bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel recombinant PHB production platform in filamentous cyanobacteria avoiding nitrogen starvation while preserving cell viability
Authors: Fink Phillipp , Menzel Claudia , Kwon Jong-Hee , Forchhammer Karl 
Published: October 2024

AbstractDuring the past decades, the importance of developing sustainable, carbon dioxide (CO2)-neutral and biodegradable alternatives to conventional plastic has become evident in the context of global pollution issues. Therefore, heterotrophic bacteria such asCupriavidussp. have been intensively explored for the synthesis of the biodegradable polymer polyhydroxybutyrate (PHB). PHB is also naturally produced by a variety of phototrophic cyanobacteria, which only need sunlight and CO2,thereby allowing a CO2negative, eco-friendly synthesis of this polymer. However, a major drawback of the use of cyanobacteria is the need of a two-stage production process, since relevant amount of PHB synthesis only occurs after transferring the cultures to conditions of nitrogen starvation, which hinders continuous, large-scale production.This study aimed at generating, by means of genetic engineering, a cyanobacterium that continuously produces PHB in large amounts. We choose a genetically amenable filamentous cyanobacterium of the genusNostocsp., which is a diazotrophic cyanobacterium, capable of atmospheric nitrogen (N2) fixation but naturally does not produce PHB. We transformed thisNostocstrain with various constructs containing the PHB synthesis operon fromCupriavidus necatorH16. In fact, while the transformants initially produced PHB, the PHB-producing strains rapidly lost cell viability. Therefore, we next attempted further optimization of the biosynthetic gene cluster. Finally, we succeeded in stabilized PHB production, whilst simultaneously avoiding decreasing cell viability. In conclusion, the recombinantNostocstrain constructed in the present work constitutes the first example of a continuous and stable PHB production platform in cyanobacteria, which has been decoupled from nitrogen starvation and, hence, harbours great potential for sustainable, industrial PHB production.
The pneumococcal bacteriocin streptococcin B is produced as part of the early competence cascade and promotes intraspecies competition
Authors: Richardson JD , Guo Emily , Wyllie Ryan M , Jensen Paul , Dawid Suzanne 
Published: October 2024

AbstractStreptococcus pneumoniaeis an important human pathogen that normally resides in the human nasopharynx. Competence mediated bacteriocin expression byS pneumoniaeplays a major role in both the establishment and persistence of colonization on this polymicrobial surface. Over 20 distinct bacteriocin loci have been identified in pneumococcal genomes, but only a small number have been characterized phenotypically. In this work, we demonstrate that 3/4th ofS. pneumoniaestrains contain a highly conservedscblocus that encodes an active lactococcin 972-like bacteriocin called Streptococcin B. In these backgrounds, thescbABClocus is part of the early competence cascade due to a ComE binding site in the promoter region. Streptococcin B producing strains target both members of the population that have failed to activate competence and the 25% of the population that carry a naturally occurring deletion of the ComE binding site and the functional bacteriocin gene. The ComR-type regulator found directly upstream of thescblocus inS. pneumoniaestrains can activatescbexpression independent of the presence of the ComE binding site but only when stimulated by a peptide that is encoded in thescblocus ofS. pseudopneumoniae, a closely related bacterium which also inhabits the human nasopharynx. Given the co-regulation with competence and the phenotypic confirmation of activity, Streptococcin B represents a previously unrecognized fratricide effector that gives producing strains an additional advantage over the naturally occurring deleted strains during colonization.ImportanceStreptococcus pneumoniaeis a common cause of pneumonia, meningitis, sinusitis and otitis media. In order to successfully colonize humans, a pre-requisite to the development of invasive disease,S. pneumoniaemust compete with other bacterial inhabitants of the nasal surface for space and nutrients. Bacteriocins are small antimicrobial peptides produced by bacteria that typically target neighboring bacteria by disruption of the cell surface.S. pnuemoniaeencodes a large number of potential bacteriocin, but, for most, their role in competitive interactions has not been defined. This work demonstrates that isolates that produce the bacteriocin Streptococcin B have an advantage over non producers. These observations contribute to our understanding of the competitive interactions that precede development ofS. pneumoniaedisease.
Structure and stabilization of the antigenic glycoprotein building blocks of the New World mammarenavirus spike complex
Authors: Paesen Guido C. , Ng Weng M. , Sutton Geoff , Doores Katie J. , Bowden Thomas A. 
Published: October 2024

