bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin
Authors: Welsh Frances C. , Eguia Rachel T. , Lee Juhye M. , Haddox Hugh K. , Galloway Jared , Chau Nguyen Van Vinh , Loes Andrea N. , Huddleston John , Yu Timothy C. , Le Mai Quynh , Nhat Nguyen T.D. , Thanh Nguyen Thi Le , Greninger Alexander L. , Chu Helen Y. , Englund Janet A. , Bedford Trevor , Matsen Frederick A. , Boni Maciej F. , Bloom Jesse D. 
Published: December 2023

ABSTRACTHuman influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population, and how this heterogeneity affects virus evolution. Here we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of the A/Hong Kong/45/2019 (H3N2) and A/Perth/16/2009 (H3N2) strains affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that fixed in influenza variants after 2020 cause the greatest escape from sera from younger individuals. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups, and suggest approaches to understand how this heterogeneous selection shapes viral evolution.
Catalytically inactive dKbCas12d guided by sgRNA and new insights into its binding through a single-molecule approach
Authors: Alekseev Aleksandr , Klimko Valerii , Abramova Marina , Franzusova Irina , Vinnik Victor , Vasileva Aleksandra , Selkova Polina , Khodorkovskii Mikhail , Arseniev Anatolii 
Published: December 2023

ABSTRACTCRISPR-Cas12d is a distinct V-D type system discovered in the metagenomes of Candidate Phyla Radiation bacteria. It stands out from most closely related systems due to its 17-19 nucleotide short spacer region and specialized stabilizing scoutRNAs. We made significant improvements to this system by modifying its scoutRNA to create sgRNA, which greatly simplifies its use. We found mutations in the RuvC domain of the effector protein KbCas12d that resulted in loss of nuclease activity. We obtained two catalytically inactive dKbCas12d variants: D827A and E913A. Using the optical tweezers technique, we demonstrated the high specificity of dKbCas12d in binding targets on individual DNA molecules. Engineered sgRNA and catalytically inactive dKbCas12d variants have promising applications in biotechnology for the precise regulation of gene expression and molecular diagnostics.
Inhibition of the UFD-1-NPL-4 complex triggers an inflammation-like response inCaenorhabditis elegans
Authors: Rao Rajneesh , Aballay Alejandro , Singh Jogender 
Published: December 2023

AbstractThe UFD-1 (ubiquitin fusion degradation 1)-NPL-4 (nuclear protein localization homolog 4) heterodimer is involved in extracting ubiquitinated proteins from several plasma membrane locations, including the endoplasmic reticulum. This heterodimer complex helps in the degradation of ubiquitinated proteins via proteasome with the help of AAA+ ATPase CDC-48. While the ubiquitin-proteasome system is known to have important roles in maintaining innate immune responses, the role of the UFD-1-NPL-4 complex in regulating immunity remains elusive. In this study, we investigate the role of the UFD-1-NPL-4 complex in maintainingCaenorhabditis elegansinnate immune responses. Inhibition of the UFD-1-NPL-4 complex activates an inflammation-like response that reduces the survival of the wild-type worms on the pathogenic bacteriumPseudomonas aeruginosadespite diminishing colonization of the gut with the bacterium. This inflammation-like response improves the survival of severely immunocompromised worms on pathogenic bacteria but is detrimental on nonpathogenic bacteria. Transcriptomics studies reveal that the GATA transcription factor ELT-2 mediates the inflammation-like response upon inhibition of the UFD-1-NPL-4 complex. Our studies uncover important roles of the UFD-1-NPL-4 complex in innate immunity and reveal the existence of inflammation-like responses inC. elegans.
The 3D ultrastructural morphology of a marine ammonia-oxidizing archaeon
Authors: Zhou Yangkai , Yan An , Yang Jiawen , He Wei , Guo Shuai , Li Yifan , Dai Yanchao , Pan Xijiang , Cui Dongyu , Pereira Olivier , Teng Wenkai , Bi Ran , Chen Songze , Fan Lu , Wang Peiyi , Liao Yan , Qin Wei , Sui Sen-Fang , Zhu Yuanqing , Zhang Chuanlun , Liu Zheng 
Published: December 2023

