bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plastid DNA sequences and oospore characters of some European species ofTolypellasectionTolypella(Obtusifolia, Characeae) indicate a new crypticTolypellaspecies from the Mediterranean island Sardinia
Authors: Holzhausen Anja , Nowak Petra , Ballot Andreas , Becker Ralf , Gebert Jasmina , Gregor Thomas , Karol Kenneth G. , Lambert Elisabeth , Pérez William , Raabe Uwe , Schneider Susanne C. , Stewart Nick , van de Weyer Klaus , Wilde Volker , Schubert Hendrik 
Published: November 2022

AbstractIn Europe, the genusTolypella(Characeae) comprises four to eightTolypellaspecies in sectionsRothiaandTolypellathat have been distinguished by vegetative morphology and gametangial characters such as antheridial size and oospore cell wall ornamentation. However, morphological species differentiation is difficult in some cases due to overlapping and variable vegetative features, which in many cases are difficult to observe clearly.To clarify the taxonomic status of the five European species ofTolypellain sectionTolypella, sequence data of the plastid genesatpB,rbcL andpsbC forTolypella glomerata(Desv.) Leonh.,Tolypella hispanicaAllen,Tolypella nidifica(O.F. Müll.) A. Braun,Tolypella normaniana(Nordst.) Nordst. andTolypella salinaCor. were combined with data on oospore morphology, including oospore wall ornamentation.Gene sequence data identified five distinct clusters, but they differed from the morphologically identified five species. ‘T. glomerata’ consisted of some of the samples morphologically identified asT. glomerataand seven samples ofT. normaniana, while the remainingT. glomeratasamples clustered with specimens of unclear affiliation (“Tolypella. sp.”). ‘T. hispanicaI’ consisted of samples from various locations, whereas “T.hispanicaII” consisted of samples ofT. hispanicafrom the Mediterranean island, Sardinia. The remaining cluster consisted of all the specimens that had been determined asT. salinaorT. nidificain addition to two specimens ofT. normaniana. Oospore morphology was most clearly distinguishable forT. glomerata. Oospore characteristics for all other taxa were not as informative but showed some geographical and/or environmentally influenced differences, especially forT. nidificaandT. salina.Our results suggest a significantly different taxonomy ofTolypellasect.Tolypellain which specimens normally identified asT. glomeratamight be two different species,T. glomerataand an unidentified species;T. nidificaandT. salinaare not separate species;T. normanianais a diminutive variant ofT. nidificaorT. salina; andT. hispanicacomprises two different species, one from the Mediterranean island Sardnia.
Mapping phosphorylation post-translational modifications along single peptides with nanopores
Authors: Nova Ian C. , Ritmejeris Justas , Brinkerhoff Henry , Koenig Theo J. R. , Gundlach Jens H. , Dekker Cees 
Published: November 2022

AbstractCurrent methods to detect post-translational modifications (PTMs) of proteins, such as phosphate groups, cannot measure single molecules and often cannot differentiate between closely spaced phosphorylation sites. Using a nanopore sequencing approach, we here report detection of PTMs at the single-molecule level on immunopeptide sequences with cancer-associated phosphate variants. We reliably discriminate peptide sequences with one or two closely spaced phosphates with 95% accuracy for individual reads of single molecules.
Risk Assessment of the newly emerged H7N9 avian influenza viruses
Authors: Chang Pengxiang , Sadeyen Jean-Remy , Bhat Sushant , Daines Rebecca , Hussain Altaf , Yilmaz Huseyin , Iqbal Munir 
Published: November 2022

ABSTRACTSince the first human case in 2013, H7N9 avian influenza viruses (AIVs) have caused more than 1500 human infections with a mortality rate of approximately 40%. Despite large-scale poultry vaccination regimes across China, the H7N9 AIVs continue to persist and evolve rapidly in poultry. Recently, several strains of H7N9 AIVs have been isolated and shown the ability to escape vaccine-induced immunity. To assess the zoonotic risk of the recent H7N9 AIV isolates, we rescued viruses with hemagglutinin (HA) and neuraminidase (NA) from these H7N9 AIVs and six internal segments from PR8 virus (A/Puerto Rico/8/34 [H1N1]) and characterized their receptor binding, pH of fusion, thermal stability, plaque morphology and in ovo virus replication. We also assessed the cross-reactivity of the viruses with human monoclonal antibodies (mAbs) against H7N9 HA and ferret antisera against H7N9 AIV candidate vaccines. The H7N9 AIVs from the early epidemic waves had dual sialic acid receptor binding characteristics, whereas the more recent H7N9 AIVs completely lost or retained only weak human sialic acid receptor binding. Compared with the H7N9 AIVs from early epidemic waves (2013-2016), the recent (2020/21) viruses formed larger plaques and increased replication titres in ovo, demonstrating increased acid stability but reduced thermal stability. Further analysis showed that these recent H7N9 AIVs had poor cross-reactivity with the human mAbs and ferret antisera, highlighting the need to update the vaccine candidates. To conclude, the newly emerged H7N9 AIVs showed characteristics of typical AIVs, posing reduced zoonotic risk but a heightened threat for poultry.
Targeting of plasmodesmal proteins requires unconventional signals
Authors: Robles Luna Gabriel , Li Jiefu , Wang Xu , Liao Li , Lee Jung-Youn 
Published: November 2022