AbstractThe spillover of New World (NW) arenaviruses from rodent reservoirs into human populations poses a continued risk to human health. NW arenaviruses present a glycoprotein (GP) complex on the envelope surface of the virion, which orchestrates host-cell entry and is a key target of the immune response arising from infection and immunization. Each protomer of the trimeric GP is composed of a stable signal peptide (SSP), a GP1 attachment glycoprotein, and a GP2 fusion glycoprotein. To glean insights into the architecture of this key therapeutic target, we determined the crystal structures of NW GP1–GP2 heterodimeric complexes from Junín virus (JUNV) and Machupo virus (MACV). Due to the metastability of the interaction between GP1 and GP2, structural elucidation required the introduction of a disulfide bond at the GP1–GP2 complex interface, but no other stabilizing modifications were required. While the overall assembly of NW GP1–GP2 is conserved with that presented by Old World (OW) arenaviruses, including Lassa virus (LASV) and lymphocytic choriomeningitis virus (LCMV), NW GP1–GP2 complexes are structurally distinct. Indeed, we note that when compared to the OW GP1–GP2 complex, the globular portion of NW GP1 undergoes limited structural alterations upon detachment from its cognate GP2. We further demonstrate that our engineered GP1–GP2 heterodimers are antigenically relevant and recognized by neutralizing antibodies. These data provide insights into the distinct assemblies presented by NW and OW arenaviruses, as well as provide molecular-level blueprints that may guide vaccine development.ImportanceAlthough the emergence of New World (NW) hemorrhagic fever mammarenaviruses poses an unceasing threat to human health, there is a paucity of reagents capable of protecting against the transmission of these pathogens from their natural rodent reservoirs. This is, in part, attributed to our limited understanding of structure and function of the NW glycoprotein spike complex presented on the NW arenavirus surface. Here, we provide a detailed molecular-level description of how the two major components of this key therapeutic target assemble to form a key building block of the NW arenaviral spike complex. The insights gleaned from this work provide a framework for guiding the structure-based development of NW arenaviral vaccines.
Expression Profiles of FABP4 and FABP5 in Breast Cancer: Clinical Implications and Perspectives
Authors: Jiang Xingshan , Xiong Yiqin , Yu Jianyu , Avellino Anthony , Liu Shanshan , Han Xiaochun , Wang Zhaohua , Shilyansky Jonathan S. , Curry Melissa A. , Hao Jiaqing , Sauter Edward R. , Sugg Sonia L. , Li Bing 
Published: October 2024

AbstractThe incidence of breast cancer continues to rise each year despite significant advances in diagnosis and treatment. Obesity-associated dysregulated lipid metabolism is believed to contribute to the increasing risk of breast cancer. However, the mechanisms linking lipid dysregulation to breast cancer risk and progression remain to be determined. The family of fatty acid binding proteins (FABPs) evolves to facilitate lipid transport and metabolism. As the predominant isoforms of FABP members expressed in breast tissue, adipose FABP (A-FABP, also known as FABP4) and epithelial FABP (E-FABP, FABP5) have been shown to play critical roles in breast carcinogenesis. In this study, we collected surgical breast tissue samples from 96 women with different subtypes of breast cancer and comprehensively analyzed the expression pattens of FABP4 and FABP5. We found that distinct expression profiles of FABP4 and FABP5 were associated with their unique roles in breast cancer development. FABP4, mainly expressed in breast stroma, especially in adipose tissue, supported neighboring tumor cell lymphvascular invasion through secretion from adipocytes. In contrast, FABP5, primarily expressed in epithelial-derived tumor cells, promoted tumor metastasis by enhancing lipid metabolism. Thus, elevated levels of FABP4 and FABP5 could serve as poor prognostic markers for breast cancer. Inhibiting the activity of FABP4 and/or FABP5 may offer a novel strategy for breast cancer treatment.
CK1α, FAM83H, and FAM83B contribute to bundling of neurofilaments and are sequestered in cellular and mice models of ARSACS
Authors: Atkinson Caitlin S. , Cheng-Boivin Zacharie , Larochelle Nancy , Minotti Sandra , Gentil Benoit J. 
Published: October 2024

