bluuebunny/crossref_metadata_2025_split huggingface dataset:
BordetellaFilamentous hemagglutinin (FhaB) and Adenylyl cyclase toxin (ACT) interactions on the bacterial surface are consistent with FhaB-mediated delivery of ACT to phagocytic cells
Authors: Nash Zachary M. , Inatsuka Carol S. , Cotter Peggy A. , Johnson Richard M. 
Published: September 2023

ABSTRACTBordetellaspecies that cause respiratory infections in mammals includeB. pertussis, which causes human whooping cough, andB. bronchiseptica, which infects nearly all mammals. Both bacterial species produce filamentous hemagglutinin (FhaB) and adenylyl cyclase toxin (ACT), prominent surface-associated and secreted virulence factors that contribute to persistence in the lower respiratory tract by inhibiting clearance by phagocytic cells. FhaB and ACT proteins interact with themselves, each other, and host cells. Using immunoblot analyses, we showed that ACT binds to FhaB preferentially on the bacterial surface before being released into the extracellular environment. We showed that SphB1, a surface protease identified based on its ability to cleave FhaB, also cleaves ACT, and we showed that the presence of ACT blocks SphB1-dependent and independent cleavage of FhaB, but the presence of FhaB does not block SphB1-dependent cleavage of ACT. SphB1-dependent cleavage of ACT occurs proximally to ACT’s active site, and hence is predicted to inactivate ACT. We also showed that FhaB-bound ACT can intoxicate host cells producing CR3, the receptor for ACT. In addition to increasing our understanding of FhaB, ACT, and ACT interactions on theBordetellasurface, our data support a model in which FhaB functions as a novel toxin delivery system by binding to ACT and allowing its release upon binding of ACT to its receptor, CR3, on phagocytic cells.AUTHOR SUMMARYBacteria need to control the variety, abundance, and conformation of proteins on the cellular surface to survive. Members of the Gram-negative bacterial genusBordetellaincludeB. pertussis, which causes whooping cough in humans, andB. bronchiseptica, which causes respiratory infections in a broad range of mammals. These extremely closely related species produce two prominent virulence factors, the two-partner secretion (TPS) effector FhaB and Adenylyl cyclase toxin (ACT), that interact with themselves, each other, and host cells. In this work, we showed that ACT binds preferentially to FhaB on the bacterial surface before being released into the extracellular environment. We showed that the exoprotease SphB1, which cleaves FhaB, also cleaves ACT. We showed that ACT that is bound to FhaB can be delivered to CR3+host cells. Our data support a model in which FhaB functions to deliver ACT specifically to phagocytic cells, and not epithelial cells. This is the first report of a TPS system facilitating delivery of a separate polypeptide toxin to target cells and expands our understanding of how these systems contribute to bacterial pathogenesis.
Effects of mild winter conditions and two pyrethroid insecticides on the development and survival of juvenile common toads (Bufo bufo)
Authors: Kásler Andrea , Bókony Veronika , Mikó Zsanett , Herczeg Dávid , Ujszegi János , Holly Dóra , Hettyey Attila 
Published: September 2023

ABSTRACTCombined effects of pollutants and climate change can have long-term negative effects on Earth’s biodiversity. We tested how amphibians are affected by exposure to pesticides around metamorphosis in combination with current winter conditions or those projected to become the norm by 2100. We applied two pyrethroid insecticides, cypermethrin or deltamethrin, to newly metamorphosed common toads (Bufo bufo) via spraying, thereafter reared animals in outdoor enclosures, and finally exposed them either to a long&cold winter (1.5 °C for 91 days) or to a short&mild one (4.5 °C for 61 days). After hibernation, we examined changes in body mass, size and gross morphology of parotoid glands and visceral organs, and determined the phenotypic sex of the surviving toadlets. In the long&cold winter scenario, we observed high mortality rate, regardless of the chemical treatment (control: 82%, cypermethrin: 78%, deltamethrin: 70%). At the same time, mortality was significantly lower in the short&mild winter scenario (control: 33%, cypermethrin: 41%, deltamethrin: 26%). The decrease in body mass during overwintering did not differ among treatment groups. Our results contradict the hypothesis of sex-biased mortality caused by chemical pollutants, harsh or mild winter conditions or by their combination. No significant deformations of the internal organs were found in either group. Our results suggest that winter conditions becoming ever milder in the temperate zone may prove beneficial for amphibian overwinter survival, and that exposure to the tested pyrethroids at ecologically relevant concentrations after metamorphosis does not interfere with the fitness of juvenile common toads.
The catalytic mechanism of the RNA methyltransferase METTL3
Authors: Corbeski Ivan , Vargas-Rosales Pablo Andrés , Bedi Rajiv Kumar , Deng Jiahua , Coelho Dylan , Braud Emmanuelle , Iannazzo Laura , Li Yaozong , Huang Danzhi , Ethève-Quelquejeu Mélanie , Cui Qiang , Caflisch Amedeo 
Published: September 2023