AbstractNitrososphaerota, formerly known asThaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their significance in Earth’s ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant question unanswered of how the machinery of these organisms underpins metabolic functions. In this study, we combined chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition ofNitrosopumilus maritimusSCM1, a representative member of marineNitrososphaerota. Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules in which one type is possibly composed of polyphosphate, while the other type is polyhydroxyalkanoate. Collectively, these findings provide visual evidence for the resilience of AOA in the vast oligotrophic marine environment.
Membrane protein sequence features direct post-translational insertion
Authors: Kalinin Ilya A. , Peled-Zehavi Hadas , Barshap Alon B.D. , Tamari Shai A. , Weiss Yarden , Nevo Reinat , Fluman Nir 
Published: December 2023

AbstractThe proper folding of multispanning membrane proteins (MPs) hinges on the accurate insertion of their transmembrane helices (TMs) into the membrane. Predominantly, TMs are inserted during protein translation, via a conserved mechanism centered around the Sec translocon. Our study reveals that the C-terminal TMs (cTMs) of numerous MPs across various organisms bypass this cotranslational route, necessitating an alternative posttranslational insertion strategy. We demonstrate that evolution has refined the hydrophilicity and length of these proteins’ C-terminal tails to optimize cTM insertion. Alterations in the C-tail sequence disrupt cTM insertion in bothE. coliand human, leading to protein defects, loss of function, and genetic diseases. InE. coli, we identify YidC, a member of the widespread Oxa1 family, as the insertase facilitating cTMs insertion, with C-tail mutations disrupting the productive interaction of cTMs with YidC. Thus, MP sequences are fine-tuned for effective collaboration with the cellular biogenesis machinery, ensuring proper membrane protein folding.
Targeting plasmid-encoded proteins that contain immunoglobulin-like domains to combat antimicrobial resistance
Authors: Prieto Alejandro , Miró Lluïsa , Margolles Yago , Bernabeu Manuel , Salguero David , Merino Susana , Tomás Joan , Corbera Juan Alberto , Pérez-Bosque Anna , Hüttener Mário , Fernández Luis Ángel , Juárez Antonio 
Published: December 2023

AbstractAntimicrobial resistance (AMR) poses a significant threat to human health. Although vaccines have been developed to combat AMR, it has proven challenging to associate specific vaccine antigens with AMR. Bacterial plasmids play a crucial role in the transmission of AMR. Our recent research has identified a group of bacterial plasmids (specifically, IncHI plasmids) that encode large molecular mass proteins containing bacterial immunoglobulin-like domains. These proteins are found on the external surface of the bacterial cells, such as in the flagella or conjugative pili. In this study, we show that these proteins are antigenic and can protect mice from infection caused by an AMRSalmonellastrain harboring one of these plasmids. Furthermore, we successfully generated nanobodies targeting these proteins, that were shown to interfere with the conjugative transfer of IncHI plasmids. Considering that these proteins are also encoded in other groups of plasmids, such as IncA/C and IncP2, targeting them could be a valuable strategy in combating AMR infections caused by bacteria harboring different groups of AMR plasmids. Since the selected antigens are directly linked to AMR itself, the protective effect extends beyond specific microorganisms to include all those carrying the corresponding resistance plasmids.
ESM-Scan - a tool to guide amino acid substitutions
Authors: Totaro Massimo G. , Vide Uršula , Zausinger Regina , Winkler Andreas , Oberdorfer Gustav 
Published: December 2023

ABSTRACTProtein structure prediction and (re)design have gone through a revolution in the last three years. The tremendous progress in these fields has been almost exclusively driven by readily available machine-learning algorithms applied to protein folding and sequence design problems. Despite these advancements, predicting site-specific mutational effects on protein stability and function remains an unsolved problem. This is a persistent challenge mainly because the free energy of large systems is very difficult to compute with absolute accuracy and subtle changes to protein structures are also hard to capture with computational models. Here, we describe the implementation and use of ESM-Scan, which uses the ESM zero-shot predictor to scan entire protein sequences for preferential amino acid changes, thus enabling in-silico deep mutational scanning experiments. We benchmark ESM-Scan on its predictive capabilities for stability and functionality of sequence changes using three publicly available datasets and proceed by experimentally evaluating the tool’s performance on a challenging test case of a blue-light-activated diguanylate cyclase from Methylotenera species (MsLadC). We used ESM-Scan to predict conservative sequence changes in a highly conserved region of this enzyme responsible for allosteric product inhibition. Our experimental results show that the ESM-zero shot model emerges as a robust method for inferring the impact of amino acid substitutions, especially when evolutionary and functional insights are intertwined. ESM-Scan is publicly available athttps://huggingface.co/spaces/thaidaev/zsp
Numerous independent gains of torpor and hibernation across endotherms, linked with adaptation to diverse environments
Authors: Kontopoulos Dimitrios - Georgios , Levesque Danielle L. , Hiller Michael 
Published: December 2023