AbstractAutosomal recessive spastic ataxia of the Charlevoix-Saguenay (ARSACS) is a rare neurodegenerative disorder characterized by mutations in theSACSgene that encodes for the sacsin protein. Sacsin dysfunction in ARSACS results in neurofilament bundling, a phenotype observed in various cellular models of ARSACS. The mechanisms underlying bundling in ARSACS remain unclear. With neurofilament phosphorylation controlling several processes of intermediate filament dynamics, its dysregulation may play a role in ARSACS. Accordingly, we investigated the interaction between CK1α (Casein Kinase 1α) and its adaptor proteins FAM83H or FAM83B (FAMily with sequence similarity 83). Here, we report that these target proteins are upregulated in ARSACS patient fibroblasts and co-localize at the sites of intermediate filament bundling. In theSacs-/-cerebellum, FAM83B compensated for the lack of FAM83H expression, suggesting a cell-type specific activity of CK1α that depends on the relative expression of its adaptor proteins. Further, CK1α inhibition with D4475 or knockdown of the target proteins with the CRISPR system caused neurofilament bundling, a phenotype that was only partially remedied by CK1α activation with SSTC3. Our findings suggest that CK1α, FAM83H, and FAM83B contribute to neurofilament bundling in ARSACS; however, the inability of CK1α to resolve neurofilament bundling may reflect an error in a priming phosphorylation event in ARSACS. Future research is needed to understand the hierarchical phosphorylation cascade to CK1α activity and its contribution to ARSACS pathology.HighlightsCK1α and its cell-specific adaptors are upregulated in ARSACS and targeted to the sites of bundlesKnockdown of CK1α, FAM83H, and FAM83B cause neurofilament bundlingActivation of CK1α partially remediates bundling
Development of a Novel Method to Fabricate Highly Functional Human Purkinje Networks
Authors: Ji Pengfei , Heinle Jeffrey S. , Birla Ravi K. 
Published: October 2024

ABSTRACTBACKGROUNDIn this study, we present a method to bioengineer functional Purkinje networks using recent advances in laser-based bioprinting.METHODSA custom bioink as formulated using optimized concentrations of polyethylene glycol diacrylate (PEGDA), gelatin methacryloyl (GELMA), lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP), and tartrazine. A standard triangle language (STL) model of Purkinje networks was developed based on the mammalian Purkinje network mapped out using India ink staining. A commercial bioprinter, the Lumen X, from CellInk, was used to bioprint Purkinje networks. The biocompatibility of the bioprinted Purkinje networks was tested using iPSCs from healthy donors. Negative molds of the Purkinje networks were designed to simulate interaction between Purkinje cells and adjacent cardiomyocytes using different degrees of overlap between the two cell types. The negative molds were also shown to be biocompatible, based on the culture of iPSCs derived from healthy donors.RESULTSWe were able to successfully bioprint over 100 Purkinje networks and demonstrate biocompatibility with iPSCs for up to 7 days. Three different configurations of the negative molds were designed and fabricated and all three shown to be biocompatible with iPSCs for up to 7 days. A co-culture system was developed by placing the Purkinje networks in proximity to the negative molds for all three configurations designed.CONCLUSIONOur results demonstrate the ability to bioprint Purkinje networks and molds and provide an in vitro system to study the functional interaction between Purkinje cells and adjacent cardiomyocytes.
Proton channel inactivation results in loss of chloroplast NDH complex activity
Authors: Strand Deserah D. , Ruf Stephanie , Sandoval-Ibáñez Omar A. , Bock Ralph 
Published: October 2024

