colocalization of MSR1 and internalised cryptococci. Together, these results identify MSR1 as a key receptor for the phagocytosis of nonopsonizedC. neoformansand demonstrate TLR4/MSR1 crosstalk in the phagocytosis ofC. neoformans.
A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic
Authors: Lubin Joseph H. , Martinusen Samantha G. , Zardecki Christine , Olivas Cassandra , Bacorn Mickayla , Balogun MaryAgnes , Slaton Ethan W. , Wu Amy Wu , Sakeer Sarah , Hudson Brian P. , Denard Carl A. , Burley Stephen K. , Khare Sagar D. 
Published: January 2023

AbstractAlthough the rapid development of therapeutic responses to combat SARS-CoV-2 represents a great human achievement, it also demonstrates untapped potential for advanced pandemic preparedness. Cross-species efficacy against multiple human coronaviruses by the main protease (MPro) inhibitor nirmatrelvir raises the question of its breadth of inhibition and our preparedness against future coronaviral threats. Herein, we describe sequence and structural analyses of 346 unique MPro enzymes from all coronaviruses represented in the NCBI Virus database. Cognate substrates of these representative proteases were inferred from their polyprotein sequences. We clustered MPro sequences based on sequence identity and AlphaFold2-predicted structures, showing approximate correspondence with known viral subspecies. Predicted structures of five representative MPros bound to their inferred cognate substrates showed high conservation in protease:substrate interaction modes, with some notable differences. Yeast-based proteolysis assays of the five representatives were able to confirm activity of three on inferred cognate substrates, and demonstrated that of the three, only one was effectively inhibited by nirmatrelvir. Our findings suggest that comprehensive preparedness against future potential coronaviral threats will require continued inhibitor development. Our methods may be applied to candidate coronaviral MPro inhibitors to evaluate in advance the breadth of their inhibition and identify target coronaviruses potentially meriting advanced development of alternative countermeasures.
A common tolerance mechanism of bacterial biofilms to antibiotics
Authors: Zhang Yuzhen , Cai Yumin , Wang Tianmin , Wu Qile 
Published: January 2023

SUMMARYA deeper mechanistic understanding of antibiotics tolerance exhibited by bacterial biofilms is crucial for clinical treatment and drug development. Here, we found a common binary distribution for various antibiotics in biofilms, which was determined by glucose distribution. Antibiotic penetration would be accompanied by glucose leakage. Surprisingly, the biofilm periphery exhibited constant glucose consumption and antibiotics patterns after drug treatment, while planktonic bacteria did not. Spatial multi-omics revealed that activation of lipid metabolism was responsible for continuous glucose consumption, which was channeled to thicken the cell membrane and subsequently weakened antibiotic penetration, leading to a low drug concentration in the biofilm interior - a common mechanism underlying biofilm drug tolerance. We further revealed that the biofilm-specific activation of lipid metabolism was derived from slower drug penetration and longer response time of biofilms to antibiotics, owing to lower energy metabolism and membrane potential in biofilms compared to planktonic bacteria.
An optimized workflow for analyzing extracellular vesicles as biomarkers in liver diseases
Authors: Paluschinski Martha , Loosen Sven , Kordes Claus , Keitel Verena , Kuebart Anne , Brandenburger Timo , Schöler David , Wammers Marianne , Neumann Ulf P , Luedde Tom , Castoldi Mirco 
Published: January 2023