ABSTRACTCellular signaling relies on precise spatial localization and dynamic interactions of proteins within the subcellular compartment or niches, including cell-cell contact sites and connections. In plants, both endogenous and pathogenic proteins gained the ability to target plasmodesmata, the membrane-lined cytoplasmic connections, to regulate or exploit cellular signaling across cell wall boundaries. Those include the receptor-like membrane protein PDLP5, a potent regulator of plasmodesmal permeability that generates feed-forward or -back signals vital for plant immunity and root development. However, little is known about what molecular features determine the plasmodesmal association of PDLP5 or other proteins. Notably, although these proteins each have the ability to target plasmodesmata, no protein motifs or sequences have been identified indicative of targeting signals. To address this knowledge gap, we combined machine learning and targeted mutagenesis approaches. Here we report that PDLP5 and its closely related proteins carry novel targeting signals comprising short stretches of amino acid residues. As for PDLP5, it contains two non-redundant, tandemly arranged signals, either of which is sufficient for both localization and biological function regulating viral movement. Strikingly, plasmodesmal targeting signals exhibit little conservation in sequence but are located similarly proximal to the membrane. These novel unconventional features appear to be a common theme in plasmodesmal targeting.
Two pup vocalization types are genetically and functionally separable in deer mice
Authors: Jourjine N. , Woolfolk M.L. , Sanguinetti-Scheck J.I. , Sabatini J.E. , McFadden S. , Lindholm A.K. , Hoekstra H.E. 
Published: November 2022

AbstractVocalization is a widespread vertebrate social behavior that is essential for fitness in the wild. While many vocal behaviors are highly conserved, heritable features of specific vocalization types can vary both within and between species, raising the questions of why and how some vocal behaviors evolve. Here, using new computational tools to automatically detect and cluster vocalizations into distinct acoustic categories, we compare pup isolation calls across neonatal development in eight taxa of deer mice (genusPeromyscus) and compare them to laboratory mice (C57Bl6/j strain) and free-living, wild house mice (Mus musculus musculus). Whereas bothPeromyscusandMuspups produce ultrasonic vocalizations (USVs),Peromyscuspups also produce a second call type with acoustic features, temporal rhythms, and developmental trajectories that are distinct from those of USVs. In deer mice, these tonal and low frequency “cries” are predominantly emitted in postnatal days one through nine, while USVs are primarily made after day nine. Using playback assays, we show that cries result in a more rapid approach byPeromyscusmothers than USVs, suggesting a role for cries in eliciting parental care early in neonatal development. Using genetic crosses between two sister species of deer mice exhibiting large, innate differences in the acoustic structure of cries and USVs, we find that variation in vocalization rate, duration, and pitch display different degrees of genetic dominance and that cry and USV features can be uncoupled in second-generation hybrids. Taken together, this work shows that vocal behavior can evolve quickly between closely related rodent species in which vocalization types, likely serving distinct functions in communication, are controlled by distinct genetic loci.
NLRP3 inflammasome is dispensable in methicillin resistantStaphylococcus aureusurinary tract infection
Authors: Paudel Santosh , Rogers Kenneth A , Kumar Rahul , Saini Yogesh , Patial Sonika , Kulkarni Ritwij 
Published: November 2022

