bluuebunny/crossref_metadata_2025_split huggingface dataset:
The landscape of antibiotic resistance genes in the nasopharynx of preterm infants: Prolonged signature of hospitalization and effects by antibiotics
Authors: Dhariwal Achal , Rajar Polona , Salvadori Gabriela , Åmdal Heidi Aarø , Berild Dag , Saugstad Ola Didrik , Fugelseth Drude , Greisen Gorm , Dahle Ulf , Haaland Kirsti , Petersen Fernanda Cristina 
Published: August 2023

ABSTRACTRespiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. Utilizing shotgun metagenomics, we investigated the nasopharynx resistome development in preterm infants, assessed early antibiotic impact on its trajectory, and explored its association with clinical covariates. Our findings revealed widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogenSerratia marcescenspersisted up to 8-10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlated with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.
Akr1b7functions as a master regulator in ovarian aging
Authors: Isayama Keishiro , Watanabe Kenji , Ohtsuka Masato , Kimura Seisuke , Murata Tomoaki , Honda Takeshi , Asagiri Masataka , Sato Shun , Tamura Hiroshi , Sugino Norihiro , Mizukami Yoichi 
Published: August 2023

AbstractAt the beginning of ovarian aging, the ovulation of immature oocytes is accelerated, leading to the arrest of ovulation despite the remaining oocytes. Here, RNA expression in the ovarian aging of mice is comprehensively analyzed during the estrous cycle after ovulation stimulation. The aldo-keto reductaseAkr1b7pathway transiently activated in the ovaries of young mice disappears in those of old mice.Akr1b7—/—mice attenuate oocyte Akt activation essential for the follicular development in primordial follicles, and enhanced ovulation in immature oocytes. The estrous cycle is extended because of the prolonged diestrous stage by a sustained progesterone level inAkr1b7—/—mice ovaries, which is caused by the decline ofCyp17a1, a major metabolic enzyme of progesterone inAkr1b7-expressed theca cell layers. In summary, the decreasedAkr1b7pathway causes ovulation of immature oocytes and a prolonged estrous cycle, typical symptoms of ovarian aging.
Comparative Analysis, Diversification and Functional Validation of Plant Nucleotide-Binding Site Domain Genes
Authors: Hussain Athar , Khan Aqsa Anwer , Aslam Muhammad Qasim , Nazar Aquib , Zaman Nadir , Amin Ayesha , Mahmood Muhammad Arslan , Mukhtar M. Shahid , Rahman Hafiz Ubaid Ur , Farooq Muhammed , Saeed Muhammed , Amin Imran , Mansoor Shahid 
Published: August 2023

AbstractNucleotide-binding site (NBS) domain genes are one of a superfamily of resistance genes involved in plant responses to pathogens. The current study identified presumably identified 12,820 NBS-containing genes across 34 species covering from mosses to monocots and dicots. These identified genes classified into 168 classes with several novel domain architectures patterns encompassing significant diversity among plant species. Several classical (NBS, NBS-LRR, TIR-NBS, TIR-NBS-LRR etc.) and species-specific structural patterns (TIR-NBS-TIR-Cupin_1-Cupin_1, TIR-NBS-Prenyltransf, Sugar_tr-NBS etc.) were discovered. We observed 603 orthogroups (OGs) with some core (most common orthogroups; OG0, OG1, OG2etc.) and unique (highly specific to species; OG80, OG82etc) OGs with tandem duplications. The expression profiling presented the putative upregulation of OG2, OG6,and OG15in different tissues under various biotic and abiotic stresses in susceptible and tolerant plants to CLCuD. The genetic variation between susceptible (Coker 312) and tolerant (Mac7)G. hirsutumaccessions identified several unique variants in NBS genes of Mac7 (6,583 varaints) and Coker312 (5,173 variants). The protein-ligand and proteins-protein interaction showed a strong interaction of some putative NBS proteins with ADP/ATP and different core proteins of cotton leaf curl disease virus. The silencing ofGaNBS(OG2) in resistant cotton through virus-induced gene silencing (VIGS) demonstrated its putative role in virus tittering. The presented study will be further helpful to understand the plant adaptation mechanism.
Characterization of a selective, iron-chelating antifungal compound that disrupts fungal metabolism and synergizes with fluconazole
Authors: Corrales Jeanne , Ramos-Alonso Lucía , González-Sabín Javier , Ríos-Lombardía Nicolás , Trevijano-Contador Nuria , Berg Henriette Engen , Skottvoll Frøydis Sved , Moris Francisco , Zaragoza Óscar , Chymkowitch Pierre , Garcia Ignacio , Enserink Jorrit M. 
Published: August 2023

