bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of SARS-CoV-2 Antibodies after the Omicron Surge, Kingston, Jamaica, 2022
Authors: Anzinger Joshua J. , Cameron-McDermott Suzette M. , Phillips Yakima Z.R. , Mendoza Leshawn , Anderson Mark , Cloherty Gavin , Strachan-Johnson Susan , Lindo John F. , Figueroa J. Peter 
Published: September 2022

AbstractA cross-sectional SARS-CoV-2 serosurvey was conducted after the Omicron surge in Jamaica using 1,540 samples collected during March – May 2022 from persons attending antenatal, STI and non-communicable diseases clinics in Kingston, Jamaica. SARS-CoV-2 spike receptor binding domain (RBD) and/or nucleocapsid IgG antibodies were detected for 88.4% of the study population, with 77.0% showing evidence of previous SARS-CoV-2 infection. Of persons previously infected with SARS-CoV-2 and/or with COVID-19 vaccination, 9.6% were negative for spike RBD IgG, most of which were unvaccinated previously infected persons. Amongst unvaccinated previously infected people, age was associated with testing spike RBD IgG negative. When considering all samples, median spike RBD IgG levels were 131.6 BAU/mL for unvaccinated persons with serological evidence of past infection, 90.3 BAU/mL for vaccinated persons without serological evidence of past infection, and 896.1 BAU/mL for vaccinated persons with serological evidence of past infection. Our study of the first reported SARS-CoV-2 serosurvey in Jamaica shows extensive SARS-CoV-2 population immunity, identifies a substantial portion of the population lacking spike RBD IgG, and provides additional evidence for increasing COVID-19 vaccine coverage in Jamaica.
From toxic waste to beneficial nutrient: acetate boostsE. coligrowth at low glycolytic flux
Authors: Millard Pierre , Gosselin-Monplaisir Thomas , Uttenweiler-Joseph Sandrine , Enjalbert Brice 
Published: September 2022

AbstractAcetate, a major by-product of glycolytic metabolism inEscherichia coliand many other microorganisms, has long been considered a toxic waste compound that inhibits microbial growth. This counterproductive auto-inhibition represents a major problem in biotechnology and has puzzled the scientific community for decades. Recent studies have revealed that acetate is also a co-substrate of glycolytic nutrients and a global regulator ofE. colimetabolism and physiology. Here, we used a systems biology strategy to investigate the mutual regulation of glycolytic and acetate metabolism. Computational and experimental results demonstrate that reducing the glycolytic flux enhances co-utilization of acetate with glucose. Acetate metabolism thus compensates for the reduction in glycolytic flux and eventually buffers carbon uptake so that acetate, far from being toxic, actually enhancesE. coligrowth under these conditions. We validated this mechanism using three orthogonal strategies: chemical inhibition of glucose uptake, glycolytic mutant strains, and alternative substrates with a natively low glycolytic flux. Acetate makesE. colimore robust to glycolytic perturbations and is a valuable nutrient, with a beneficial effect on microbial growth.
Regulation of cellular LDL uptake by PROX1 and CHD7
Authors: Serrano-Zayas Candilianne , Holding Matthew L. , Khan Taslima G. , Tang Vi T. , Skidmore Jennifer M , Martin Donna M , Ginsburg David , Emmer Brian T. 
Published: September 2022

AbstractAn elevated level of low-density lipoprotein (LDL) in the bloodstream is a causal risk factor for atherosclerotic cardiovascular disease (ASCVD). The low-density lipoprotein receptor (LDLR) is a critical regulator of circulating LDL, and increasing LDLR activity is an effective therapeutic approach to reduce circulating LDL cholesterol levels. In this study, we characterize PROX1 and CHD7, two genes we previously identified in a genome-scale CRISPR screen as positive regulators of LDL uptake in HuH7 cells. We found that although disruption of either PROX1 or CHD7 significantly reduced LDL uptake, only PROX1 disruption significantly reduced the cellular levels of LDLR mRNA and surface-displayed LDLR protein. Consistent with a direct role for PROX1 in LDLR gene regulation, we also observed in publicly available data sets the presence of two liver-specific PROX1 binding sites near the LDLR locus, one of which colocalized with biochemical hallmarks of enhancer activity in hepatic tissue. Both PROX1 LDLR binding sites contained predicted PROX1 transcription factor binding motifs and colocalized with binding sites for HNF4α, a known interactor for PROX1 and regulator of hepatic lipid metabolism and LDL uptake. In contrast to PROX1, no CHD7 binding sites were detected near the LDLR locus. Together, our results support a model in which both PROX1 and CHD7 promote cellular LDL uptake through distinct mechanisms, with PROX1 directly promoting LDLR gene expression and CHD7 functioning through an LDLR-independent pathway.
The effect of metal remediation on the virulence and antimicrobial resistance of the opportunistic pathogenPseudomonas aeruginosa
Authors: Lear Luke , Hesse Elze , Newsome Laura , Gaze William , Buckling Angus , Vos Michiel 
Published: September 2022