AbstractMany endotherms from diverse taxonomic groups can respond to environmental changes through dormancy, i.e., by greatly reducing their energy expenditure for up to 24 hours (daily torpor) or longer (hibernation). We currently have a poor understanding of how dormancy evolved across endotherms and its associations with physiological traits and ecological factors. To fill this gap, we thoroughly examine the evolutionary patterns of dormancy and its links with 21 key ecophysiological variables across 1,338 extant endotherms. We find that daily torpor and hibernation are parts of a dormancy continuum, and that there are several, albeit weak, associations between dormancy and species’ physiological or environmental characteristics. Furthermore, we show that early endotherm ancestors likely did not hibernate and that this trait evolved multiple times in independent lineages. Overall, our results provide an explanation for the remarkable variation in dormancy patterns, even among species occupying highly similar niches.
Paleocene origin of a streamlined digestive symbiosis in leaf beetles
Authors: García-Lozano Marleny , Henzler Christine , Porras Miguel Ángel González , Pons Inès , Berasategui Aileen , Lanz Christa , Budde Heike , Oguchi Kohei , Matsuura Yu , Pauchet Yannick , Goffredi Shana , Fukatsu Takema , Windsor Donald , Salem Hassan 
Published: December 2023

AbstractTiming the acquisition of a beneficial microbe relative to the evolutionary history of its host can shed light on the adaptive impact of a partnership. Here, we investigated the onset and molecular evolution of an obligate symbiosis between Cassidinae leaf beetles andCandidatusStammera capleta, a γ-proteobacterium. Residing extracellularly within foregut symbiotic organs,Stammeraupgrades the digestive physiology of its host by supplementing plant cell wall-degrading enzymes. We observe thatStammerais a shared symbiont across tortoise and hispine beetles that collectively comprise the Cassidinae subfamily, despite differences in their folivorous habits. In contrast to its transcriptional profile during vertical transmission,Stammeraelevates the expression of genes encoding digestive enzymes while in the foregut symbiotic organs, matching the nutritional requirements of its host. Symbiont acquisition during the Paleocene (∼62 Mya) did not coincide with the origin of Cassidinae beetles, despite the widespread distribution ofStammeraacross the subfamily. Early-diverging lineages lack the symbiont and the specialized organs that house it. Reconstructing the ancestral state of host-beneficial factors revealed thatStammeraencoded three digestive enzymes at the onset of symbiosis, including polygalacturonase – a pectinase that is universally shared. While non-symbiotic cassidines encode polygalacturonase endogenously, their repertoire of plant cell wall-degrading enzymes is more limited compared to symbiotic beetles supplemented with digestive enzymes fromStammera. Highlighting the potential impact of a symbiotic condition and an upgraded metabolic potential,Stammera-harboring beetles exploit a greater variety of plants and are more speciose compared to non-symbiotic members of the Cassidinae.
ERK1/2 inhibition disrupts alcohol memory reconsolidation and prevents relapse
Authors: Rahamim Nofar , Liran Mirit , Aronovici Coral , Flumin Hila , Gordon Tamar , Urshansky Nataly , Barak Segev 
Published: December 2023