AbstractFungal infections are a growing global health concern due to the limited number of available antifungal therapies as well as the emergence of fungi that are resistant to first-line antimicrobials, particularly azoles and echinocandins. Development of novel, selective antifungal therapies is challenging due to similarities between fungal and mammalian cells. An attractive source of potential antifungal treatments is provided by ecological niches co-inhabited by bacteria, fungi and multicellular organisms, where complex relationships between multiple organisms has resulted in evolvement of a wide variety of selective antimicrobials. Here, we characterized several analogs of the one such natural compound, Collismycin A. We show that NR-6226C has antifungal activity against several pathogenicCandidaspecies, includingC. albicansandC. glabrata, whereas it only has little toxicity against mammalian cells. Mechanistically, NR-6226C selectively chelates iron, which is a limiting factor for pathogenic fungi during infection. As a result, NR-6226C treatment causes severe mitochondrial dysfunction, leading to formation of reactive oxygen species, metabolic reprogramming and a severe reduction in ATP levels. Using anin vivomodel for fungal infections, we show that NR-6226C significantly increases survival ofCandida-infectedGalleria mellonellalarvae. Finally, our data indicate that NR-6226C synergizes strongly with fluconazole in inhibition ofC. albicans. Taken together, NR-6226C is a promising antifungal compound that acts by chelating iron and disrupting mitochondrial functions.Importance statementDrug-resistant fungal infections are an emerging global threat, and pan-resistance to current antifungal therapies is an increasing problem. Clearly, there is a need for new antifungal drugs. In this study, we characterized a novel antifungal agent, the Collismycin analog NR-6226C. NR-6226C has a favorable toxicity profile for human cells, which is essential for further clinical development. We unraveled the mechanism of action of NR-6226C and found that it disrupts iron homeostasis and thereby depletes fungal cells of energy. Importantly, NR-6226C strongly potentiates the antifungal activity of fluconazole, thereby providing inroads for combination therapy that may reduce or prevent azole resistance. Thus, NR-6226C is a promising compound for further development into antifungal treatment.
Tetrapod vocal evolution: higher frequencies and faster rates of evolution in mammalian vocalizations
Authors: Muñoz Matías I. , Marsot Myriam , Ellers Jacintha , Halfwerk Wouter 
Published: August 2023

AbstractUsing the voice to produce sound is a widespread form of communication and plays an important role in contexts as diverse as parent-offspring interactions and courtship. Variation in the tempo and mode of vocal signal evolution has been studied in a phylogenetic context within orders or classes, but understanding vocal signal evolution ultimately requires comparison across all major lineages involved. Here we used comparative analyses to investigate the evolution of dominant frequency (i.e., the frequency with the highest energy content) and its association with body weight across 873 species of mammals, birds and frogs. In agreement with previous studies, we found that the negative allometric relationship between body weight and vocal frequency is a general feature of vocal systems. In addition, we found mammals to consistently vocalize at higher frequencies, and evolved their vocalizations at around 6-fold faster rates than those of birds and frogs. Although all three groups strongly rely on vocal communication, our findings show that only mammals have extensively explored the spectral acoustic space. We argue that such high vocal diversity of mammals is made possible by their unique hearing system, which evolved in the context of a small, parental-caring, nocturnal and insectivore ancestor, and has allowed them to detect, and therefore to evolve, a richer array of frequencies than other tetrapods.
Basolateral amygdala parvalbumin interneurons coordinate oscillations to drive reward behaviors
Authors: Amaya Kenneth A. , Teboul Eric , Weiss Grant L. , Antonoudiou Pantelis , Maguire Jamie L. 
Published: August 2023