AbstractNLRP3 inflammasome is a cytoplasmic complex that senses molecular patterns from pathogens or damaged cells to trigger an innate immune defense response marked by the production of proinflammatory cytokines IL-1β and IL-18 and an inflammatory death called pyroptosis. The NLRP3 inflammasome is activated in the urinary tract by a variety of infectious and non-infectious insults. In this study, we investigated the role of NLRP3 inflammasome by inducing methicillin resistantStaphylococcus aureus(MRSA) ascending UTI in WT andNlrp3-/-mice. At 24 and 72 hpi, compared to the WT, the MRSA-infectedNlrp3-/-showed ∼100-fold lower median CFUs, although this reduction was not statistically significant. The ablation of NLRP3 did not affect MRSA-induced urinary immune defenses as indicated by the similar levels of pro-inflammatory cytokines and chemokines and the similar numbers of granulocytes in the bladder and the kidneys of WT andNlrp3-/-mice at 24 h after MRSA infection. However, MRSA-infectedNlrp3-/-bladders, but not kidneys, showed significantly higher monocyte infiltration. The histopathological analysis of bladder and kidney sections showed similar inflammation in MRSA-infectedNlrp3-/-and WT mice. Overall, these results suggest that MRSA-induced urinary NLRP3 activity is dispensable to the host.ImportanceIndwelling urinary catheter usage increased susceptibility to methicillin-resistantStaphylococcus aureus(MRSA) urinary tract infections (UTI) which can be difficult to treat and can result in potentially fatal complications such as bacteremia, urosepsis, and shock. In this work, we examined the role of NLRP3 inflammasome in MRSA uropathogenesis. In comparison to the WT, mice deficient in NLRP3 activity showed similar MRSA burden and similar inflammation in the bladder and kidney tissues at 24 h after the experimental induction of ascending UTI. These results suggest that NLRP3 inflammasome is not involved in shaping urinary immune defenses during acute MRSA-UTI.
Regulation of multidrug efflux pumps by TetR family transcriptional repressor negatively affects secondary metabolism inStreptomyces coelicolorA3(2)
Authors: Lei Yukun , Asamizu Shumpei , Ishizuka Takumi , Onaka Hiroyasu 
Published: November 2022

ABSTRACTStreptomycesspp. are well-known producers of bioactive secondary metabolites (SMs) that serve as pharmaceutical agents. In addition to their ability to produce SMs,Streptomycesspp. have evolved diverse membrane transport systems to protect cells against antibiotics produced by itself or other microorganisms. We previously screened mutants ofStreptomyces coelicolorthat show a phenotype of reduced undecylprodigiosin (RED) production in a combined-culture withTsukamurella pulmonis. Here, we identified a point mutation, which reduced RED production, by performing genome resequencing and genetic complementation. We found that inactivation of thesco1718gene encoding the TetR family transcriptional regulator (TFR) produced a deficient phenotype for several SMs inStreptomyces coelicolorA3(2). Electrophoretic mobility shift assay and quantitative reverse transcription-PCR experiments demonstrated that SCO1718 repressed the expression of adjacent two-component ATP-binding cassette (ABC) transporter genes (sco1719-20) by binding to the operator sequence in the 5′-UTR. Notably, the Δsco1718mutant showed increased resistance to several antibiotics of other actinomycete origin. In the genome ofS. coelicolorA3(2), two other sets of TFR and two-component ABC transporter genes (sco4358-4360andsco5384-5382) were found, which had similar effects on the phenotype for both secondary metabolism and antibiotic resistance. Our results imply the switching of cell metabolism to direct offence (antibiotic production) or defense (efflux pump activation) using costly and limited quantities of cell energy sources (e.g., ATP) in the soil ecosystem.IMPORTANCEThe bacterial metabolic potential to synthesize diverse secondary metabolites (SMs) in the environment has been revealed by recent (meta-)genomics of both unculturable and culturable bacteria. These studies imply that bacteria are continuously exposed to harmful chemical compounds in the environment.Streptomycesspp. contain antibiotic efflux pumps and SM biosynthetic gene clusters. However, the mechanism by which soil bacteria, includingStreptomyces, survive against toxic compounds in the environment remains unclear. Here, we identified three sets of TFR-ABC transporter genes inStreptomyces coelicolorA3(2). We found that each TFR controlled the expression of a respective ABC transporter, and the expression of all ABC transporters negatively impacted SM production and increased antibiotic resistance. Notably, bioinformatic analysis indicated that these TFR-ABC transporter gene sets are highly conserved and widely distributed in the genome ofStreptomycesspecies, indicating the importance of systematic regulation that directs antibiotic production and xenobiotic excretion.
NhaR, LeuO and H-NS are part of an expanded regulatory network for ectoine biosynthesis expression
Authors: Boas Lichty Katherine E. , Gregory Gwendolyn J. , Boyd E. Fidelma 
Published: November 2022