AbstractMetal contamination poses both a direct threat to human health as well as an indirect threat through its potential to affect bacterial pathogens. Metals can not only co-select for antibiotic resistance, but also might affect pathogen virulence via increased siderophore production. Siderophores are extracellular compounds released to increase ferric iron uptake — a common limiting factor for pathogen growth within hosts – making them an important virulence factor. However, siderophores can also be positively selected for to detoxify non-ferrous metals, and consequently metal stress can potentially increase bacterial virulence. Anthropogenic methods to remediate environmental metal contamination commonly involve amendment with lime-containing materials, but whether this reducesin situco-selection for antibiotic resistance and virulence remains unknown. Here, using microcosms containing metal-contaminated river water and sediment, we experimentally test whether metal remediation by liming reduces co-selection for these traits in the opportunistic pathogenPseudomonas aeruginosaembedded within a natural microbial community. To test for the effects of environmental structure, which can impact siderophore production, microcosms were incubated under either static or shaking conditions. EvolvedP. aeruginosapopulations had greater fitness in the presence of toxic concentrations of copper than the ancestral strain, but this effect was reduced in the limed treatments. EvolvedP. aeruginosapopulations showed increased resistance to the clinically-relevant antibiotics apramycin, cefotaxime, and trimethoprim, regardless of lime addition or environmental structure. Although we found virulence to be significantly associated with siderophore production, neither virulence nor siderophore production significantly differed between the four treatments. We therefore demonstrate that although remediation via liming reduced the strength of selection for metal resistance mechanisms, it did not mitigate metal-imposed selection for antibiotic resistance or virulence inP. aeruginosa. Consequently, metal-contaminated environments may select for antibiotic resistance and virulence traits even when treated with lime.Graphical abstract
Zika virus spreads through infection of lymph node-resident macrophages
Authors: Reynoso Glennys V. , Gordon David N. , Kalia Anurag , Aguilar Cynthia C. , Malo Courtney S. , Aleshnick Maya , Dowd Kimberly A. , Cherry Christian R. , Shannon John P. , Vrba Sophia M. , Maciejewski Sonia , Asano Kenichi , Pierson Theodore C. , Hickman Heather D. 
Published: September 2022

SummaryZika virus (ZIKV) is an arthopod-vectored flavivirus that disseminates from the infection site into peripheral tissues, where it can elicit virus-induced pathology. To move through the body, ZIKV is thought to exploit the mobility of myeloid cells, in particular monocytes and dendritic cells. However, multiple distinct steps during viral spread culminate in peripheral tissue infection, and the timing and mechanisms underlying mobile immune cell shuttling of virus remain unclear. To understand the very early steps in ZIKV dissemination from the skin, we kinetically and spatially mapped ZIKV-infected lymph nodes (LNs), an intermediary stop en route to the blood. Contrary to dogma, migratory immune cells were not required for large quantities of virus to reach the LN or blood. Instead, ZIKV rapidly infected a subset of immobile macrophages in the LN, which shed virus through the lymphatic pathway into the blood. Importantly, infection of LN macrophages alone was sufficient to initiate viremia. Together, our studies indicate that sessile macrophages that live and die in the LN contribute to initial ZIKV spread to the blood. These data build a more complete picture of ZIKV movement through the body and identify an alternate anatomical site for potential antiviral intervention.HighlightsZIKV infects and replicates in distinct LN macrophage populationsLN macrophage infection results in infectious virus in the bloodVirus reaches the blood in the absence of DC migration or monocyte infectionNodal macrophage infection does not sustain viremia or induce morbidityGraphical abstractCaption:ZIKV infects lymph node macrophages, which shed infectious virus into the lymph and then blood.
DNA-encoded immunoassay in picoliter drops: a minimal cell-free approach
Authors: Jacková Barbara , Mottet Guillaume , Rudiuk Sergii , Morel Mathieu , Baigl Damien 
Published: September 2022

