bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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

Liquid 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

RNA-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

The 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

Sensing 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

Over 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

Chloroform (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.

SYNOPSIS

Dechlorination 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

Apicomplexan 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.
HIV-Tocky system to visualize proviral expression dynamics
Authors: Reda Omnia , Monde Kazuaki , Sugata Kenji , Rahman Akhinur , Sakhor Wajihah , Rajib Samiul Alam , Sithi Sharmin Nahar , Tan Benjy Jek Yang , Niimura Koki , Motozono Chihiro , Maeda Kenji , Ono Masahiro , Takeuchi Hiroaki , Satou Yorifumi
Published: August 2023

The stably integrated pool of HIV-1 proviruses in the host genome stands against curative strategies. This reservoir is extremely heterogeneous with respect to host cell type, anatomical location, integration site, and replication fitness. During the initial phase of infection, only a few infected cells can resist host immune clearance or cytopathic effect and establish this resistant pool. The mechanisms underlying HIV latency initiation are not fully resolved yet. In the current study, we propose and validate a new reporter model for monitoring HIV-1 provirus silencing and reactivation using Timer of cell kinetics and activity (Tocky). HIV-Tocky system uses a fluorescent Timer protein whose emission spectrum spontaneously shifts from blue to red to reveal HIV-1 provirus dynamics. We dissected provirus transcriptional phases into early, persistent, recently silenced, and latent. To our knowledge, this is the first report to distinguish two latent subsets: a directly non-expressing population and a recently silenced after brief expression. In-depth integration site analysis suggested that the distribution of proviruses in directly latent cells was similar to that in actively transcribing cell population, whereas recently silenced cells tended to harbor proviruses integrated into heterochromatin. Furthermore, we established a library of various single integration clones at which we utilized to demonstrate the efficiency of the block-and-lock strategy by capturing the fast dynamics of silencing that were overlooked in previous models. In summary, we propose HIV-Tocky system to serve as a time-sensitive model that can capture the dynamics of provirus expression, making it a useful tool for HIV latency research.

Significance Statement

Determinants of HIV-1 latency establishment are yet to be elucidated. This reservoir comprises a rare fraction of infected cells that can survive host and virus-mediated killing.In vitroreporter models so far offered a feasible means to inspect this population, but with limited capabilities to dissect provirus silencing dynamics. Here, we describe a new HIV reporter model (HIV-Tocky) with dual fluorescence spontaneous shifting to reveal provirus silencing and reactivation dynamics. This unique feature allowed; for the first time, identifying two latent populations: a directly latent, and a recently silenced subset, with the latter having integration features suggestive of stable latency. Our proposed model can help address the heterogeneous nature of HIV reservoirs and offers new possibilities for evaluating eradication strategies.

Classification

Biological Sciences, Microbiology.
Plasmodium, theApicomplexaoutlier when it comes to protein synthesis
Authors: Jaramillo Ponce José R. , Frugier Magali
Published: August 2023

Plasmodiumis an obligate intracellular parasite that makes numerous interactions with different hosts during its elaborate life cycle. This is also the case for other parasites that belong to the same phylumApicomplexa. In this study, we identified bioinformatically the components of the multi-synthetase complexes (MSC) of severalApicomplexaparasites. By using AlphaFold2 modeling to compare their assembly, it appears that none of these MSCs resemble those identified inPlasmodium. In particular, the discrepancies between the core components ofPlasmodiumcomplexes, tRip and its homologs indicate that tRip-dependent exogenous tRNA import is not conserved in the otherApicomplexaparasites. Based on this observation, we looked for obvious differences that could explain this singularity inPlasmodium. The content of tRNA genes and amino acid usage in the different genomes highlighted the originality ofPlasmodiatranslation. This is evident with respect to asparagine amino acid, which is highly used in thePlasmodiumproteomes, and the scarcity of tRNAAsnrequired for protein synthesis, regardless of long homorepeats or AT content of the genomes.
Cell division machinery drives cell-specific gene activation during bacterial differentiation
Authors: Chareyre Sylvia , Li Xuesong , Anjuwon-Foster Brandon R. , Clifford Sarah , Brogan Anna , Su Yijun , Shroff Hari , Ramamurthi Kumaran S.
Published: August 2023