Background & AimsExtracellular vesicles (EVs) play an important role in intercellular communication, serving as vehicles for the exchange of biological materials and being involved in the regulation of physiological processes. EVs and their associated cargoes are considered a promising source of disease-associated biomarkers. The purpose of this study was to establish an easy-to-use, reproducible, and scalable workflow to efficiently analyze EVs in the context of liver disease.MethodsAn optimized workflow was established for the pre-analytical processing and isolation of EVs from plasma and serum. Nanoparticle Tracking Analysis (NTA) was used to characterize circulating EVs in the serum of patients with nonalcoholic fatty liver disease (NAFLD), autoimmune liver disease (AIH), and animal models with impaired liver function. EVs were separated from soluble proteins by an optimized, polyethylene glycol (PEG)-based enrichment protocol. Enriched EVs were either labeled and functionally characterized by monitoring cellular uptake or lysed for biomarker identification.ResultsCirculating EVs in the serum of patients with NAFLD or AIH and in different animal models have been characterized by NTA. Here we show that both the quantity and size of EVs in the serum of patients/animal models are significantly different from those of healthy individuals. We show that isolated EVs are functional, and their uptake by acceptor cells can be quantified after fluorescence labelling. Enriched EVs were directly used to analyze RNA biomarkers. Several microRNAs, including miR-15b, -16, -21, -122 and -223, were found to be significantly up-regulated in EVs isolated from the sera of patients with NAFLD and AIH. We show that EVs transport cytokines, and that IL-2, IL-6 and IL-8 were significantly up-regulated in EVs enriched from patients with cholangiocarcinoma (CCA) compared to healthy controls.ConclusionsThe workflow presented here represents an accessible and easy-to-use approach that enables the analysis and enrichment of EVs from complex biological fluids and their preparation for functional characterization or downstream analysis. In this study, the levels of several miRNAs were found to be significantly increased in EVs isolated from AIH and NAFLD patients compared with healthy controls.HighlightsEVs circulating in crude serum reflect the diseased stage of the donors.Enrichment of EVs with the approach presented here efficiently separates soluble proteins from EVs, providing optimal material for further characterization.Exosomal markers are present in the EVs-enriched fraction.Enriched EVs are intact and are functionally taken up by acceptor cells.Enriched EVs are suitable, and have been used for, biomarkers identification both at RNA and protein level.
Homeostatic control of an iron repressor in a GI tract resident
Authors: Wang Yuanyuan , Mao Yinhe , Chen Xiaoqing , Yang Kaiyan , Huang Xinhua , Tian Lixing , Jiang Tong , Zou Yun , Ma Xiaoyuan , Xu Chaoyue , Zhou Zili , Wu Xianwei , Pan Lei , Liang Huaping , Chen Changbin 
Published: January 2023

AbstractThe transition metal iron plays a crucial role in living cells. However, high level of iron is potentially toxic through the production of reactive oxygen species (ROS), serving as a deterrent to the commensal fungusCandida albicansfor colonization in the iron-rich gastrointestinal (GI) tract. We observe that the mutant lacking an iron-responsive transcription factor Hap43 is hyper-fit for colonization in murine gut. We demonstrate that high iron specifically triggers multiple post-translational modifications (PTMs) and proteasomal degradation of Hap43, a vital process guaranteeing the precision of intestinal ROS detoxification. Reduced levels of Hap43 lead to de-repression of antioxidant genes and therefore alleviate the deleterious ROS derived from iron metabolism. Our data reveal that Hap43 functions as a negative regulator for oxidative stress-adaptation ofC. albicansto gut colonization and thereby provide a new insight into understanding the interplay between iron homeostasis and fungal commensalism.ImportanceIron homeostasis is critical for creatures.Candida albicansis one of the major commensals in the GI tract where is iron-replete environment. Transcriptional factor Hap43 was believed to repress iron utilizations genes in iron-depleted conditions for decades. However, the mystery in iron-replete conditions of Hap43 has never been uncovered. We discovered that reduced levels of Hap43 via phosphorylation-dependent nuclear export, followed by proteosome-mediated protein degradation, leads to de-repression of downstream antioxidant genes and promote its colonization in GI tract. We propose thatC. albicanshas a strict detoxification process to ensure its survival, which has important implications for understanding how the fungi survives in the mammalian host.
Co-evolutionary patterns shown inOstreococcus-virus system from the Western Baltic Sea in freshly isolated hosts and viruses
Authors: Listmann Luisa , Peters Carina , Rahlff Janina , Esser Sarah P. , Schaum Elisa 
Published: January 2023