AbstractThe plastidal photosynthetic complex I (formerly NAD(P)H dehydrogenase-like complex, NDH) remains enigmatic in its function within the electron transport chain of higher plants. While the NDH complex shares high homology with complex I, a key component of the respiratory electron transport chain, electron transport rates through the NDH complex in thylakoids are relatively low. In this study, we took a structure-function approach and mutated the plastid genome-encodedndhFgene to abolish the NdhF proton channel of the NDH complex. These mutations led to loss of plastoquinone reductase activity, indicating tight coupling between the proton and electron transfer reactions within NDH. Additionally, loss of the transverse helix of NdhF led to loss of the NDH complex, suggesting that this region of the NdhF subunit is required for complex stability. In agreement with previous studies usingndhknockout mutants, loss of NDH complex activity did not result in measurable changes in rates of steady-state cyclic electron flow. However, all mutants displayed a shift in the sensitivity of pH-dependent feedback regulation of the photosystem II antennae to total protonmotive force (pmf), indicating a defect in either stromal redox state orpmfdistribution into ΔpH and Δψ.
Interrogating the plasma proteome of repetitive head impact exposure and chronic traumatic encephalopathy
Authors: Saloner Rowan , Casaletto Kaitlin B. , Rayaprolu Sruti , Chakrabarty Paramita , Abisambra Jose F. , Spina Salvatore , Grinberg Lea T. , Seeley William W. , Miller Bruce L. , Kramer Joel H. , Rabinovici Gil D. , Asken Breton M. 
Published: October 2024

ABSTRACTBackgroundExposure to repetitive head impacts (RHI) is associated with increased risk for chronic traumatic encephalopathy (CTE), a neurodegenerative tauopathy, and other neuropathological changes. Biological drivers of RHI-related neurodegeneration are not well understood. We interrogated the plasma proteome in aging adults with prior RHI compared to healthy controls (CTL) and individuals with Alzheimer’s disease (AD), including a subset characterized neuropathologically at autopsy.MethodsProximity extension assay (Olink Explore®) quantified 2,779 plasma proteins in 22 RHI patients (all AD-biomarker negative), 39 biomarker-confirmed AD, and 44 CTL. A subset of participants went to autopsy (N=16) allowing for comparisons of the antemortem plasma proteome between autopsy-confirmed CTE+ (N=7) and CTE-(N=9). Differential abundance and co-expression network analyses identified plasma proteomic signatures of RHI, which were functionally annotated using gene ontology and cell type enrichment analysis. Nonparametric correlations examined plasma proteomic associations with orthogonally-measured plasma biomarkers, global cognitive function, and semi-quantitative ratings of neuropathology burden at autopsy.ResultsDifferential abundance analysis revealed 434 increased (vs. 6 decreased) proteins in RHI vs. CTL and 193 increased (vs. 14 decreased) in RHI vs. AD. Network analysis identified 9 protein co-expression modules (M1-M9), of which 7 were elevated in RHI compared to AD or CTL. Modules with increased abundance in RHI were enriched for mitochondrial/metabolic, cell division, and immunovascular (e.g., cell adhesion, TNF-signaling) processes. RHI-related modules exhibited strong and selective correlations with immunoassay-based plasma IL-6 in RHI cases, including the M2 TNF-signaling/cell adhesion module which harbored proteins that strongly tracked with cognitive function. RHI-related plasma protein signatures were similar in the subset of participants with autopsy-confirmed CTE, including immune and metabolic modules that positively correlated with medial temporal lobe tau and TDP-43 burden.ConclusionsMolecular pathways in plasma most consistently implicated in RHI were tied to immune response, mitochondrial function, and cell metabolism. RHI-related proteomic signatures tracked with antemortem cognitive severity and postmortem neuropathological burden, providing converging evidence for their role in disease progression. Differentially abundant proteins and co-expression modules in RHI may inform mechanisms linking RHI to increased dementia risk, thus guiding diagnostic biomarker and therapeutic development for at-risk populations.
Late-life short-term dietary restriction ameliorates intestinal stem cell function and impacts intestinal stem cell DNA methylation
Authors: Kurup Kavitha , Chan Michael , Moore Eric , Ranjo-Bishop Michelle , Pham Kevin , Stanford David R , Freeman Willard M , Unnikrishnan Archana 
Published: October 2024