When faced with starvation, the bacteriumBacillus subtilistransforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σFis exclusively activated in the smaller daughter cell. Compartment specific activation of σFrequires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σFin both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that a unique feature of the sporulation septum, defined by the cell division machinery, drives the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.
Spatial transcriptomics map of the embryonic mouse brain: a tool to explore neurogenesis
Authors: Marco Barbara Di , Vázquez-Marín Javier , Monyer Hannah , Centanin Lázaro , Alfonso Julieta
Published: August 2023

The developing brain has a well-organized anatomical structure comprising different types of neural and non-neural cells. Stem cells, progenitors, and newborn neurons tightly interact with their neighbouring cells and tissue microenvironment, and this intricate interplay ultimately shapes the output of neurogenesis. Given the relevance of spatial cues during brain development, we acknowledge the necessity for a spatial transcriptomics map accessible to the neurodevelopmental community. To fulfil this need, we generated spatially-resolved RNAseq data from E13.5 mouse brain sections immunostained for mitotic active neural and vascular cells. Unsupervised clustering defined specific cell type populations of diverse lineages and differentiation states. Differential expression analysis revealed unique transcriptional signatures across specific brain areas, uncovering novel features inherent to particular anatomical domains. Finally, we integrated existing single-cell RNAseq datasets into our Spatial Transcriptomics map, adding tissue context to single-cell RNAseq data. In summary, we provide a valuable tool that enables the exploration and discovery of unforeseen molecular players involved in neurogenesis, particularly in the crosstalk between different cell types.

Summary Statement

Di Marco, Vázquez-Marín et al. provide an open-access spatial transcriptomics atlas of the embryonic mouse brain. This spatial map enables the exploration and discovery of gene functions within tissue context.
Utilization of 5’-deoxy-nucleosides as Growth Substrates by Extraintestinal PathogenicE. colivia the Dihydroxyacetone Phosphate Shunt
Authors: Huening Katherine A. , Groves Joshua T. , Wildenthal John A. , Tabita F. Robert , North Justin A.
Published: August 2023

All organisms utilizeS-adenosyl-L-methionine (SAM) as a key co-substrate for methylation of biological molecules, synthesis of polyamines, and radical SAM reactions. When these processes occur, 5’-deoxy-nucleosides are formed as byproducts such asS-adenosyl-L-homocysteine (SAH), 5’-methylthioadenosine (MTA), and 5’-deoxyadenosine (5dAdo). One of the most prevalent pathways found in bacteria for the metabolism of MTA and 5dAdo is the DHAP shunt, which converts these compounds into dihydroxyacetone phosphate (DHAP) and 2-methylthioacetaldehyde or acetaldehyde, respectively. Previous work has shown that the DHAP shunt can enable methionine synthesis from MTA or serve as an MTA and 5dAdo detoxification pathway. Here we show that in Extraintestinal PathogenicE. coil(ExPEC), the DHAP shunt serves none of these roles in any significant capacity, but rather physiologically functions as an assimilation pathway for use of MTA and 5dAdo as growth substrates. This is further supported by the observation that when MTA is the substrate for the ExPEC DHAP shunt, the sulfur components is not significantly recycled back to methionine, but rather accumulates as 2-methylthioethanol, which is slowly oxidized non-enzymatically under aerobic conditions. While the pathway is active both aerobically and anaerobically, it only supports aerobic ExPEC growth, suggesting that it primarily functions in oxygenic extraintestinal environments like blood and urine versus the predominantly anoxic gut. This reveals a heretofore overlooked role of the DHAP shunt in carbon assimilation and energy metabolism from ubiquitous SAM utilization byproducts and suggests a similar role may occur in other pathogenic and non-pathogenic bacteria with the DHAP shunt.