AbstractBased on the remarkably specific antibody-antigen interaction, immunoassays have emerged as indispensable bioanalytical tools for both fundamental research and biomedical applications but necessitate long preliminary steps for the selection, production and purification of the antibody(ies) to be used. Here, we adopt a paradigm shift exploring the concept of creating a rapid and purification-free assay where the antibody is replaced by its coding DNA as a starting material, while exploiting a drop microfluidic format to dramatically decrease sample volume and accelerate throughput and sorting capability. The methodology consists in the co-encapsulation of a DNA coding for the variable domain of the heavy chain of heavy-chain only antibodies (VHH), a reconstituted cell-free expression medium, the target antigen and a capture scaffold where VHH:antigen accumulate to create a detectable signal, inside picoliter drop compartments. We first demonstrate successful synthesis of a functional hemagglutinin (HA)-tagged anti-GFP VHH, referred to as NanoGFP, at a high yield (15.3 ± 2.0 µg·mL-1) in bulk and in less than 3 h using PURExpress cell-free expression medium. We then use a microfluidic device to generate stable water-in-oil drops (30 pL) encapsulating NanoGFP-coding DNA, PURExpress medium, EGFP antigen and HA tag-specific magnetic nanoparticles prior to incubating at 37 °C the resulting emulsion under a magnetic field, inducing bothin situsynthesis of NanoGFP and accumulation of NanoGFP:EGFP complexes on magnetically assembled particles. This allows us to assess, for the first time and in less than 3 hours, the binding of an antigen to a cell-free synthesized antibody, in a large number of picoliter drops down to a DNA concentration as low as 12 plasmids per drop. We also show that the drops of this immunoassay can be further sequentially analyzed at high throughput (500 Hz), thus offering capability for library screening, sorting and/or rare event detection. We finally demonstrate the versatility of this method by using DNA coding for different VHH (e.g., anti-mCherry protein), by characterizing VHH specificity in the presence of antigen mixtures, and by showing that antigens can be either inherently fluorescent or not. We thus anticipate that the ultraminiaturized format (pL), rapidity (3 h), programmability (DNA-encoded approach) and versatility of this novel immunoassay concept will constitute valuable assets for faster discovery, better understanding and/or expanded applications of antibodies.
Femora from an exceptionally large population of coeval ornithomimosaurs yield evidence of sexual dimorphism in extinct theropod dinosaurs
Authors: Pintore R. , Cornette R. , Houssaye A. , Allain R. 
Published: September 2022

AbstractSexual dimorphism is challenging to detect among fossils, due to a lack of statistical representativeness. The Angeac-CharenteLagerstätte(France) represents a remarkable “snapshot” from a Berriasian (Early Cretaceous) ecosystem and offers a unique opportunity to study intraspecific variation among a herd of at least 61 coeval ornithomimosaurs. Herein, we investigated the hindlimb variation across the best-preserved specimens from the herd through 3D Geometric Morphometrics and Gaussian Mixture Modelling. Our results based on complete and fragmented femora evidenced a dimorphism characterized by variations in the shaft curvature and the distal epiphysis width. Since the same features vary between sexes among modern avian dinosaurs, crocodilians, and more distant amniotes, we attributed this bimodal variation to sexual dimorphism based on the extant phylogenetic bracketing approach. Documenting sexual dimorphism in fossil dinosaurs allows a better characterization and accounting of intraspecific variations, which is particularly relevant to address ongoing taxonomical and ecological questions relative to dinosaur evolution.
Bacteria evolve macroscopic multicellularity via the canalization of phenotypically plastic cell clustering
Authors: Chavhan Yashraj , Dey Sutirth , Lind Peter A. 
Published: September 2022