SummaryAging reduces the function of intestinal stem cells (ISCs) and dietary restriction (DR) has been shown to improve ISC function in young mice. However, there are no studies to-date that has evaluated the effect of short-term DR (stDR) implemented late-in-life on ISC function. Data from our laboratory shows for thefirst timethatstDR can ameliorate the age-related decline in ISC function by in-vitroenteroid forming assay. Transcriptomic analysis of the Lgr5+ISCs identified genes not commonly known for ISC function but showed a robust change with age which were reversed by stDR. Evaluation of the methylation status of selected genes (Slc28a3, Ly9, Cd2, Platr4) showed association between changes in 5mCG levels in the cis-acting regions of the genes and their expression. Our data suggest a potential role for DNA methylation in stDR’s effect on ISC function.
Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing
Authors: Shi Honglue , Al-Sayyad Noor , Wasko Kevin M. , Trinidad Marena I. , Doherty Erin E. , Vohra Kamakshi , Boger Ron S. , Colognori David , Cofsky Joshua C. , Skopintsev Petr , Bryant Zev , Doudna Jennifer A. 
Published: October 2024

SUMMARYRNA-guided CRISPR-Cas enzymes initiate programmable genome editing by recognizing a 20-base-pair DNA sequence adjacent to a short protospacer-adjacent motif (PAM). To uncover the molecular determinants of high-efficiency editing, we conducted biochemical, biophysical and cell-based assays onS. pyogenesCas9 (SpyCas9) variants with wide-ranging genome editing efficiencies that differ in PAM binding specificity. Our results show that reduced PAM specificity causes persistent non-selective DNA binding and recurrent failures to engage the target sequence through stable guide RNA hybridization, leading to reduced genome editing efficiency in cells. These findings reveal a fundamental trade-off between broad PAM recognition and genome editing effectiveness. We propose that high-efficiency RNA-guided genome editing relies on an optimized two-step target capture process, where selective but low-affinity PAM binding precedes rapid DNA unwinding. This model provides a foundation for engineering more effective CRISPR-Cas and related RNA-guided genome editors.
Group B streptococci lyse endothelial cells to infect the brain in a zebrafish meningitis model
Authors: Ravishankar Sumedha , Tuohey Samantha M. , Ramos Nicole O. , Uchiyama Satoshi , Hayes Megan I. , Nizet Victor , Madigan Cressida A. 
Published: October 2024

AbstractTo cause meningitis, bacteria move from the bloodstream to the brain, crossing the endothelial cells of the blood-brain barrier. Most studies on how bacteria cross the blood-brain barrier have been performedin vitrousing cultured endothelial cells, due to a paucity of animal models. Group BStreptococcus(GBS) is the leading cause of bacterial meningitis in neonates and is primarily thought to cross the blood-brain barrier by transcytosis through endothelial cells. To test this hypothesisin vivo, we used optically transparent zebrafish larvae. Timelapse confocal microscopy revealed that GBS forms extracellular microcolonies in brain blood vessels and causes perforation and lysis of blood-brain barrier endothelial cells, which promotes bacterial entry into the brain. Vessels infected with GBS microcolonies were distorted and contained thrombi. Inhibition of clotting worsened brain invasion, suggesting a host-protective role for thrombi. The GBS lysincylE, implicated in brain invasionin vitro,was found dispensablein vivo. Instead, pro-inflammatory mediators associated with endothelial cell damage and blood-brain barrier breakdown were specifically upregulated in the zebrafish head upon GBS entry into the brain. Therefore, GBS crosses the blood-brain barrierin vivonot by transcytosis, but by endothelial cell lysis and death. Given that we observe the same invasion route for a meningitis-associated strain ofStreptococcus pneumoniae,our findings suggest that streptococcal infection of brain blood vessels triggers endothelial cell inflammation and lysis, thereby facilitating brain invasion.