Importance

Acquisition and utilization of organic compounds that can serve as growth substrates is essential for pathogenicE. colito survive and multiply. Ubiquitous enzymatic reactions involvingS-adenosyl-L-methionine as a co-substrate result in the formation of the 5’-deoxy-nucleoside byproducts, 5’-methylthioadenosine and 5’-deoxyadenosine. AllE. colipossess a conserved nucleosidase that cleaves these 5’-deoxy-nucleosides into 5-deoxy-pentose sugars for adenine salvage. The DHAP shunt pathway, which is found in ExPEC strains but neither in intestinal pathogenic nor commensalE. coli,enables utilization of 5’-deoxy-nucleosides and 5-deoxy-pentose sugars as growth substrates by ExPEC strains. This provides insight into the diversity of sugar compounds accessible by ExPEC strains in recalcitrant and nutrient-poor environments such as the urinary tract during infection. Furthermore, given the dihydroxyacetone phosphate shunt pathway appears to only support aerobicE. coligrowth, this suggests an explanation as to why intestinal strains that primarily exist in anoxic environments lack this pathway.
Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistantKlebsiella pneumoniaeST258
Authors: Piña-Iturbe Alejandro , Hoppe-Elsholz Guillermo , Suazo Isidora D. , Kalergis Alexis M. , Bueno Susan M.
Published: August 2023

The ICEKp258.2 genomic island (GI) has been proposed as an important factor for the emergence and success of the globally spread carbapenem-resistantKlebsiella pneumoniaesequence type (ST) 258. However, a characterization of this horizontally acquired element is lacking. Using bioinformatic and experimental approaches, we found that ICEKp258.2 is not confined to ST258 and ST512 but also carried by ST3795 strains and emergent invasive multidrug-resistant pathogens from ST1519. We also identified several ICEKp258.2-like GIs spread among differentK. pneumoniaeSTs, otherKlebsiellaspecies, and even other pathogen genera, uncovering horizontal gene transfer events between different STs and bacterial genera. Also, in agreement with the origin of ST258 from ST11, the comparative and phylogenetic analyses of the ICEKp258.2-like GIs suggested that ICEKp258.2 was acquired from an ST11 strain. Importantly, we found that subinhibitory concentrations of antibiotics used in treatingK. pneumoniaeinfections can induce the excision of this GI and modulate its gene expression. Our findings provide the basis for the study of ICEKp258.2 and its role in the success ofK. pneumoniaeST258. They also highlight the potential role of antibiotics in the spread of ICEKp258.2-like GIs among bacterial pathogens.
A Genomic View of Environmental and Life History Controls on Microbial Nitrogen Acquisition Strategies
Authors: Reji Linta , Darnajoux Romain , Zhang Xinning
Published: August 2023

Microorganisms have evolved diverse strategies to acquire the vital element nitrogen (N) from the environment. Ecological and physiological controls on the distribution of these strategies among microbes remain unclear. Here we examine the distribution of 10 major N-acquisition strategies in taxonomically and metabolically diverse microbial genomes, including those from the Genomic Catalog of Earth’s Microbiomes dataset. We utilize a marker gene-based approach to assess relationships between N acquisition strategy prevalence and microbial life history strategies. Our results underscore energetic costs of assimilation as a broad control on strategy distribution. The most prevalent strategies are the uptake of ammonium and simple amino acids, while biological nitrogen fixation is the least common. Deviations from this energy-based framework include the higher-than-expected prevalence of the assimilatory pathway for chitin, a large organic polymer. Notably, oxygen-respiring chemoorganotrophic and phototrophic microbes possess ∼2-fold higher numbers of total strategies compared to anaerobic microbes. Environmental controls on N acquisition are evidenced by the enrichment of inorganic N assimilation strategies among free-living taxa compared to host-associated taxa. Physiological constrains such as pathway incompatibility add further complexity to N-acquisition strategy distributions. Finally, we discuss the necessity for microbially-relevant environmental metadata for improving mechanistic and prediction-oriented analyses of genomic data.
Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease
Authors: Quinn-Bohmann Nick , Freixas-Coutin Jose A. , Seo Jin , Simmons Ruth , Diener Christian , Gibbons Sean M.
Published: August 2023