AbstractThe evolutionary transition from unicellular to multicellular life was a key innovation in the history of life. Given scarce fossil evidence, experimental evolution has been an important tool to study the likely first step of this transition, namely the formation of undifferentiated cellular clusters. Although multicellularity first evolved in bacteria, the extant experimental evolution literature on this subject has primarily used eukaryotes. Moreover, it focuses on mutationally driven (and not environmentally induced) phenotypes. Here we show that both Gram-negative and Gram-positive bacteria exhibit phenotypically plastic (i.e., environmentally induced) cell clustering. Under high salinity, they grow as elongated ~ 2 cm long clusters (not as individual planktonic cells). However, under habitual salinity, the clusters disintegrate and grow planktonically. We used experimental evolution withEscherichia colito show that such clustering can be canalized successfully: the evolved bacteria inherently grow as macroscopic multicellular clusters, even without environmental induction. Highly parallel mutations in genes linked to cell wall assembly formed the genomic basis of canalized multicellularity. While the wildtype also showed cell shape plasticity across high versus low salinity, it was either canalized or reversed after evolution. Interestingly, a single mutation could canalize multicellularity by modulating plasticity at multiple levels of organization. Taken together, we show that phenotypic plasticity can prime bacteria for evolving undifferentiated macroscopic multicellularity.
The DNA-relaxation-dependent Off-to-On biasing of the type 1 fimbrial genetic switch requires the Fis nucleoid-associated protein
Authors: Conway Colin , Beckett Michael C , Dorman Charles J 
Published: September 2022

AbstractThe structural genes expressing type 1 fimbriae in Escherichia coli alternate between expressed (phase ON) and non-expressed (phase OFF) states due to inversion of the 314-bp fimS genetic switch. The FimB tyrosine integrase inverts fimS by site-specific recombination, alternately connecting and disconnecting the fim operon, encoding the fimbrial subunit protein and its associated secretion and adhesin factors, to and from its transcriptional promoter within fimS. Site-specific recombination by the FimB recombinase becomes biased towards phase ON as DNA supercoiling is relaxed, a condition that occurs when bacteria approach the stationary phase of the growth cycle. This effect can be mimicked in exponential phase cultures by inhibiting the negative DNA supercoiling activity of DNA gyrase. We report that this bias towards phase ON depends on the presence of the Fis nucleoid-associated protein. We mapped the Fis binding to a site within the invertible fimS switch by DNase I footprinting. Disruption of this binding site by base substitution mutagenesis abolishes both Fis binding and the ability of the mutated switch to sustain its phase ON bias when DNA is relaxed, even in bacteria that produce the Fis protein. In addition, the Fis binding site overlaps one of the sites used by the Lrp protein, a known directionality determinant of fimS inversion that also contributes to phase ON bias. The Fis-Lrp relationship at fimS is reminiscent of that between Fis and Xis when promoting DNA-relaxation-dependent excision of bacteriophage λ from the E. coli chromosome. However, unlike the co-binding mechanism used by Fis and Xis at λ attR, the Fis-Lrp relationship at fimS involves competitive binding. We discuss these findings in the context of the link between fimS inversion biasing and the physiological state of the bacterium.
N6-Adenosine methylation regulates the translation of insulin mRNA
Authors: Wilinski Daniel , Dus Monica 
Published: September 2022

AbstractRelatively little is known about the first step of insulin synthesis: the translation of the mRNA. Here we show that the translation of D. melanogaster insulin 2 mRNA (dilp2) is controlled by methylation of N6-adenosine (m6A) in the 3’ UTR. Mutations in the m6A writer Mettl3 and methylated-residues in the dilp2 3’UTR decreased the levels of dilp2 mRNA associated with the polysomes, and the total amount of dilp2 protein produced. This resulted in aberrant energy homeostasis and diabetic-like phenotypes, consistent with the specific function of dilp2 in adult metabolism. Conserved m6A signatures were also identified in the 3’ UTRs of vertebrate insulin mRNAs. These data identify m6A as a key regulator of insulin protein synthesis and energy homeostasis in metazoans and demonstrate an essential role for m6A in translation, with important implications for diabetes and metabolic disease.One-Sentence SummaryThe most abundant modification in eukaryotic mRNAs controls the synthesis of insulin protein in D. melanogaster.
Peroxisome biogenesis initiated by protein phase separation
Authors: Ravindran Rini , Bacellar Isabel O. L. , Castellanos-Girouard Xavier , Zhang Zhenghao , Kisley Lydia , Michnick Stephen W. 
Published: September 2022