AbstractMarine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. In recent years, an understanding of the potential importance of phytoplankton-targeting viruses on ecosystem dynamics has emerged, but experimental investigations of host-virus interactions on a broad spatial and temporal scale are still missing. Here, we investigated in detail a phytoplankton host’s responses reacting to infections by species-specific viruses from i) distinct geographical regions and ii) different sampling seasons. Specifically, we used two species of picophytoplankton (1 µm)Ostreococcus tauriandO. mediterraneusand their viruses (size ca. 100 nm), which represent systems well-known in marine biology, but almost entirely ignored in evolutionary biology. The strains stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature. Using an experimental cross-infection set-up, we show that in this natural system evolutionary history, and thus the timing of when hosts and their associated viruses coexisted, was the main driver of infection patterns. In addition species and strain specificity underline the present understanding of rapid host-virus co-evolution.
The virus-encoded ion channel “viroporin” activity of the agnoprotein is required for BK Polyomavirus release from infected kidney cells
Authors: Swinscoe Gemma , Prescott Emma L , Hurdiss Daniel L , Morgan Ethan L , Dobson Samuel J , Edwards Thomas , Foster Richard , Welberry Smith Matthew , Macdonald Andrew 
Published: January 2023

AbstractBK polyomavirus (BKPyV) is a common opportunistic pathogen and the causative agent of several diseases in transplant patients and the immunosuppressed. Despite its importance, aspects of the virus lifecycle such as how the virus exits an infected cells, remain poorly understood. The late region of the BKPyV genome encodes an auxillery protein called agnoprotein. We and others have shown that agnoprotein is an essential factor in virus release, and the loss of agnoprotein results in an accumulation of virus particles within the nucleus of an infected cell. The functions of agnoprotein necessary for this egress phenotype are not known. Here we demonstrate that agnoprotein shows properties associated with viroporins, a group of virus-encoded membrane spanning proteins that play key roles in virus infection and release. We demonstrate that agnoprotein oligomerises and perturbs membranes in cells. The development of a novel recombinant agnoprotein expression system permitted the identification of the first small molecules targeting agnoprotein. These compounds abrogated agnoprotein viroporin activity in vitro and reduced virus release, indicating that viroporin activity contributes to the phenotype observed in agnoprotein knockout viruses. The identification of channel activity should enhance the future understanding of the physiological function of agnoprotein and could represent an important target for antiviral intervention.
Coregulation of extracellular vesicle production and fluconazole susceptibility inCryptococcus neoformans
Authors: Rizzo Juliana , Trottier Adèle , Moyrand Frédérique , Coppee Jean-Yves , Maufrais Corinne , Zimbres Ana Claudia G. , Dang Thi Tuong Vi , Alanio Alexandre , Desnos-Ollivier Marie , Mouyna Isabelle , Péhau-Arnaudet Gérard , Commere Pierre-Henri , Novault Sophie , Ene Iuliana V. , Nimrichter Leonardo , Rodrigues Marcio L. , Janbon Guilhem 
Published: January 2023

ABSTRACTResistance to fluconazole (FLC), the most widely used antifungal drug, is typically achieved by altering the azole drug target and/or drug efflux pumps. Recent reports have suggested a link between vesicular trafficking and antifungal resistance. Here, we identified novelCryptococcus neoformansregulators of extracellular vesicle (EV) biogenesis that impact FLC resistance. In particular, the transcription factor Hap2 does not affect the expression of the drug target or efflux pumps, yet it impacts the cellular sterol profile. Subinhibitory FLC concentrations also downregulate EV production. Moreover,in vitrospontaneous FLC-resistant colonies showed altered EV production, and the acquisition of FLC resistance was associated with decreased EV production in clinical isolates. Finally, the reversion of FLC resistance was associated with increased EV production. These data suggest a model in which fungal cells can regulate EV production in place of regulating the drug target gene expression as a first line of defense against antifungal assault in this fungal pathogen.IMPORTANCEExtracellular vesicles (EVs) are membrane-enveloped particles that are released by cells into the extracellular space. Fungal EVs can mediate community interactions and biofilm formation but thier functions remain poorly understood. Here, we report the identification of the first regulators of EV production in the major fungal pathogenCryptococcus neoformans.Surprisingly, we uncover a novel role of EVs in modulating antifungal drug resistance. Disruption of EV production was associated with altered lipid composition and changes in fluconazole susceptibility. Spontaneous azole-resistant mutants were deficient in EV production, while loss of resistance restored initial EV production levels. These findings were recapitulated inC. neoformansclinical isolates, indicating that azole resistance and EV production are coregulated in diverse strains. Our study reveals a new mechanism of drug resistance in which cells adapt to azole stress by modulating EV production.
The E3 ubiquitin ligase DTX3L and the deubiquitinase USP28 fine-tune DNA double strand repair through mutual regulation of their protein levels
Authors: Mennerich Daniela , Ashok Yashwanth , Vela-Rodríguez Carlos , Hentilä Heli I. , Rall-Scharpf Melanie , Wiesmüller Lisa , Prunskaite-Hyyryläinen Renata , Lehtiö Lari , Kietzmann Thomas 
Published: January 2023