The human upper respiratory tract (URT) microbiome, like the gut microbiome, varies across individuals and between health and disease states. However, study-to-study heterogeneity in reported case-control results has made the identification of consistent and generalizable URT-disease associations difficult. In order to address this issue, we assembled 26 independent 16S amplicon sequencing data sets from case-control URT studies, with approximately 2-3 studies per respiratory condition and ten distinct conditions covering common chronic and acute respiratory diseases. We leveraged the healthy control data across studies to investigate URT associations with age, sex and geographic location, in order to isolate these associations from health and disease states. We found several robust genus-level associations, across multiple independent studies, with either health or disease status. We identified disease associations specific to a particular respiratory condition and associations general to all conditions. Ultimately, we reveal robust associations between the URT microbiome, health, and disease, which hold across multiple studies and can help guide follow-up work on potential URT microbiome diagnostics and therapeutics.
Mycobacterial formation of intracellular lipid inclusions is a dynamic process associated with rapid replication
Authors: Fines DM , Schichnes D , Knight M , Anaya-Sanchez A , Thuong NTT , Cox J , Stanley SA
Published: August 2023

Intracellular lipid inclusions (ILI) are triacylglyceride rich organelles produced by mycobacteria thought to serve as energy reservoirs. It is believed that ILI are formed as a result of adosRmediated transition from replicative growth to non-replicating persistence (NRP). ILI richMycobacterium tuberculosis(Mtb) bacilli have been reported during infection and in sputum, establishing their importance in Mtb pathogenesis. Studies conducted in mycobacteria such asMycobacterium smegmatis, Mycobacterium abscessus,or lab Mtb strains have demonstrated ILI formation in the presence of hypoxic, nitric oxide, nutrient limitation, or low nitrogen stress, conditions believed to emulate the host environment within which Mtb resides. Here, we show thatM. marinumand clinical Mtb isolates make ILI during active replication in axenic culture independent of environmental stressors. By tracking ILI formation dynamics we demonstrate that ILI are quickly formed in the presence of fresh media or exogenous fatty acids but are rapidly depleted while bacteria are still actively replicating. We also show that the cell envelope is an alternate site for neutral lipid accumulation observed during stationary phase. In addition, we screen a panel of 60 clinical isolates and observe variation in ILI production during early log phase growth between and among Mtb lineages. Finally, we show thatdosRexpression level does not strictly correlate with ILI accumulation in fresh clinical isolates. Taken together, our data provide evidence of an active ILI formation pathway in replicating mycobacteria cultured in the absence of stressors, suggesting a decoupling of ILI formation from NRP.
Metabolic changes to host cells withToxoplasma gondiiinfection
Authors: Gallego-López Gina M. , Guzman Emmanuel Contreras , Knoll Laura J. , Skala Melissa
Published: August 2023

Toxoplasma gondii, the causative agent of toxoplasmosis, is an obligate intracellular parasite that infects warm-blooded vertebrates across the world. In humans, seropositivity rates ofT. gondiirange from 10% to 90%. Despite its prevalence, few studies address howT. gondiiinfection changes the metabolism of host cells. Here, we investigate howT. gondiimanipulates the host cell metabolic environment by monitoring metabolic response over time using non-invasive autofluorescence lifetime imaging of single cells, seahorse metabolic flux analysis, reactive oxygen species (ROS) production, and metabolomics. Autofluorescence lifetime imaging indicates that infected host cells become more oxidized and have an increased proportion of bound NAD(P)H with infection. These findings are consistent with changes in mitochondrial and glycolytic function, decrease of intracellular glucose, fluctuations in lactate and ROS production in infected cells over time. We also examined changes associated with the pre-invasion “kiss and spit” process using autofluorescence lifetime imaging, which similarly showed a more oxidized host cell with an increased proportion of bound NAD(P)H over 48 hours. Glucose metabolic flux analysis indicated that these changes are driven by NADH and NADP+ inT. gondiiinfection. In sum, metabolic changes in host cells withT. gondiiinfection were similar during full infection, and kiss and spit. Autofluorescence lifetime imaging can non-invasively monitor metabolic changes in host cells over a microbial infection time-course.
A systematic analysis of the qualitative and quantitative evidence on the purpose of animal-assisted therapy in improving patients wellbeing
Authors: Himanshu K. , Gunjan K. , Mukherjee Riya , Pandey Ramendra Pati , Chang Chung-Ming
Published: August 2023

Background

Animal-assisted therapy, also known as pet therapy, is a therapeutic intervention that involves animals to enhance the well-being of individuals across various populations and settings. This systematic study aims to assess the outcomes of animal-assisted therapy interventions and explore the associated policies.

