bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic imprint of an intracellular pathogen drives histone hypermethylation and tunes the host transcriptional response to infection
Authors: Charendoff Chloé I. , Louchez Félix V. , Wu Yongzheng , Dolat Lee , Velasco Guillaume , Perrinet Stéphanie , Torres Adrian Gabriel , Blanchet Laure , Duchateau Magalie , Gianetto Quentin Giai , Matondo Mariette , Maestro Laurence Del , Ait-Si-Ali Slimane , Bonhomme Frédéric , Millot Gaël A. , Ribas de Pouplana Lluís , Martinez Elisabeth D. , Valdivia Raphael H. , Subtil Agathe 
Published: June 2024

ABSTRACTChlamydia trachomatis, an intracellular bacterium, highjacks metabolites from the host cell. We provide evidence of global hypermethylation of the host proteome, including histones, during the late stages of infection and that histone hypermethylation is the result of metabolic imbalance favoring the activity of lysine methyl transferases over demethylases. We find that histones hypermethylated at residues H3K4 and H3K9 are distributed throughout the chromatin. Inhibition of bacterial growth, or supplementation of the culture medium with iron or with dimethyl-ketoglutarate (DMKG) reduced histone hypermethylation. DMKG supplementation modified the transcription of about one third of the infection-responsive genes, including genes involved in the innate response to infection. Transfer RNA (tRNA) levels decreased late in infection and DMKG supplementation prevented this phenomenon. Finally, we uncovered a robust, histone demethylase dependent shut-down of the innate response in the mouse genital tract shortly after the acute phase of infection. Overall, our data show that the metabolic pressure exerted by a pathogen with an intracellular lifestyle drives an epigenetic imprint that tunes the transcriptional response of its host.
A high-throughput search for intracellular factors that affect RNA folding identifiesE. coliproteins PepA and YagL as RNA chaperones that promote RNA remodeling
Authors: Rojano-Nisimura Alejandra Matsuri , Miller Lucas G. , Anantharaman Aparna , Middleton Aaron T. , Kibret Elroi , Jung Sung H. , Russell Rick , Contreras Lydia M. 
Published: June 2024

AbstractGeneral RNA chaperones are RNA-binding proteins (RBPs) that interact transiently and non-specifically with RNA substrates and assist in their folding into native state. In bacteria, these chaperones impact both coding and non-coding RNAs and are particularly important for large, structured RNAs which are prone to becoming kinetically trapped in misfolded states. Currently, due to the limited number of well-characterized examples and the lack of a consensus structural or sequence motif, it is difficult to identify general RNA chaperones in bacteria. Here, we adapted a previously publishedin vivoRNA regional accessibility probing assay to screen genome wide for intracellular factors inE. coliaffecting RNA folding, among which we aimed to uncover novel RNA chaperones. Through this method, we identified and validated eight proteins whose deletion gives changes in regional accessibility within the exogenously expressedTetrahymenagroup I intron ribozyme. Further, we purified and measuredin vitroproperties of two of these proteins, YagL and PepA, which were especially attractive as general chaperone candidates. We showed that both proteins bind RNA and that YagL accelerates native refolding of the ribozyme from a long-lived misfolded state. Further dissection of YagL showed that a putative helix-turn-helix (HTH) domain is responsible for most of its RNA binding activity but only the full protein shows chaperone activity. Altogether, this work expands the current repertoire of known general RNA chaperones in bacteria.
Phosphatases control the duration and range of cAMP/PKA microdomains
Authors: Conca Filippo , Bayburtlu Doruk Kaan , Vismara Mauro , Surdo Nicoletta C. , Tavoni Alessandra , Nogara Leonardo , Sarra Adamo , Ciciliot Stefano , Di Benedetto Giulietta , Iannucci Liliana F. , Lefkimmiatis Konstantinos 
Published: June 2024