AbstractThe complex of methyltransferase-like proteins 3 and 14 (METTL3-14) is the major enzyme that deposits N6-methyladenosine (m6A) modifications on mRNA in humans. METTL3-14 plays key roles in various biological processes through its methyltransferase (MTase) activity. However, little is known about its substrate recognition and methyl transfer mechanism from its cofactor and methyl donor S-adenosylmethionine (SAM). Here, we study the MTase mechanism of METTL3-14 by a combined experimental and multiscale simulation approach using bisubstrate analogues (BAs), conjugates of a SAM-like moiety connected to the N6-atom of adenosine. Molecular dynamics simulations based on crystal structures of METTL3-14 with BAs suggest that the Y406 side chain of METTL3 is involved in the recruitment of adenosine and release of m6A. A crystal structure with a bisubstrate analogue representing the transition state of methyl transfer shows a direct involvement of the METTL3 side chains E481 and K513 in adenosine binding which is supported by mutational analysis. Quantum mechanics/molecular mechanics (QM/MM) free energy calculations indicate that methyl transfer occurs without prior deprotonation of adenosine-N6. Furthermore, the QM/MM calculations provide further support for the role of electrostatic contributions of E481 and K513 to catalysis. The multidisciplinary approach used here sheds light on the (co)substrate binding mechanism, catalytic step, and (co)product release catalysed by METTL3, and suggests that the latter step is rate-limiting. The atomistic information on the substrate binding and methyl transfer reaction of METTL3 can be useful for understanding the mechanisms of other RNA MTases and for the design of transition state analogues as their inhibitors.One sentence summaryA combined structural, biochemical, and computational approach reveals two distinct binding conformations of adenosine, the transition state of methyl transfer, and the catalytic mechanism of the human m6A RNA methyltransferase METTL3-14.
Optimisation of cell fate determination for cultured muscle differentiation
Authors: Melzener Lea , Schaeken Lieke , Fros Marion , Messmer Tobias , Raina Dhruv , Kiessling Annemarie , van Haaften Tessa , Spaans Sergio , Doǧan Arin , Post Mark J. , Flack Joshua E. 
Published: September 2023

AbstractProduction of cultured meat requires defined medium formulations for the robust differentiation of myogenic cells into mature skeletal muscle fibers in vitro. Whilst such formulations can drive myogenic differentiation to an extent similar to serum-starvation based protocols, these cultures are invariably heterogeneous in nature, with a significant proportion of cells not participating in myofusion, limiting maturation of the muscle. Here, we use RNA sequencing to characterise this heterogeneity at single-nucleus resolution, identifying distinct cellular subpopulations, including proliferative cells that fail to exit the cell cycle, and ’reserve cells’ that do not commit to myogenic differentiation. We show that the ERK, NOTCH and RXR pathways act during the first stages of myogenic cell fate determination, and by targeting these pathways, cell cycle exit can be promoted whilst abrogating reserve cell formation. Under these improved culture conditions, fusion indices close to 100% can be robustly obtained in 2D culture. Finally, we demonstrate that this translates to higher levels of myotube formation and muscle protein accumulation in animal component-free bioartificial muscle constructs, providing proof of principle for the generation of highly differentiated cultured muscle with excellent mimicry to traditional muscle.
SARS-CoV-2 ORF7a mutation found in BF.5 and BF.7 sublineages impacts its functions
Authors: Timilsina Uddhav , Duffy Sean R. , Plianchaisuk Arnon ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito Jumpei , Sato Kei , Stavrou Spyridon 
Published: September 2023