Methods

A total of 16 papers published between 2015 and 2023 were selected for analysis. These papers were chosen based on their relevance to the research topic of animal-assisted therapy and their availability in scholarly databases. Thematic synthesis and meta-analysis were employed to synthesize the qualitative and quantitative data extracted from the selected papers.

Results

The analysis included sixteen studies that met the inclusion criteria and were deemed to be of moderate or higher quality. Among these studies, four demonstrated positive results for therapeutic mediation and one for supportive mediation in psychiatric disorders. Additionally, all studies showed positive outcomes for depression and neurological disorders. Regarding stress and anxiety, three studies indicated supportive mediation while two studies showed activating mediation.

Conclusion

The overall assessment of animal-assisted therapy shows promise as an effective intervention in promoting well-being among diverse populations. Further research and the establishment of standardized outcome assessment measures and comprehensive policies are essential for advancing the field and maximizing the benefits of animal-assisted therapy.
Inter-species gene flow drives ongoing evolution ofStreptococcus pyogenesandStreptococcus dysgalactiaesubsp.equisimilis
Authors: Xie Ouli , Morris Jacqueline M. , Hayes Andrew J. , Towers Rebecca J. , Jespersen Magnus G. , Lees John A. , Ben Zakour Nouri L. , Berking Olga , Baines Sarah L. , Carter Glen P. , Tonkin-Hill Gerry , Schrieber Layla , McIntyre Liam , Lacey Jake A. , James Taylah B. , Sriprakash Kadaba S. , Beatson Scott A. , Hasegawa Tadao , Giffard Phil , Steer Andrew C. , Batzloff Michael R. , Beall Bernie W. , Pinho Marcos D. , Ramirez Mario , Bessen Debra E. , Dougan Gordon , Bentley Stephen D. , Walker Mark J. , Currie Bart J. , Tong Steven Y. C. , McMillan David J. , Davies Mark R.
Published: August 2023

Streptococcus dysgalactiaesubsp.equisimilis(SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species,Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE andS. pyogenes.More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were found across species. Assessing potential cross-protection from leadingS. pyogenesvaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.
Thyroid hormone rewires cortical circuits to coordinate body-wide metabolism and exploratory drive
Authors: Hochbaum Daniel R. , Dubinsky Alexandra C. , Farnsworth Hannah C. , Hulshof Lauren , Kleinberg Giona , Urke Amanda , Wang Wengang , Hakim Richard , Robertson Keira , Park Canaria , Solberg Alyssa , Yang Yechan , Baynard Caroline , Nadaf Naeem M. , Beron Celia C. , Girasole Allison E. , Chantranupong Lynne , Cortopassi Marissa , Prouty Shannon , Geistlinger Ludwig , Banks Alexander , Scanlan Thomas , Greenberg Michael E. , Boulting Gabriella L. , Macosko Evan Z. , Sabatini Bernardo L.
Published: August 2023

Animals adapt to varying environmental conditions by modifying the function of their internal organs, including the brain. To be adaptive, alterations in behavior must be coordinated with the functional state of organs throughout the body. Here we find that thyroid hormone— a prominent regulator of metabolism in many peripheral organs— activates cell-type specific transcriptional programs in anterior regions of cortex of adult mice via direct activation of thyroid hormone receptors. These programs are enriched for axon-guidance genes in glutamatergic projection neurons, synaptic regulators across both astrocytes and neurons, and pro-myelination factors in oligodendrocytes, suggesting widespread remodeling of cortical circuits. Indeed, whole-cell electrophysiology recordings revealed that thyroid hormone induces local transcriptional programs that rewire cortical neural circuits via pre-synaptic mechanisms, resulting in increased excitatory drive with a concomitant sensitization of recruited inhibition. We find that thyroid hormone bidirectionally regulates innate exploratory behaviors and that the transcriptionally mediated circuit changes in anterior cortex causally promote exploratory decision-making. Thus, thyroid hormone acts directly on adult cerebral cortex to coordinate exploratory behaviors with whole-body metabolic state.
Exploring beam size measurement based on the Talbot effect at BEPCII
Authors: Zhang Wan , Zhu Dechong , Sui Yanfeng , Yue Junhui , Cao Jianshe , He Jun
Published: August 2023