AbstractThe spatiotemporal interplay between the second messenger cyclic AMP (cAMP) and its main effector, Protein Kinase A (PKA) is crucial for the pleotropic nature of this cascade. To maintain a high degree of specificity, the cAMP/PKA axis is organized into functional multiprotein complexes, called microdomains, precisely distributed within the cell. While the subcellular allocation of PKA is guaranteed by a family of tethers called A-Kinase-anchoring Proteins (AKAPs), the mechanisms underlying the efficient confinement of a microdomain’s functional effects are not fully understood. Here we used FRET-based sensors to detect cAMP levels and PKA-dependent phosphorylation within specific subcellular compartments and found that, while free cAMP is responsible for the activation of local PKA enzymes, the dephosphorylating actions of phosphatases dictate the duration of the microdomain’s effects. To test the range of action of PKA microdomains we used rigid aminoacidic nanorulers to distance our FRET sensors from their original location for 10 or 30 nm. Interestingly, we established that cAMP levels do not affect the spatial range of the microdomain while on the contrary, phosphatase activity acts as the main functional boundary for phosphorylated PKA targets. Our findings contribute to the design of a picture where two microdomain-forming events have distinct roles. Cyclic AMP elevations trigger the initial activation of subcellular PKA moieties, while the temporal and spatial extent of the PKA’s actions is regulated by phosphatases.
Conserved residues of the immunosuppressive domain of MLV are essential for regulating the fusion-critical SU-TM disulfide bond
Authors: Hogan Victoria A. , Harmon Julia , Cid-Rosas Miguel , Hall Laura R. , Johnson Welkin E. 
Published: June 2024

ABSTRACTThe ENV protein of murine leukemia virus (MLV) is the prototype of a large clade of retroviral fusogens, collectively known as gamma-type Envs. Gamma-type ENVs are found in retroviruses and related endogenous retroviruses (ERV) representing a broad range of vertebrate hosts. All gamma-type Envs contain a highly conserved stretch of 26-residues in the transmembrane subunit (TM) comprising two motifs, a putative immunosuppressive domain (ISD) and a CX6CC motif. The extraordinary conservation of the ISD and its invariant association with the CX6CC suggests a fundamental contribution to Env function. To investigate function of the ISD, we characterized several mutants with single amino acid substitutions at conserved positions in the MLV ISD. A majority abolished infectivity, although we did not observe a corresponding loss in intrinsic ability to mediate membrane fusion. Ratios of the surface subunit (SU) to capsid protein (CA) in virions were diminished for a majority of the mutants, while TM/CA ratios were similar to wild type. Specific loss of SU reflected premature isomerization of the labile disulfide bond that links SU and TM prior to fusion and entry. Indeed, all non-infectious mutants displayed significantly lower disulfide stability than wild type MLV Env. These results reveal a role for residues at MLV ISD positions 2, 3, 4, 7, and 10 in regulating a late step in fusion, and suggest that the ISD is part of a larger domain, encompassing both the ISD and CX6CC motifs, that is critical for formation and regulation of the metastable, intersubunit disulfide bond.IMPORTANCEThe gamma-type Env is an extremely prevalent viral fusogen, extensively found within retroviruses and endogenous loci across vertebrate species and are further found in filoviruses such as Ebola virus. The fusion mechanism of gamma-type Envs is unique from other Class I fusogens such as those of IAV and HIV-1. Gamma-type Envs contain a hallmark feature known as the immunosuppressive domain (ISD) that has been the subject of some controversy in the literature surrounding its putative immunosuppressive effects. Despite the distinctive conservation of the ISD, little has been done to investigate the role of this region for the function of this widespread fusogen. Our work demonstrates the importance of the ISD for the function of gamma-type Envs in infection, particularly in regulating the intermediate steps of fusion with the host membrane. Understanding the fusion mechanism of gamma-type Envs has broad implications for understanding entry of extant viruses and aspects of host biology connected to co-opted endogenous gamma-type Envs.
A mouse model of TB-associated lung fibrosis reveals persistent inflammatory macrophage populations during treatment
Authors: Boucau Julie , Naidoo Threnesan , Liu Yuming , Dasgupta Shatavisha , Jain Neha , Castillo Jennie Ruelas , Jacobson Nicholas E. , Nargan Kievershen , Cimini Beth A. , Eliceiri Kevin W. , Steyn Adrie J.C. , Barczak Amy K. 
Published: June 2024