ABSTRACTA feature of the SARS-CoV-2 Omicron subvariants BF.5 and BF.7 that recently circulated mainly in China and Japan was the high prevalence of ORF7a: H47Y mutation. Here we evaluated the effect of this mutation on the three main functions ascribed to SARS-CoV-2 ORF7a protein. Our findings show that H47Y mutation impairs the ability of SARS-CoV-2 ORF7a to antagonize type-I interferon (IFN-I) response and to downregulate Major Histocompatibility Complex-I (MHC-I) cell surface levels, but had no effect in its anti-SERINC5 function. Overall, our results suggest that the H47Y mutation of ORF7a affects important functions of this protein resulting in changes in virus pathogenesis.ImportanceIn late 2021, the Omicron (B.1.1.529) VOC emerged and outcompeted the circulating VOC Delta (B.1.617.2). Soon afterwards, Omicron VOC has expanded and diversified in the world. Among the emerged subvariants of Omicron are BF.5 and BF.7 that are characterized by the presence of a number of mutations across their genome and spread quite effectively across China and other countries later on. One such mutation that was found in the vast majority of isolates of the BF.5 and BF.7 subvariants was ORF7a: H47Y, whose effect on ORF7a is unknown. In this report, we show that H47Y inhibits a number of ORF7a functions, which can potentially affect virus pathogenesis.
Emerging many-to-one weighted mapping in hippocampus-amygdala network underlies memory formation
Authors: Liu Jun , Hall Arron F , Wang Dong V 
Published: September 2023

AbstractMemories are crucial for our daily lives, yet the network-level organizing principle that governs neural representations of our experiences remains to be determined. Employing dual-site electrophysiology recording in freely behaving mice, we discovered that hippocampal dorsal CA1 (dCA1) and basolateral amygdala (BLA) utilize distinct coding strategies to represent novel experiences. A small assembly of BLA neurons rapidly emerged during memory acquisition and remained active during subsequent consolidation, whereas the majority of dCA1 neurons engaged in the same processes. Machine learning decoding revealed that dCA1 population spikes predicted the BLA assembly firing rate. This suggests that most dCA1 neurons concurrently index an episodic event by rapidly establishing weighted communications with a specific BLA assembly, a process we call “many-to-one weighted mapping.” Furthermore, we demonstrated that closed-loop optoinhibition of BLA activity triggered by dCA1 ripples after new learning resulted in impaired memory. These findings highlight a new principle of hippocampus-amygdala communication underlying memory formation and provide new insights into how the brain creates and stores memories.
Immunogenicity and tolerability of a SARS-CoV-2 TNX-1800, a live recombinant poxvirus vaccine candidate, in Syrian Hamsters and New Zealand White Rabbits
Authors: Awasthi Mayanka , Macaluso Anthony , Goebel Scott J , Luea Erin , Noyce Ryan S , Nasar Farooq , Daugherty Bruce , Bavari Sina , Lederman Seth 
Published: September 2023

AbstractTNX-1800 is a preclinical stage synthetic derived live chimeric horsepox virus vaccine that comprises an engineered SARS-CoV-2 spike (S) gene expression cassette. The objectives of this study were to assess the immunogenicity and tolerability of TNX-1800 administration in Syrian golden hamsters and New Zealand white rabbits. Animals were vaccinated via percutaneous inoculation and evaluated for dose tolerance and immunogenicity at three different dose levels. The 28-day study data showed that the single percutaneous administration of three TNX-1800 vaccine dose levels was well tolerated in both hamsters and rabbits. For all dose levels, rabbits had more dermal observations than hamsters at the same dose levels. Vaccine-induced viral load four weeks post-dosing was below the detection level for both species.
Mycobacterium tuberculosisrequires conditionally essential metabolic pathways for infection
Authors: Block Alisha M. , Wiegert Parker C. , Namugenyi Sarah B. , Tischler Anna D. 
Published: September 2023