Vertical beam size measurements were carried out at Beijing Electron–Positron Collider II (BEPCII) using a phase grating and an absorption grating based on the Talbot effect. The transverse coherence of synchrotron radiation is closely related to beam size. Due to the partial coherence of the synchrotron radiation source, the coherence length can be calculated by measuring the visibility decay of interferograms recorded at different distances behind the gratings. A vertical beam size of 68.19 ± 2 µm was obtained based on the relationship between the coherence length and beam size at the 3W1 beamline of BEPCII. A comparison of the vertical emittance derived from the grating Talbot method and the synchrotron radiation visible light interferometer method was presented. The vertical emittances from the two methods are 1.41 nm rad and 1.40 nm rad, respectively. The 0.1% difference indicates that the grating Talbot method for beam size measurement is reliable. This technique has great potential for small beam size measurement of fourth-generation synchrotron radiation light sources, considering its small diffraction limitation and simple experimental setups.
Pb speciation and elemental distribution in leeks by micro X-ray fluorescence and X-ray absorption near-edge structure
Authors: Sun Jianling , Yang Yongqiang , Luo Liqiang
Published: August 2023

Vegetables are crucial to a human diet as they supply the body with essential vitamins, minerals,etc. Heavy metals that accumulate in plants consequently enter the food chain and endanger people's health. Studying the spatial distribution and chemical forms of elements in plant/vegetable tissues is vital to comprehending the potential interactions between elements and detoxification mechanisms. In this study, leek plants and soil from vegetable gardens near lead–zinc mines were collected and cultivated with 500 mg L−1PbNO3solutions for three weeks. Micro X-ray fluorescence was used to map the distribution of Pb and other chemical elements in leek roots, and X-ray absorption near-edge spectroscopy was used to assess the Pb speciation in leek roots and leaves. These findings demonstrated that Pb, Cu, Mn, Cr, Ti and Fe were detected in the outer rings of the root's cross section, and high-intensity points were observed in the epidermis. Zn, K and Ca, on the other hand, were distributed throughout the root's cross section. Leek root and leaf contained significant quantities of lead phosphate and basic lead carbonate at more than 80%, followed by lead sulfide (19%) and lead stearate (11.1%). The capacity of leek roots to convert ambient lead into precipitated lead and fix it on the root epidermis and other inner surfaces is a key mechanism for reducing the toxic effects of Pb.
Combinatorial aspects of the Löwenstein avoidance rule. Part III: the relational system of configurations
Authors: Moreira de Oliveira Jr Montauban , Eon Jean-Guillaume
Published: August 2023

This paper introduces a new method of determining the independence ratio of periodic nets, based on the observation that, in any maximum independent set of the whole net, be it periodic or not, the vertices of every unit cell should constitute an independent set, called here a configuration. For 1-periodic graphs, a configuration digraph represents possible sequences of configurations of the unit cell along the periodic line. It is shown that maximum independent sets of the periodic graph are based on directed cycles with the largest ratio. In the case of 2-periodic nets, it is necessary to draw a different configuration digraph for each crystallographic direction defining a linkage between neighbouring cells, a concept known as a binary relational system. The two possible systems are analysed in this paper: \overrightarrow{\bf{sql}} is associated to nets displaying linkages between unit cells along the directions 10 and 01, and \overrightarrow{\bf{hxl}} is associated to nets also displaying linkages between cells along the direction 11. For both kinds of nets, a maximum independent set is obtained as a homomorphic image from \overrightarrow{\bf{sql}} or \overrightarrow{\bf{hxl}} to the respective configuration system. The method is illustrated with some of the 2-periodic nets listed on the Reticular Chemistry Structure Resource site; it is shown that it provides a rigorous solution to the case of the net sdh that was not satisfactorily solved in Part II [Moreira de Oliveira, de Abreu Mendes & Eon (2022). Acta Cryst. A78, 115–127]. The method is extended to relational systems based on non-translational symmetry operations. The successive steps are then summarized and a simple application to the 3-periodic net qtz is discussed; analysis of zeolites and aluminosilicates may proceed along the same lines. It is shown that the new method enables the analysis of disordered distributions in periodic nets.
Paths leading contractual disputes to litigation
Authors: Jagannathan Murali , Delhi Venkata Santosh Kumar
Published: August 2023