AbstractPost-TB lung disease (PTLD) causes a significant burden of global disease. Fibrosis is a central component of many clinical features of PTLD. To date, we have a limited understanding of the mechanisms of TB-associated fibrosis and how these mechanisms are similar to or dissimilar from other fibrotic lung pathologies. We have adapted a mouse model of TB infection to facilitate the mechanistic study of TB-associated lung fibrosis. We find that the morphologies of fibrosis that develop in the mouse model are similar to the morphologies of fibrosis observed in human tissue samples. Using Second Harmonic Generation (SHG) microscopy, we are able to quantify a major component of fibrosis, fibrillar collagen, over time and with treatment. Inflammatory macrophage subpopulations persist during treatment; matrix remodeling enzymes and inflammatory gene signatures remain elevated. Our mouse model suggests that there is a therapeutic window during which adjunctive therapies could change matrix remodeling or inflammatory drivers of tissue pathology to improve functional outcomes after treatment for TB infection.
Emergence of Slc11 clade MCbgut: a parsimonious hypothesis for the dawn of Lactobacillales in the gut of early vertebrates
Authors: Cellier M. FM 
Published: June 2024

AbstractThe Lactobacillales (LB) stand apart among bacterial orders, using manganese (Mn) instead of iron to support their growth and swiftly ferment complex foods while acidifying their environment. The present work investigates whether a shift in the use of Mn could mark the origin of LB. Transmembrane carriers of the ubiquitous Slc11 family play key roles in LB physiology by catalyzing proton-dependent Mn import. In prior studies, the Slc11 clade found in LB (MntH Cb, MCb) showed both remarkable structural plasticity and highly efficient Mn uptake, and another Slc11 clade, MCg1, demonstrated divergent evolution coinciding with emergence of bacterial genera (e.g.,Bordetella,Achromobacter). Herein, Slc11 clade MCb is subdivided in sister groups: MCbieand MCbgut. MCbiederives directly from Slc11 clade MCa, pointing an intermediate stage in the evolution of MCbgut. MCbiepredominates in marine Bacillaceae, is more conserved than MCbgut, lacks the structural plasticity that typify MCbgutcarriers, and responds differently to identical mutagenesis. Exchanging MCbie/MCbgutamino acid residues at sites that distinguish these clades showed conformation-dependent effects with both MCbieand MCbguttemplates and the 3D location of the targeted sites in the carrier structure together suggest the mechanism to open the inner gate, and release Mn into the cytoplasm, differs between MCbieand MCbgut. Building on the established phylogeny forEnterococcusrevealed that a pair of genes encoding MCbgutwas present in the common ancestor of LB, as MCbgu1and MCbgu2templates exhibit distinct structural dynamics properties. These data are discussed examining whether MCb+LB could emerge in the upper gut of early vertebrates (ca. 540 mya), through genome contraction and evolution toward Mn-centrism, as they specialized as gastric aids favoring stomach establishment in jawed vertebrates through bi-directional communication with host nervous, endocrine and immune systems.
High-affinity PQQ import is widespread in Gram-negative bacteria
Authors: Munder Fabian , Voutsinos Marcos , Hantke Klaus , Venugopal Hari , Grinter Rhys 
Published: June 2024