ABSTRACTNew drugs are needed to shorten and simplify treatment of tuberculosis caused byMycobacterium tuberculosis. Metabolic pathways thatM. tuberculosisrequires for growth or survival during infection represent potential targets for anti-tubercular drug development. Genes and metabolic pathways essential forM. tuberculosisgrowth in standard laboratory culture conditions have been defined by genome-wide genetic screens. However, whetherM. tuberculosisrequires these essential genes during infection has not been comprehensively explored because mutant strains cannot be generated using standard methods. Here we show thatM. tuberculosisrequires functional phenylalanine (Phe) andde novopurine and thiamine biosynthetic pathways for mammalian infection. We used a defined collection ofM. tuberculosistransposon (Tn) mutants in essential genes, which we generated using a custom nutrient-rich medium, and transposon sequencing (Tn-seq) to identify multiple central metabolic pathways required for fitness in a mouse infection model. We confirmed by individual retesting and complementation that mutations inpheA(Phe biosynthesis) orpurF(purine and thiamine biosynthesis) cause death ofM. tuberculosisin the absence of nutrient supplementationin vitroand strong attenuation in infected mice. Our findings show that Tn-seq with defined Tn mutant pools can be used to identifyM. tuberculosisgenes required during mouse lung infection. Our results also demonstrate thatM. tuberculosisrequires Phe and purine/thiamine biosynthesis for survival in the host, implicating these metabolic pathways as prime targets for the development of new antibiotics to combat tuberculosis.AUTHOR SUMMARYMycobacterium tuberculosiscauses more than 10 million new cases of active tuberculosis (TB) disease and 1.6 million deaths worldwide each year. Individuals with active TB must take a combination of four antibiotics for a minimum of 6-9 months to cure the infection. New anti-tubercular drugs are needed to simplify TB treatment and combat drug resistance. Here, we describe a novel collection ofM. tuberculosismutants lacking metabolic pathways essential for growth in standard laboratory conditions. Using these mutants, a mouse infection model, and deep sequencing we identified those metabolic pathways thatM. tuberculosisalso requires during infection. We find thatM. tuberculosismutants that cannot synthesize purine nucleotides, riboflavin, or certain amino acids are unable to grow in mice. We also find that mutant strains which cannot synthesize purine nucleotides or the amino acid phenylalanine die rapidly in laboratory cultures without nutrient supplementation, suggesting that new drugs targeting these pathways would killM. tuberculosis. Overall, our work reveals multiple metabolic pathways thatM. tuberculosisrequires during infection, which could be pursued as new targets for development of anti-tubercular drugs.
Interim influenza vaccine effectiveness estimates during the 2023 Southern Hemisphere season
Authors: Acevedo-Rodriguez J Gonzalo , Zamudio Carlos , Kojima Noah , Krapp Fiorella , Tsukayama Pablo , Neciosup-Vera C Stefany , Gotuzzo Eduardo 
Published: September 2023

AbstractOur findings suggest that a substantial number of people sought care for CLI during an early Southern Hemisphere season during which A/H1N1pdm09 clade 6B.1A.5a.2a viruses predominated. The minority vaccinated benefitted from the A/Victoria/2570/2019 (H1N1)pdm09-like antigen which afforded good protection against illness.
Beneficial changes in the gut microbiome of patients with multiple sclerosis after consumption of Neu-REFIX B-glucan in a clinical trial
Authors: Dedeepiya Vidyasagar Devaprasad , Vetrievel Chockanathan , Ikewaki Nobunao , Yamamoto Naoki , Kawashima Hiroto , Ichiyama Koji , Senthilkumar Rajappa , Preethy Senthilkumar , Abraham Samuel JK 
Published: September 2023

AbstractBackgroundMultiple sclerosis (MS) is a debilitating demyelinating disease and recent evidences are giving cues towards correlation of disease severity to gut microbiome dysbiosis. However, there haven’t been any reported interventions that beneficially modifies the gut microbiome to yield a clinically discernible improvement. Having earlier reported the clinical effects of a biological response modifier beta-glucan (BRMG) produced by the N-163 strain ofAureobasidum pullulans, commercially available as Neu-REFIX, which decreased the biomarkers of inflammation and produced beneficial immune-modulation in twelve MS patients in 60 days, we evaluated their gut microbiome in the present study.MethodsTwelve patients diagnosed with MS participated in the study. Each consumed 16 g gel of the NEU-REFIX beta-Glucan for 60 days. Whole genome metagenomic sequencing was performed on the fecal samples before and after Neu-REFIX intervention.ResultsPost-intervention analysis showed thatActinobacteriafollowed byBacteroideswas the major family. Abundance of beneficial genera such asBifidobacterium, Collinsela, Prevotella, Lactobacillusand species such asPrevotella copri (p-value=0.4), Bifidobacterium longum (p-value=0.2), Faecalibacterium prausnitzii (p-value=0.06), Siphoviridae (p-value=0.06)increased while inflammation associated genera such asBlautia (p-value=0.06),Ruminococcus (p-value=0.007)andDorea (p-value = 0.03)decreased in abundance.ConclusionRestoration of gut eubiosis in terms of both increase in abundance of the good microbiome and suppression of the harmful ones which also correlate with earlier reported clinical improvement in MS patients makes this Neu-REFIX beta-glucan, a potential disease modifying therapy (DMT) requiring larger studies for validation in MS and other auto-immune-inflammatory conditions where a safe intervention for immune modulation is vital.
Convergent alterations in the tumor microenvironment of MYC-driven human and murine prostate cancer
Authors: Graham Mindy K , Wang Rulin , Chikarmane Roshan , Wodu Bulouere , Vaghasia Ajay , Gupta Anuj , Zheng Qizhi , Hicks Jessica , Sysa-Shah Polina , Pan Xin , Castagna Nicole , Liu Jianyong , Meyers Jennifer , Skaist Alyza , Zhang Yan , Schuebel Kornel , Simons Brian W , Bieberich Charles J. , Nelson William G , Lupold Shawn E. , DeWeese Theodore L , De Marzo Angelo M , Yegnasubramanian Srinivasan 
Published: September 2023