AbstractThe basolateral amygdala (BLA) has been implicated in mediating both fear and reward learning. Parvalbumin interneurons (PVs) in the BLA have previously been shown to contribute to BLA oscillatory states integral to fear expression, but whether BLA oscillatory states and PV interneurons also contribute to reward learning is unknown and critical to our understanding of reward processing. Local field potentials in the BLA were collected as animals consumed a sucrose reward, where prominent changes in the beta band (15-30 Hz) emerged with reward experience. Rhythmic optogenetic stimulation of PV interneurons to entrain the BLA network to 20Hz during consumption of one bottle during a two-bottle choice test produced a robust bottle preference. Finally, to demonstrate that PV activity is necessary for reward value use, PVs were chemogenetically targeted and inhibited following outcome devaluation, rendering those animals incapable of using updated reward value information to guide their behavior. Taken together, these experiments provide novel information regarding the physiological signatures of reward learning while highlighting the importance of PV interneurons in reward learning. This work builds upon the field’s established knowledge of PV involvement in fear expression and provides evidence that PV orchestration of unique BLA network states is involved in both learning types.
Open-source milligram-scale, four channel, automated protein purification system
Authors: Puccinelli Robert R. , Sama Samia S. , Worthington Caroline M. , Puschnik Andreas S. , Pak John E. , Gómez-Sjöberg Rafael 
Published: August 2023

AbstractLiquid chromatography purification of multiple recombinant proteins, in parallel, could catalyze research and discovery if the processes are fast and approach the robustness of traditional, “one-protein-at-a-time” purification. Here, we report an automated, four channel chromatography platform that we have designed and validated for parallelized protein purification at milligram scales. The device can purify up to four proteins (each with its own single column), has inputs for up to eight buffers or solvents that can be directed to any of the four columns via a network of software-driven valves, and includes an automated fraction collector with ten positions for 1.5 or 5.0 mL collection tubes and four positions for 50 mL collection tubes for each column output. The control software can be accessed either via Python scripting, giving users full access to all steps of the purification process, or via a simple-to-navigate touch screen graphical user interface that does not require knowledge of the command line or any programming language. Using our instrument, we report milligram-scale, parallelized, single-column purification of a panel of mammalian cell expressed coronavirus (SARS-CoV-2, HCoV-229E, HCoV-OC43, HCoV-229E) trimeric Spike and monomeric Receptor Binding Domain (RBD) antigens, and monoclonal antibodies targeting SARS-CoV-2 Spike (S) and Influenza Hemagglutinin (HA). We include a detailed hardware build guide, and have made the controlling software open source, to allow others to build and customize their own protein purifier systems.
Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes
Authors: Yoon Peter H. , Skopintsev Petr , Shi Honglue , Chen Lin-Xing , Adler Benjamin A. , Al-Shimary Muntathar , Craig Rory J. , Li Zheng , Amerasekera Jasmine , Trinidad Marena , Nisonoff Hunter , Chen Kai , Lahiri Arushi , Boger Ron , Jacobsen Steve , Banfield Jillian F. , Doudna Jennifer A. 
Published: August 2023

ABSTRACTRNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12. In eukaryotes and their viruses, TnpB homologs occur as two distinct types, Fanzor1 and Fanzor2. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, revealing that a clade of IS607 TnpBs with unusual active site arrangement found primarily in Cyanobacteriota likely gave rise to both types of Fanzors. The wide-spread nature of Fanzors imply that the properties of this particular group of IS607 TnpBs were particularly suited to adaptation and evolution in eukaryotes and their viruses. Experimental characterization of a prokaryotic IS607 TnpB and virally encoded Fanzor1s uncovered features that may have fostered coevolution between TnpBs/Fanzors and their cognate transposases. Our results provide insight into the evolutionary origins of a ubiquitous family of RNA-guided proteins that shows remarkable conservation across domains of life.
Craniofacial diversity across Danionins and the effects of TH status on craniofacial morphology of two Danio species
Authors: Nguyen Stacy , Lee Rachel S , Mohlmann Emma , Petrullo Gabriella , Blythe John , Ranieri Isabella , McMenamin Sarah 
Published: August 2023