ABSTRACTPQQ is a soluble redox cofactor used by diverse bacteria to oxidise fuel compounds as a source of electrons for the respiratory chain. Many Gram-negative bacteria that encode PQQ-dependent enzymes do not possess the biosynthetic machinery for its production and instead obtain it from the environment. To achieve this the bacteriumEscherichia coliuses the TonB-dependent transporter PqqU as a high-affinity PQQ importer, allowing it to use PQQ at an external concentration as low as 1 nM. Here, we show that PqqU achieves this by binding PQQ with a very high affinity. Using cryo-electron microscopy we determine the structure of the PqqU-PQQ complex at a resolution of 1.99 Å, revealing that the extracellular loops of PqqU undergo significant conformational changes upon PQQ binding, which captures the cofactor in an internal cavity. This cavity likely facilitates an airlock-style gating mechanism that prevents non-specific import through PqqU. Using structural modelling we show that the change in PqqU structure upon PQQ binding precludes the binding of bacteriophage, which targets it as a cell surface receptor. Guided by the PqqU-PQQ complex structure we use phenotypic analysis to identify the amino acids essential for PQQ import and leverage this information to map the presence of PqqU across Gram-negative bacteria. This reveals that PqqU is encoded by Gram-negative bacteria from at least 22 phyla from diverse habitats, including those found in aquatic, soil, host-associated, and extreme environments. This indicates that PQQ is a ubiquitous nutrient in many environments, and an important cofactor for bacteria that adopt diverse lifestyles and metabolic strategies.Significance StatementMany enzymes form complexes with molecules called cofactors to perform their function. PQQ is a cofactor used by bacterial enzymes that provide energy by breaking down food molecules. While some bacteria make their own PQQ, other bacteria use the transport protein PqqU to bind PQQ from the environment and import it into their cells. We show that PqqU binds PQQ very tightly, allowing bacteria to acquire it at very low concentrations. Using cryo-electron microscopy we image the PqqU-PQQ complex on an atomic level, revealing how PQQ is bound so tightly. Using this the information to analyse microbial genomes, we show that PQQ scavenging is employed by diverse bacteria, implying that PQQ is an important common good of diverse microbiomes.
Multiplexed optical barcoding and sequencing for spatial omics
Authors: Venkatramani Aditya , Ciftci Didar , Cohen Limor , Li Christopher , Pham Khanh , Zhuang Xiaowei 
Published: June 2024

AbstractSpatial omics has brought a fundamental change in the way that we study cell and tissue biology in health and disease. Among various spatial omics methods, genome-scale imaging allows transcriptomic, 3D-genomic, and epigenomic profiling of individual cells with high spatial (subcellular) resolution but often requires a preselection of targeted genes or genomic loci. On the other hand, spatially dependent barcoding of molecules followed by sequencing provides untargeted, genome-wide profiling but typically lacks single-cell resolution. Here, we report a spatial omics method that could potentially combine the power of the two approaches by optically controlled spatial barcoding followed by sequencing. Specifically, we utilize patterned light to encode the locations of cells in tissues using oligonucleotide-based barcodes and then identify the barcoded molecular content, such as mRNAs, by sequencing. This optical barcoding method is designed with multiplexing and error-correction capacity and achieved by a light-directed ligation chemistry that attaches distinct nucleic-acid sequences to the reverse transcribed cDNA products at different locations. As a proof of principle for this method, we demonstrated high-efficiency in situ light-directed ligation, spatially dependent barcoding with multiplexed light-controlled ligations, and high-accuracy detection of spatially barcoded mRNAs in cells.
How many vector charmoniumlike states lie in the mass range 4.2–4.35 GeV?
Authors: von Detten Leon , Baru Vadim , Hanhart Christoph , Wang Qian , Winney Daniel , Zhao Qiang 
Published: June 2024

In recent years many vector charmonium(like) states were reported by different electron-positron collider experiments above 4.2 GeV. However, so far, there not only exists sizable tension in the parameters of those states, but there is also no consensus on the number of the vector states in this energy range. To some extend, this might be caused by the fact that the experimental data were typically analyzed in single channel analyses employing overlapping Breit-Wigner functions, in particular ignoring the effect of opening thresholds. In this study, we focus on the mass range between 4.2 GeV and 4.35 GeV, conducting a comprehensive analysis of eight different final states in e+e− annihilation. Our findings demonstrate that, within this mass range, a single vector charmoniumlike state, exhibiting properties consistent with a D1D¯ molecular structure and characterized by a pole location spoleY(4230)=(4227±4−i2(50−2+8))  MeV, can effectively describe all the collected data. This is made possible by allowing for an interference with the well-established vector charmonium ψ(4160) along with the inclusion of the D1D¯ threshold effect. Moreover, in contrast to experimental analyses, our study reveals that the highly asymmetric total cross sections for e+e−→J/ψππ and e+e−→J/ψKK¯ around 4230 MeV stem from the same physics, rooted in the approximate SU(3) flavor symmetry of QCD.