SummaryPeroxisomes are organelles that perform beta-oxidation of fatty acids and amino acids. Both rare and prevalent diseases are caused by their disfunction1. Among disease-causing mutant genes are those required for protein transport into the peroxisome. The peroxisomal protein import machinery, also shared with chloroplasts, is unique in transporting folded and large, up to 10 nm in diameter, protein complexes into peroxisomes2 and current models postulate a large pore formed by transmembrane proteins3. To date, however, no pore structure has been observed. In the budding yeast Saccharomyces cerevisiae, the minimum transport machinery includes membrane proteins Pex13 and Pex14 and cargo protein-binding transport receptor, Pex5. Here we show that Pex13 undergoes liquid-liquid phase separation (LLPS) with Pex5-cargo. Intrinsically disordered regions (IDR) in Pex13 and Pex5 resemble those found in nuclear pore complex (NPC) proteins. Cargo transport into peroxisomes depends on the number but not patterns of aromatic residues in these IDRs, consistent with their roles as ‘stickers’ in associative polymer models of LLPS4,5. Finally, imaging Fluorescence Cross-Correlation Spectroscopy (iFCCS) shows that the transport of cargo correlates with transient focusing of GFP-Pex13/14 on the peroxisome membrane. Pex13 and Pex14 form foci in distinct time-frames, suggesting that they may form channels at different saturating concentrations of Pex5-cargo. Our results suggest a model in which LLPS of Pex5-cargo with Pex13/14 results in transient protein transport channels.
Pseudomonas aeruginosa FpvB is a high-affinity transporter for xenosiderophores ferrichrome and ferrioxamine B
Authors: Chan Derek C. K. , Burrows Lori L. 
Published: September 2022

ABSTRACTIron is essential for many biological functions in bacteria but its poor solubility is a limiting factor for growth. Bacteria produce siderophores, soluble natural products that bind iron with high affinity, to overcome this challenge. Siderophore-iron complexes return to the cell through specific outer-membrane transporters. The opportunistic pathogen Pseudomonas aeruginosa makes multiple transporters that recognize its own siderophores, pyoverdine and pyochelin, and xenosiderophores produced by other bacteria, which gives it a competitive advantage. Some antibiotics exploit these transporters to bypass the membrane to reach their intercellular targets – including the thiopeptide antibiotic, thiostrepton (TS), which uses the pyoverdine transporters FpvA and FpvB to cross the outer membrane. Here, we assessed TS susceptibility in the presence of various siderophores and discovered that ferrichrome and ferrioxamine B antagonized TS uptake via FpvB. Unexpectedly, we found that FpvB transports ferrichrome and ferrioxamine B with higher affinity than pyoverdine. Site-directed mutagenesis of FpvB coupled with competitive growth inhibition and affinity label quenching studies suggested that the siderophores and antibiotic share a common binding site in an aromatic pocket formed by the plug and barrel domains, but have differences in their binding mechanism and molecular determinants for uptake. This work describes an alternative uptake pathway for ferrichrome and ferrioxamine B in P. aeruginosa and emphasizes the promiscuity of siderophore transporters, with implications for Gram-negative antibiotic development via the Trojan horse approach.
Loss of the first β-strand of human prion protein generates an aggregation-competent partially “open” form
Authors: Hosszu Laszlo L. P. , Sangar Daljit , Batchelor Mark , Risse Emmanuel , Hounslow Andrea M. , Waltho Jonathan P. , Collinge John , Bieschke Jan 
Published: September 2022

AbstractPrion diseases, a group of incurable, lethal neurodegenerative disorders of mammals including humans, are caused by prions, assemblies of misfolded host prion protein (PrP). The pathway of PrP misfolding is still unclear, though previous data indicate the presence of a structural core in cellular PrP (PrPC), whose cooperative unfolding presents a substantial energy barrier on the path to prion formation. PrP is a GPI-anchored membrane protein, and a number of studies suggest that membrane interactions play an important role in the conversion of PrPC to its disease-associated form, including a transmembrane form of PrP in which a highly conserved region (residues 110 - 136) spans the ER membrane. Insertion of this region results in the detachment of the PrPC first β-strand from the structural core. The effect of this removal on the structure, stability and self-association of the folded domain of PrPC is determined here through a biophysical characterisation of a truncated form of PrPC lacking this region. Whilst markedly destabilised, NMR chemical shifts show that the truncated protein exhibits tertiary structure characteristic of a fully folded protein and retains its native secondary structure elements, including the second strand of the PrP β-sheet, but with altered conformational flexibility in the β2-α2 loop and first α-helix. The latter is destabilised relative to the other helical regions of the protein, with markedly increased solvent exposure. This truncated form of PrP fibrilises more readily than the native form of the protein. These data suggest a stepwise mechanism, in which a destabilised “open” form of PrPC may be a key intermediate in the refolding to the fibrillar, pathogenic form of the protein.