SummaryThe DNA damage response (DDR) relies on a complex protein network to maintain genomic integrity, yet the interplay between post-translational modifiers remains poorly understood. Here, we uncover a novel regulatory axis between the E3 ubiquitin ligase DTX3L and the deubiquitinase USP28 at DNA double-strand breaks (DSBs). Our results reveal a sophisticated feedback mechanism in which DTX3L ubiquitinates USP28, leading to its proteasomal degradation, while USP28 counteracts by deubiquitinating both itself and DTX3L. This cross-regulation fine-tunes DSB repair in multiple pathways, including non-homologous end joining (NHEJ), homologous recombination (HR), single-strand annealing (SSA), and microhomology-mediated end joining (MMEJ). Strikingly, the detrimental effects of USP28 depletion on these repair pathways were rescued by concurrent DTX3L knockdown. Collectively, our work uncovers a novel layer of DDR regulation in which DTX3L and USP28’s antagonistic activities calibrate cellular responses to genotoxic stress, thus identifying promising therapeutic targets to combat diseases associated with genomic instability.HighlightsDTX3L and USP28 physically interact and colocalize in cellular sub-compartments, with the N-terminal D1-D3 domains of DTX3L primarily mediating the interactionDTX3L ubiquitinates USP28 for degradation, while USP28 deubiquitinates itself and DTX3L, creating a sophisticated feedback mechanism.The DTX3L-USP28 circuit influences levels of key proteins like HIF-1α, p53, and c-MYC, suggesting broader impacts on cellular stress responses.DTX3L and USP28 cooperatively regulate multiple DSB repair pathways, including NHEJ, HR, SSA, and MMEJ, with USP28 depletion effects rescued by DTX3L silencing.
G-quadruplexes regulate miRNA biogenesis in live zebrafish embryos
Authors: Steeman Tomás J. , Weiner Andrea M. J. , David Aldana P. , Binolfi Andrés , Calcaterra Nora B. , Armas Pablo 
Published: January 2023

AbstractRNA guanine quadruplexes (G4s) regulate RNA functions, metabolism, and processing. G4s formed within precursors of microRNAs (pre-miRNAs) may impair pre-miRNAs maturation by Dicer, thus repressing mature miRNA biogenesis. As miRNAs are essential for proper embryonic development, we studied the role of G4s on miRNA biogenesisin vivoduring zebrafish embryogenesis. We performed a computational analysis on zebrafish pre-miRNAs to find putative G4 forming sequences (PQSs). The precursor of the miRNA 150 (pre-miR-150) was found to contain an evolutionarily conserved PQS formed by three G-tetrads and able to foldin vitroas G4. MiR-150 controls the expression ofmyb, which shows a well-defined knock-down phenotype in zebrafish developing embryos. We microinjected zebrafish embryos within vitrotranscribed pre-miR-150 synthesized using either GTP (G-pre-miR-150) or 7-Deaza-GTP, a GTP analogue unable to form G4s (7DG-pre-miR-150). Compared to embryos injected with G-pre-miR-150, embryos injected with 7DG-pre-miR-150 showed higher levels of miRNA 150 (miR-150) and lower levels ofmybmRNA and stronger phenotypes associated withmybknock-down. The incubation of pre-miR-150 prior to the injection with the G4 stabilizing ligand pyridostatin (PDS) reverted gene expression variations and rescued the phenotypes related tomybknock-down. Overall, results suggest that the G4 formed in pre-miR-150 functionsin vivoas a conserved regulatory structure competing with the stem-loop structure necessary for miRNA biogenesis.