ABSTRACTThe tissue microenvironment in prostate cancer is profoundly altered. While such alterations have been implicated in driving prostate cancer initiation and progression to aggressive disease, how prostate cancer cells and their precursors mediate those changes is unclear, in part due to the inability to longitudinally study the disease evolution in human tissues. To overcome this limitation, we performed extensive single-cell RNA-sequencing (scRNA-seq) and rigorous molecular pathology of the comparative biology between human prostate cancer and key time points in the disease evolution of a genetically engineered mouse model (GEMM) of prostate cancer. Our studies of human tissues, with validation in a large external data set, revealed that cancer cell-intrinsic activation of MYC signaling was the top up-regulated pathway in human cancers, representing a common denominator across the well-known molecular and pathological heterogeneity of human prostate cancer. Likewise, numerous non-malignant cell states in the tumor microenvironment (TME), including non-cancerous epithelial, immune, and fibroblast cell compartments, were conserved across individuals, raising the possibility that these cell types may be a sequelae of the convergent MYC activation in the cancer cells. To test this hypothesis, we employed a GEMM of prostate epithelial cell-specific MYC activation in two mouse strains. Cell communication network and pathway analyses suggested that MYC oncogene-expressing neoplastic cells, directly and indirectly, reprogrammed the TME during carcinogenesis, leading to the emergence of cascading cell state alterations in neighboring epithelial, immune, and fibroblast cell types that paralleled key findings in human prostate cancer. Importantly, among these changes, the progression from a precursor-enriched to invasive-cancer-enriched state was accompanied by a cell-intrinsic switch from pro-immunogenic to immunosuppressive transcriptional programs with coinciding enrichment of immunosuppressive myeloid and Treg cells in the immune microenvironment. These findings implicate activation of MYC signaling in reshaping convergent aspects of the TME of prostate cancer as a common denominator across the otherwise well-documented molecular heterogeneity of human prostate cancer.
Speciation in kleptoparasites of oak gall wasps often correlates with a shift into a new tree habitat, tree organ, or gall morphospace
Authors: Ward Anna K.G. , Zhang Y. Miles , Brown Guerin E. , Hippee Alaine C. , Prior Kirsten M. , Rollins Shannon , Sierra Nicolas , Sheikh Sofia I. , Tribull Carly M. , Forbes Andrew A. 
Published: September 2023

AbstractHost shifts to new plants can drive speciation for plant-feeding insects, but how commonly do host shifts also drive diversification for the parasites of those same insects? Oak gall wasps induce galls on oak trees and shifts to novel tree hosts and new tree organs have been implicated as drivers of oak gall wasp speciation. Gall wasps are themselves attacked by many insect parasites, which must find their hosts on the correct tree species and organ, but which also must navigate the morphologically variable galls with which they interact. Thus, we ask whether host shifts to new trees, organs, or gall morphologies correlate with gall parasite diversification. We delimit species and infer phylogenies for two genera of gall kleptoparasites,SynergusandCeroptres, reared from a variety of North American oak galls. We find that most species were reared from galls induced by just one gall wasp species, and no parasite species was reared from galls of more than four species. Most kleptoparasite divergence events correlate with shifts to non-ancestral galls. These shifts often involved changes in tree habitat, gall location, and gall morphology. Host shifts are thus implicated in driving diversification for both oak gall wasps and their kleptoparasitic associates.