AbstractBacteria accumulate compatible solutes, to maintain cellular turgor pressure when exposed to high salinity. In the marine halophileVibrio parahaemolyticus,the compatible solute ectoine is biosynthesizedde novo, which is energetically more costly than uptake; therefore, tight regulation is required. To uncover novel regulators of the ectoine biosynthesisectABC-asp_ectoperon, a DNA affinity pulldown of proteins interacting with theectABC-asp_ectregulatory region was performed. Mass spectrometry analysis identified, amongst others, three regulators: LeuO, NhaR, and the nucleoid associated protein H-NS. In-frame non-polar deletions were made for each gene and PectA-gfppromoter reporter assays were performed in exponential and stationary phase cells. PectA-gfpexpression was significantly repressed in the ΔleuOmutant and significantly induced in the ΔnhaRmutant compared to wild type, suggesting positive and negative regulation, respectively. In the Δhnsmutant, PectA-gfpshowed increased expression in exponential phase cells, but no change compared to wild type in stationary phase cells. To examine whether H-NS interacts with LeuO or NhaR at the ectoine regulatory region, double deletion mutants were created. In a ΔleuO/Δhnsmutant, PectA-gfpshowed reduced expression, but significantly more than ΔleuOsuggesting H-NS and LeuO interact to regulate ectoine expression. Whereas ΔnhaR/Δhnshad no additional effect as compared to ΔnhaRsuggesting NhaR regulation is independent of H-NS. To examineleuOregulation further, a PleuO-gfpreporter analysis was examined that showed significantly increased expression in the ΔleuO, Δhnsand ΔleuO/Δhnsmutants as compared to wild type, indicating both are repressors. Growth pattern analysis of the mutants in M9G 6%NaCl, showed growth defects compared to wild type, indicating that these regulators play an important physiological role in salinity stress tolerance.ImportanceEctoine is a commercially used compatible solute that acts as a biomolecule stabilizer because of its additional role as a chemical chaperone. A better understanding of how the ectoine biosynthetic pathway is regulated in natural bacterial producers can be used to increase efficient industrial production. Thede novobiosynthesis of ectoine is essential for bacteria to survive osmotic stress when exogenous compatible solutes are absent. This study identified LeuO as a positive regulator and NhaR as a negative regulator of ectoine biosynthesis and also showed that similar to enteric species, LeuO is an anti-silencer of H-NS. In addition, defects in growth in high salinity among all the mutants suggest that these regulators play a broader role in the osmotic stress response beyond ectoine biosynthesis regulation.
Early induction of cytokine release syndrome by rapidly generated CAR T cells in a preclinical mouse model
Authors: Ho Naphang , Jamali Arezoo , Braun Angela , Adabi Elham , Thalheimer Frederic B. , Buchholz Christian J. 
Published: November 2022

SummaryChimeric antigen receptor (CAR) T cells have emerged as effective strategy against B cell malignancies. Since the long manufacturing process limits patient accessability, short-term (st) CAR T cells are under investigation. Here, we evaluated CD19-CAR T cells 24 hours after exposure to lentiviral vectors. In co-culture with tumor cells and monocytes, stCAR T cells exhibited anti-tumoral activity and strong release of CRS-relevant cytokines (IL-6, IFN-γ, TNF-α, GM-CSF, IL-2, IL-10). When administered into tumor engrafted NSG-SGM3 mice, severe acute adverse events encompassing high body scoring, temperature and weight drop arised rapidly within 24 hours. Human (IFN-Y, TNF-α, IL-2, IL-10) and murine (MCP-1, IL-6, G-CSF) cytokines typical for severe cytokine release syndrome (CRS) were systemically elevated. Our data highlight potential safety risks of CAR T cells manufactured within short time and suggest simple models for their preclinical safety evaluation.
PD-1 is induced on tumor-associated macrophages in obesity to directly restrain anti-tumor immunity
Authors: Bader Jackie E. , Wolf Melissa M. , Madden Matthew Z. , Reinfeld Bradley I. , Arner Emily N. , Hathaway Emma S. , Steiner KayLee K. , Needle Gabriel A. , Landis Madelyn D. , Cottam Matthew A. , Ye Xiang , Christofides Anthos , Boussiotis Vassiliki A. , Haake Scott M. , Beckermann Kathryn E. , Rathmell W. Kimryn , Hasty Alyssa H. , Rathmell Jeffrey C. 
Published: November 2022