AbstractRelapse to alcohol abuse after periods of abstinence, often caused by cue-induced alcohol craving, is a major challenge in the treatment of alcohol addiction. Therefore, disruption of the cue-alcohol associative memories can diminish the risk of relapse. Upon retrieval, memories become temporarily labile before they reconsolidate in a process that requires protein synthesis. Accumulating evidence suggests that the mammalian target of rapamycin complex 1 (mTORC1), which is responsible for the translation of a subset of dendritic proteins, is crucial for memory reconsolidation. Here, we explored the involvement of two regulatory pathways of mTORC1, namely phosphoinositide 3-kinase (PI3K)-AKT and extracellular regulated kinase1/2 (ERK1/2), in the reconsolidation process in a rat model of non-operant alcohol self-administration. We found that retrieval of alcohol memories using an odor-taste cue increased ERK1/2 activation in the amygdala, but did not affect the PI3K-AKT pathway. Importantly, inhibition of ERK1/2 shortly after alcohol memory retrieval impaired reconsolidation and led to long-lasting suppression of relapse to alcohol drinking. Additionally, we show that attenuation of alcohol memories and relapse was also induced by post-retrieval administration of lacosamide, an inhibitor of collapsin response mediator protein-2 (CRMP2) – a translational product of mTORC1 that is functionally regulated by PI3K-AKT signaling. Together, our findings provide evidence for the crucial role of ERK1/2 and CRMP2 in the reconsolidation of alcohol memories, and mark the FDA-approved drug, lacosamide, as a potential treatment for alcohol use disorder.
Lsr2, a pleiotropic regulator at the core of the infectious strategy ofMycobacterium abscessus
Authors: Gerges Elias , del Pilar Rodríguez-Ordoñez María , Durand Nicolas , Herrmann Jean-Louis , Crémazy Frédéric 
Published: December 2023

ABSTRACTMycobacterium abscessusis a non-tuberculous mycobacterium, causing lung infections in cystic fibrosis patients. During pulmonary infection,M. abscessusswitches from smooth (Mabs-S) to rough (Mabs-R) morphotypes, the latter being hyper-virulent. Previously, we isolated thelsr2gene as differentially expressed during S-to-R transition.lsr2encodes a pleiotropic transcription factor that falls under the superfamily of nucleoid-associated proteins (NAPs). Here, we used two functional genomics methods, RNA-seq and ChIP-seq, to elucidate the molecular role of Lsr2 in the pathobiology ofM. abscessus. Transcriptomic analysis shows that Lsr2 differentially regulates gene expression across both morphotypes, most of which are involved in several key cellular processes ofM. abscessus, including host adaptation and antibiotic resistance. These results were confirmed through RT-qPCR, as well as by minimum inhibitory concentration (MIC) tests and infection tests on macrophages in the presence of antibiotics. ChIP-seq analysis revealed that Lsr2 extensively binds theM. abscessusgenome at AT-rich sequences and appears to form long domains that participate in the repression of its target genes. Unexpectedly, the genomic distribution of Lsr2 revealed no distinctions between Mabs-S and Mabs-R, implying more intricate mechanisms at play for achieving target selectivity.IMPORTANCELsr2 is a crucial transcription factor and chromosome organizer involved in intracellular growth and virulence in the smooth and rough morphotypes ofMycobacterium abscessus(Mabs). Using RNA-seq and ChIP-seq, we investigated the molecular role of Lsr2 in gene expression regulation along with its distribution on Mabs genome. Our study demonstrates the pleiotropic regulatory role of Lsr2, regulating the expression of many genes coordinating essential cellular and molecular processes in both morphotypes. In addition, we have elucidated the role of Lsr2 in antibiotic resistance bothin vitroandin vivo, wherelsr2mutant strains display heightened sensitivity to antibiotics. Through ChIP-seq, we reported the widespread distribution of Lsr2 on Mabs genome, revealing a direct repressive effect due to its extensive binding on promoters or coding sequences of its targets. This study unveils the significant regulatory role of Lsr2, intricately intertwined with its function in shaping the organization of the Mabs genome.
A heptavalent O-antigen bioconjugate vaccine exhibits differential functional antibody responses against diverseKlebsiella pneumoniaeisolates
Authors: Wantuch Paeton L. , Knoot Cory J. , Robinson Lloyd S. , Vinogradov Evgeny , Scott Nichollas E. , Harding Christian M. , Rosen David A. 
Published: December 2023