Purpose

Judiciary plays a pivotal role in the overall development of a nation's economy and its involvement assures process transparency and impartiality. However, litigation is often expensive, uncertain and prone to delays. Notwithstanding such inherent challenges associated with litigation, it is observed that parties in construction disputes do resort to litigation. This study attempts to understand the potential paths triggering litigation of contractual disputes in construction. While extant researchers have identified focus areas or factors influencing litigation, the underlying paths connecting these focus areas, leading parties to litigation, is explored in this study.

Design/methodology/approach

Considering the framework of Rachlinski's “framing theory of litigation” and the mixed-methods approach (qualitative and quantitative approaches), this study proposes and validates a model that identifies the paths to litigation of contractual disputes in construction.

Findings

The results of in-depth interviews, followed by validation through structural equation modelling (SEM), reveal four critical paths, namely positional focus (PF) – contract and dispute characteristics (CDC) – decision to litigate (DTL), milieu influence (MI) – CDC – DTL, MI-PF-DTL and CDC-DTL.

Practical implications

The identified paths highlight the areas policymakers can consider while developing policy interventions to mitigate litigation.

Originality/value

Researchers have identified factors causing litigation in construction. However, attempts to examine the existence of multi-factor “paths” on the decision to litigate (DTL) have hitherto received a muted response, so this study focuses on identifying the project-level path(s) leading to the litigation of contractual disputes in construction.
The optimum use of high-strength steel in the construction of gas transmission pipeline
Authors: Guillal Abdelkader , Abdelbaki Noureddine
Published: August 2023

Purpose

The aim of this study is to assess the opportunity for the development of hydrocarbon transportation using high-strength steel (HSS) in pipeline construction in terms of cost savings and reliability.

Design/methodology/approach

Several optimizations of pipeline design and operations were performed to estimate the total life-cycle cost variation associated with different grades of high-strength steel. The generalized reduced gradient (GRG) method was used in an Excel table to determine optimal total life cycle each pipeline. Variables used in this optimization with respect to each steel grade were as follows: pipeline external diameter, wall thickness, number of compression stations and installed power in each compression station. The reliability of a pipeline with optimal cost was assessed to highlight the impact of steel grade on pipeline reliability.

Findings

The study showed that the cost reduction is strongly dependent on the adopted gas pipeline configuration. The number of compression stations and external diameter are the main factors influencing the pipeline total life cycle cost, while the steel price seems to have a minor effect, the reduction of the gas pipeline total life cycle does not exceed 5% even with a 50% difference in pipe steel prices between X70 and X100 steels. On the other side, for the same external diameter, X100 steel presents better pipeline reliability against carbonic corrosion compared to X70 steel.

Practical implications

The main contribution of this study is to provide a decision-support tool to help pipeline constructors enhance the profitability of natural gas transmission pipelines. The optimization method used is simple to use for design engineers during a feasibility study.

Originality/value

The present study presents one step to fill the gap concerning the question of balancing the trade-off between cost savings and structural reliability in high-strength steel pipelines during the early stages of feasibility studies. The optimal design and operations parameters ensuring cost savings on total life cycle costs are identified via an optimization method. The impact of selected optimal parameters on the long-term pipeline service life was estimated via a structural reliability analysis.