SummaryObesity is a leading risk factor for progression and metastasis of many cancers1,2, yet can also promote improved survival for some cancers3-5and enhance responses to some immune checkpoint blockade therapies6-8. The role of the immune system in the obesity-cancer connection and how obesity influences immunotherapy, however, remain unclear. While PD-1 expression by macrophages has been described9-12, we found that obesity selectively induced PD-1 on macrophages and that PD-1 directly impaired macrophage function. Single cell RNA sequencing of murine colorectal carcinoma tumors showed obesity remodeled myeloid and T cell populations, with fewer clonally expanded effector T cells and increased abundance of PD-1+tumor-associated macrophages (TAM). Cytokines and molecules associated with obesity, including IL-6, leptin, and insulin, and the unsaturated fatty acid palmitate, induced PD-1 expression on macrophages in a glycolysis-dependent manner. PD-1+TAMs had increased mitochondrial respiration and expression of genes regulating oxidative phosphorylation, lipid uptake and cell cycle while PD-1-TAMs showed greater signatures of phagocytosis and antigen presentation to T cells. These patterns were directly regulated by PD-1, as recombinant PD-L1 reduced macrophage glycolysis and phagocytic capacity, and this was reversed with blocking PD-1 antibody. Conversely, PD-1-deficientPdcd1-/-TAMs had high rates of glycolysis, phagocytosis, and expression of MHC-II. Myeloid-specific PD-1 deficiency correlated with slower tumor growth, enhanced TAM antigen presentation capability, and increased CD8 T cell activation together with reduced markers of exhaustion. These findings show metabolic signaling in obesity induces PD-1-mediated suppression of TAM function and reveal a unique macrophage-specific mechanism to modulate immune tumor surveillance and checkpoint blockade. This may contribute to increased cancer risk yet improved response to PD-1 blockade in TAM-enriched tumors and obesity.
Genome-scale CRISPR screening reveals host factors required for ribosome formation and viral replication
Authors: Ohlson Maikke B. , Kumar Ashwani , Eitson Jennifer L. , Jang Seoyeon , Ni Chunyang , Xing Chao , Buszczak Michael , Schoggins John W. 
Published: November 2022

ABSTRACTViruses are known to co-opt host machinery for translation initiation, but less is known about which host factors are required for the formation of ribosomes used to synthesize viral proteins. Using a loss of function CRISPR screen, we show that synthesis of a flavivirus encoded reporter depends on multiple host factors, including several 60S ribosome biogenesis proteins. Viral phenotyping revealed that two of these factors, SBDS, a known ribosome biogenesis factor, and the relatively uncharacterized protein SPATA5, were broadly required for replication of flaviviruses, coronaviruses, alphaviruses, paramyxoviruses, an enterovirus, and a poxvirus. Mechanistic studies revealed that loss of SPATA5 caused defects in ribosomal RNA processing and ribosome assembly, suggesting that this human protein may be a functional ortholog of yeastDrg1. These studies implicate specific ribosome biogenesis proteins as viral host dependency factors that are required for synthesis of virally encoded protein and accordingly, optimal viral replication.
RUNX1 is regulated by androgen receptor to promote cancer stem markers and chemotherapy resistance in triple negative breast cancer
Authors: Fernández Natalia B , Sosa Sofía M , Roberts Justin T , Recouvreux María S , Rocha-Viegas Luciana , Christenson Jessica L , Spoelstra Nicole S , Couto Facundo L , Raimondi Ana R , Richer Jennifer K , Rubinstein Natalia 
Published: November 2022

ABSTRACTTriple negative breast cancer (TNBC) is an aggressive breast cancer subtype for which no effective targeted therapies are available. Growing evidence suggests that chemotherapy-resistant cancer cells with stem-like properties (CSC) may repopulate the tumor. Androgen receptor (AR) is expressed in up to 50% of TNBC, and AR inhibition decreases CSC and tumor initiation. Runt-related transcription factor 1 (RUNX1) correlates with poor prognosis in TNBC and is regulated by AR in prostate cancer. Our group has shown that RUNX1 promotes TNBC cell migration and regulates tumor gene expression. We hypothesized that RUNX1 is regulated by AR and that both may work together in TNBC CSC to promote disease recurrence following chemotherapy. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) experiments in MDA-MB-453 revealed AR binding toRUNX1regulatory regions. RUNX1 expression is upregulated by dihydrotestosterone (DHT) in MDA-MB-453 and in HCI-009 patient-derived xenograft (PDX) tumors (p<0.05). RUNX1 is increased in a CSC-like experimental model in MDA-MB-453 and SUM-159PT cells (p<0.05). Inhibition of RUNX1 transcriptional activity reduced the expression of CSC markers. Interestingly, RUNX1 inhibition reduced cell viability and enhanced paclitaxel and enzalutamide sensitivity. Targeting RUNX1 may be an attractive strategy to potentiate the anti-tumor effects of AR inhibition, specifically in the slow growing CSC-like populations that resist chemotherapy leading to metastatic disease.