AbstractKlebsiella pneumoniaeis a concerning pathogen that is now the leading cause of neonatal sepsis and is increasingly difficult to treat due to heightened antibiotic resistance. Thus, there is an urgent need for preventive and effective immunotherapies targetingK. pneumoniae. Vaccination represents a tractable approach to combat this resistant bacterium in some settings; however, there is currently not a licensedK. pneumoniaevaccine available.K. pneumoniaesurface polysaccharides, including the terminal O-antigen polysaccharides of lipopolysaccharide, have long been attractive candidates for vaccine inclusion. Herein we describe the generation of a bioconjugate vaccine targeting seven of the predominant O-antigen subtypes inK. pneumoniae. Each of the seven bioconjugates were immunogenic in isolation, with limited cross-reactivity among subtypes. Vaccine-induced antibodies demonstrated varying degrees of binding to a wide variety ofK. pneumoniaestrains, including suspected hypervirulent strains, all expressing different O-antigen and capsular polysaccharide combinations. Further, sera from vaccinated mice induced complement-mediated killing of many of theseK. pneumoniaestrains. Finally, we found that increased quantity of capsule interferes with O-antigen antibodies’ ability to bind and mediate killing of someK. pneumoniaestrains, including those carrying hypervirulence-associated genes. Taken together, these data indicate that this novel heptavalent O-antigen bioconjugate vaccine formulation exhibits promising efficacy against some, but not all,K. pneumoniaeisolates.
Impact of CRISPR/HDR-editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques
Authors: Lee Byung-Chul , Gin Ashley , Wu Chuanfeng , Singh Komudi , Grice Max , Mortlock Ryland , Abraham Diana , Fan Xing , Zhou Yifan , AlJanahi Aisha , Choi Uimook , de Ravin Suk See , Shin Taehoon , Hong Sogun , Dunbar Cynthia E. 
Published: December 2023

AbstractFor precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) requires both sufficient HDR efficiency and protection of LT-HSC function and number. The impact of HDR on true LT-HSCs clonal dynamics in a relevant large animal model has not previously been studied. To track the HDR-edited cells, autologous rhesus macaque (RM) CD34+cells were electroporated with the gRNA/Cas9 ribonucleoprotein (RNP) and HDR cassette barcode library structure and reinfused into RMs following myeloablation. For competitive model animals, fractionated CD34+cells were transduced with a barcoded GFP-expressing lentiviral vector (LV) and electroporated via HDR machinery, respectively.CD33knockout (KO) neutrophils were prevalent early following engraftment and then rapidly decreased, resulting in less than 1% total editing efficiency. Interestingly, in competitive animals, a higher concentration of i53 mRNA result in a less steep reduction inCD33KO cells, presented a modest decrease in HDR rate (0.1-0.2%) and total indels (1.5-6.5%). In contrast, the drop off of LV-transduced GFP+cells stabilized at 20% after 2 months. We next retrieved embedded barcodes and revealed that various clones contributed to early hematopoietic reconstitution, then after dominant clones appeared at steady state throughout the animals. In conclusion, CRISPR/HDR edited cells disappeared rapidly after the autologous transplantation in RM despite substantial gene editing outcome, whereas LV-transduced cells were relatively well maintained. Clonality of HDR-edited cells drastically shrank at early stage and then relied on several dominant clones, which can be mildly mitigated by the introduction of i53 mRNA.
The effects of situational and dispositional factors on audit quality threatening behaviour: exploring the moderating influence of religiosity
Authors: Liu Shilin , Sulaiman Noor Adwa , Shahimi Suhaily 
Published: December 2023

PurposeUsing attribution theory, this study examined the effects of situational factors [time budget pressure (TBP), organisational ethical culture (OEC) and quality control procedures (QCPs)] and dispositional factors [auditor professional commitment (APC) and internal locus of control (ILOC)] on audit quality threatening behaviour (AQTB). In addition, it observed the moderating role of religiosity in the relationship between situational and dispositional factors and AQTB.Design/methodology/approachA total of 189 external auditors responded to the survey questionnaire. This study employed structural equation modelling via SmartPLS to analyse the proposed model.FindingsThe results documented that the OEC and QCPs situational factors were negatively related to the incidence of AQTB, whilst TBP was positively linked to the incidence of AQTB. Dispositional factors APC and ILOC were negatively connected to AQTB. Furthermore, the findings recorded the moderating effect of religiosity on most of the situational and dispositional factors related to AQTB.Practical implicationsRegulators and accounting firms' efforts to promote high audit quality (AQ) may consider the theological/religious lens and reinforce ethical culture and quality control to reduce AQTB.Originality/valueThe findings provide further insights into situational and dispositional factors that may cause or impede the incidence of AQTB in auditing practices, as well as the moderating role of religiosity in curbing AQTB.