Published by the American Physical Society
2024
Sustainability and development of EWE communities in Ghana through indigenous knowledge management practices
Authors: Dei De-Graft Johnson 
Published: June 2024

Purpose
Losing indigenous knowledge is to lose the future and impoverish the societies because indigenous knowledge is considered one of the cornerstones and survival of communities, societies and economies. This study, thus, aims to explore and assess the contextual enablers of indigenous knowledge and their role in developing and sustaining the Ewe communities in Ghana.

Design/methodology/approach
The qualitative research design, which enabled the researcher to engage the participants in an interview process and observation, was used in this study. It was augmented with a quantitative design using structured questions. Data analysis was guided by the basic principles of grounded theory. The coding system was aided by NVivo to analyze the qualitative data, while the quantitative data was analyzed using the SPSS. Descriptive analysis and graphs were deployed in the presentation of the findings.

Findings
The study discovered that the communities are in possession of several types of indigenous knowledge, ranging from tacit to explicit knowledge, which are embedded in their cultural and traditional systems and unique to every community; the culture of trust among the citizens and motivation to create and share knowledge in communities was high. Same time, family heads, farmer groups, libraries and museums played key roles in the preservation and management of indigenous knowledge in the communities. On the other hand, information officers and institutions like churches and police posts played insignificant roles in the management and preservation of knowledge in the communities just as the absence of a culture of willingness by the community members to create and share knowledge. Additionally, there was an absence of technological infrastructure, platforms, databases and policies to aid the management and preservation of knowledge in the communities. The study concludes that indigenous knowledge plays a vital role in the development and sustainability of communities in Ghana.

Practical implications
Community leaders and political leaders need to invest in systems and structures that will promote the management and preservation of indigenous knowledge for the development of the communities and the state as a whole.

Originality/value
The study demonstrates its originality in terms of scope, setting, population and empirical evidence by focusing on the role of indigenous knowledge in the sustainability and development of Ewe communities in Ghana.
A generic numerical method for treating a system of Volterra integro-differential equations with multiple delays and variable bounds
Authors: Kürkçü Ömür Kıvanç , Sezer Mehmet 
Published: June 2024

PurposeThis study aims to treat a novel system of Volterra integro-differential equations with multiple delays and variable bounds, constituting a generic numerical method based on the matrix equation and a combinatoric-parametric Charlier polynomials. The proposed method utilizes these polynomials for the matrix relations at the collocation points.Design/methodology/approachThanks to the combinatorial eligibility of the method, the functional terms can be transformed into the generic matrix relations with low dimensions, and their resulting matrix equation. The obtained solutions are tested with regard to the parametric behaviour of the polynomials with $\alpha$, taking into account the condition number of an outcome matrix of the method. Residual error estimation improves those solutions without using any external method. A calculation of the residual error bound is also fulfilled.FindingsAll computations are carried out by a special programming module. The accuracy and productivity of the method are scrutinized via numerical and graphical results. Based on the discussions, one can point out that the method is very proper to solve a system in question.Originality/valueThis paper introduces a generic computational numerical method containing the matrix expansions of the combinatoric Charlier polynomials, in order to treat the system of Volterra integro-differential equations with multiple delays and variable bounds. Thus, the method enables to evaluate stiff differential and integral parts of the system in question. That is, these parts generates two novel components in terms of unknown terms with both differentiated and delay arguments. A rigorous error analysis is deployed via the residual function. Four benchmark problems are solved and interpreted. Their graphical and numerical results validate accuracy and efficiency of the proposed method. In fact, a generic method is, thereby, provided into the literature.