AbstractThe model zebrafish (Danio rerio) belongs to the Danioninae subfamily with a range of informative phenotypes. However, the craniofacial diversity across the subfamily is not fully described. To better understand craniofacial phenotypes across Danioninae we used microCT and 3D geometric morphometrics to capture skull shapes from nine species. TheDaniospecies examined showed largely similar skull shapes, althoughD. aesculapii, the sister species toD. rerioshowed a unique morphology. Two non-Daniospecies examined,Chela dadiburjoriandDevario aequipinnatusshowed distinct skull morphologies unique from those of other species examined. Thyroid hormone regulates skeletal development and remodeling, and we asked if changes in developmental thyroid hormone metabolism could underlie some of the craniofacial diversity across Danioninae. We reared twoDaniospecies under altered thyroid profiles, finding that hypothyroid individuals from both species showed corresponding morphological shifts in skull shape. HypothyroidDaniosshowed skull morphologies closer to that ofChelaand unlike any of the examined wild-typeDaniospecies. We provide an examination of the evolved craniofacial diversity across Danioninae, and demonstrate that alterations to thyroid hormone have the capacity to create unique skull phenotypes.
Unique and shared functions of the Rad9–Hus1–Rad1 and Mre11–Rad50–Nbs1 complexes in ATR checkpoint activation and long-range DNA end resection inXenopusegg extracts
Authors: Tatsukawa Kensuke , Sakamoto Reihi , Kawasoe Yoshitaka , Kubota Yumiko , Tsurimoto Toshiki , Takahashi Tatsuro S. , Ohashi Eiji 
Published: August 2023

ABSTRACTSensing and processing of DNA double-strand breaks (DSBs) are vital to genome stability. DSBs are primarily detected by the ATM checkpoint pathway, where the Mre11–Rad50–Nbs1 (MRN) complex serves as the DSB sensor. Subsequent DSB end resection promotes the transition from the ATM to the ATR checkpoint pathway, where replication protein A, MRN, and the Rad9–Hus1–Rad1 (9–1–1) checkpoint clamp serve as the DNA structure sensors. 9–1–1 and MRN recruit Topbp1, a critical checkpoint mediator that activates the ATR kinase. However, how multiple sensors contribute to regulating end resection and checkpoint activation remains ambiguous. Using DNA substrates that mimic extensively resected DSBs, we show here that MRN and 9–1–1 redundantly stimulate Dna2-dependent long-range end resection and ATR activation inXenopusegg extracts. MRN serves as the loading platform for Dna2, ATM, and Topbp1. In contrast, 9–1–1 is dispensable for bulk Dna2 loading, and Topbp1 loading is interdependent with 9–1–1 in this pathway. ATR facilitates Mre11 phosphorylation and ATM dissociation. Our results delineate the molecular mechanism of and interplay between two redundant pathways that stimulate ATR checkpoint activation and long-range DSB end resection in vertebrates.
The reference genome of the paradise fish (Macropodus opercularis)
Authors: Fodor Erika , Okendo Javan , Szabó Nóra , Szabó Kata , Czimer Dávid , Tarján-Rácz Anita , Szeverényi Ildikó , Low Bi Wei , Liew Jia Huan , Koren Sergey , Rhie Arang , Orbán László , Miklósi Ádám , Varga Máté , Burgess Shawn M. 
Published: August 2023

AbstractOver the decades, a small number of model species, each representative of a larger taxa, have dominated the field of biological research. Amongst fishes, zebrafish (Danio rerio) has gained popularity over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (Macropodus opercularis), an “air-breather” species from Southeast Asia, has a highly complex behavioral repertoire and has been the subject of many ethological investigations, but lacks genomic resources. Here we report the reference genome assembly ofMacropodus opercularisusing long-read sequences at 150-fold coverage. The final assembly consisted of ≈483 Mb on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ≈90% of them to orthogroups. Completeness analysis showed that 98.5% of the Actinopterygii core gene set (ODB10) was present as a complete ortholog in our reference genome with a further 1.2 % being present in a fragmented form. Additionally, we cloned multiple genes important during early development and using newly developedin situhybridization protocols, we showed that they have conserved expression patterns.
A multifunctionalDehalobacter? Tandem chloroform and dichloromethane degradation in a mixed microbial culture
Authors: Bulka Olivia , Webb Jennifer , Dworatzek Sandra , Mahadevan Radhakrishnan , Edwards Elizabeth A. 
Published: August 2023

ABSTRACTChloroform (CF) and dichloromethane (DCM) contaminate groundwater sites around the world, which can be remediated through bioaugmentation. Although several strains ofDehalobacter restrictuscan reduce CF to DCM, and multiple Peptococcaceae can ferment DCM, these processes cannot happen simultaneously due to CF sensitivity in the known DCM-degraders or electron donor competition. Here we present a mixed microbial culture that can simultaneously metabolize CF and DCM to carbon dioxide and create an additional enrichment culture fed only DCM. Through species-specific qPCR, we find that aDehalobacterstrain grows both while CF alone and DCM alone are converted, indicating its involvement in both metabolic steps. Additionally, the culture was maintained for over 1400 days without addition of exogenous electron donor, and through electron balance calculations we show that DCM mineralization produces sufficient reducing equivalents (likely hydrogen) for CF respiration. Together, these results suggest intraspecies electron transfer could occur to continually reduce CF in the culture. Minimizing the addition of electron donor reduces the cost of bioremediation, and understanding this mechanism informs strategies for culture maintenance and scale-up, and benefits contaminated sites where the culture is employed for remediation worldwide.SYNOPSISDechlorination of chloroform to dichloromethane and dichloromethane mineralization are performed concurrently by aDehalobacter-containing mixed microbial community without provision of exogenous electron donor.TOC ART
TheToxoplasmasubpellicular network is highly interconnected and defines parasite shape for efficient motility and replication
Authors: Back Peter S. , Senthilkumar Vignesh , Choi Charles P. , Ly Andrew M. , Snyder Anne K. , Lau Justin G. , Ward Gary E. , Bradley Peter J. 
Published: August 2023

AbstractApicomplexan parasites possess several specialized structures to invade their host cells and replicate successfully. One of these is the inner membrane complex (IMC), a peripheral membrane-cytoskeletal system underneath the plasma membrane. It is composed of a series of flattened, membrane-bound vesicles and a cytoskeletal subpellicular network (SPN) comprised of intermediate filament-like proteins called alveolins. While the alveolin proteins are conserved throughout the Apicomplexa and the broader Alveolata, their precise functions and interactions remain poorly understood. Here, we describe the function of one of these alveolin proteins, TgIMC6. Disruption of IMC6 resulted in striking morphological defects that led to aberrant motility, invasion, and replication. Deletion analyses revealed that the alveolin domain alone is largely sufficient to restore localization and partially sufficient for function. As this highlights the importance of the IMC6 alveolin domain, we implemented unnatural amino acid photoreactive crosslinking to the alveolin domain and identified multiple binding interfaces between IMC6 and two other cytoskeletal proteins – IMC3 and ILP1. To our knowledge, this provides the first direct evidence of protein-protein interactions in the alveolin domain and supports the long-held hypothesis that the alveolin domain is responsible for filament formation. Collectively, our study features the conserved alveolin proteins as critical components that maintain the parasite’s structural integrity and highlights the alveolin domain as a key mediator of SPN architecture.