bluuebunny/crossref_metadata_2025_split huggingface dataset:
PANDAA-monium: Intentional violations of conventional qPCR design enables rapid, HIV-1 subtype-independent drug resistance SNP detection
Authors: MacLeod Iain J. , Rowley Christopher F. , Essex M. 
Published: October 2019

ABSTRACTGlobal efforts to ensure that 90% of all HIV-infected people receiving antiretroviral therapy (ART) will be virally suppressed by 2020 could be crippled by increases in acquired and transmitted HIV drug resistance (HIVDR), which challenge ART efficacy. The long-term sustainability of ART treatment programs is contingent on effective HIVDR monitoring yet current Sanger sequencing genotypic resistance tests are inadequate for large-scale implementation in low- and middle-income countries (LMICs). A simple, rapid, affordable HIVDR diagnostic would radically improve the treatment paradigm in LMICs by facilitating informed clinical decision-making upon ART failure. Although point mutation assays can be broadly deployed in this context, the primary challenge arises from extensive sequence variation surrounding targeted drug resistance mutations (DRMs). Here, we systematically and intentionally violate the canonical principles of qPCR design to develop a novel assay, Pan-Degenerate Amplification and Adaptation (PANDAA), that mitigates the impact of DRM-proximal secondary polymorphisms on probe-based qPCR performance to enable subtype-independent, focused resistance genotyping. Using extremely degenerate primers with 3’ termini overlapping the probe-binding site, the HIV-1 genome is adapted through site-directed mutagenesis to replace secondary polymorphisms flanking the target DRM during the initial qPCR cycles. We show that PANDAA can quantify key HIV DRMs present at ≥5% and has diagnostic sensitivity and specificity of 96.9% and 97.5%, respectively, to detect DRMs associated with ART failure. PANDAA is an innovative solution for HIVDR genotyping and is an advancement in qPCR technology that could be applicable to any scenario where target-proximal genetic variability has been a roadblock in diagnostic development.
Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes
Authors: Ogrodzinski Martin P. , Lunt Sophia Y. 
Published: October 2019

AbstractBreast cancer is a heterogeneous disease with several subtypes that currently do not have targeted therapy options. Metabolomics has the potential to uncover novel targeted treatment strategies by identifying metabolic pathways required for cancer cells to survive and proliferate. Here, we used tumor-derived cell lines derived from the MMTV-Myc mouse model to investigate metabolic pathways that are differentially utilized between two subtypes of breast cancer. Using mass spectrometry-based metabolomics techniques, we identified differences in glycolysis, the tricarboxylic acid cycle, glutathione metabolism, and nucleotide metabolism between subtypes. We further show the feasibility of targeting these pathways in a subtype-specific manner using metabolism-targeting compounds.
Chromatin accessibility and histone acetylation in the regulation of competence in early development
Authors: Esmaeili Melody , Blythe Shelby A. , Tobias John W. , Zhang Kai , Yang Jing , Klein Peter S. 
Published: October 2019

AbstractAs development proceeds, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner. While key inductive signaling pathways within competent cells are well-described at a molecular level, the mechanisms by which tissues lose responsiveness to inductive signals are not well understood. Localized activation of Wnt signaling before zygotic gene activation inXenopus laevisleads to dorsal development, but competence to induce dorsal genes in response to Wnts is lost by the late blastula stage. We hypothesize that loss of competence is mediated by changes in histone modifications leading to a loss of chromatin accessibility at the promoters of Wnt target genes. We use ATAC-seq to evaluate genome-wide changes in chromatin accessibility across several developmental stages. Based on overlap with p300 binding, we identify thousands of putative cis-regulatory elements at the gastrula stage, including sites that lose accessibility by the end of gastrulation and are enriched for pluripotency factor binding motifs. Dorsal Wnt target gene promoters are not accessible after the loss of competence in the early gastrula while genes involved in mesoderm and neural crest development maintain accessibility at their promoters. Inhibition of histone deacetylases increases acetylation at the promoters of dorsal Wnt target genes and extends competence for dorsal gene induction by Wnt signaling. Histone deacetylase inhibition, however, is not sufficient to extend competence for mesoderm or neural crest induction. These data suggest that chromatin state regulates the loss of competence to inductive signals in a context-dependent manner.
Comparative genomics identifies putative signatures of sociality in spiders
Authors: Tong Chao , Najm Gabriella M. , Pinter-Wollman Noa , Pruitt Jonathan N. , Linksvayer Timothy A. 
Published: October 2019

AbstractComparative genomics has begun to elucidate the genomic basis of social life in insects but insight into the genomic basis of spider sociality has lagged behind. To begin to characterize genomic signatures associated with the evolution of social life in spiders, we performed one of the first spider comparative genomics studies including five solitary species and two social species, representing two independent origins of sociality in the genus Stegodyphus. We found that the two social spider species had a large expansion of gene families associated with transport and metabolic processes and an elevated genome-wide rate of molecular evolution compared with the five solitary spider species. Genes that were rapidly evolving in the two social species relative to the five solitary species were enriched for transport, behavior, and immune functions, while genes that were rapidly evolving in the solitary species were enriched for energy metabolism processes. Most rapidly evolving genes in the social species S. dumicola were broadly expressed across four tissues and enriched for transport functions, but 12 rapidly evolving genes showed brain-specific expression and were enriched for social behavioral processes. Altogether, our study identifies putative genomic signatures and potential candidate genes associated with spider sociality. These results indicate that future spider comparative genomic studies, including broader sampling and additional independent origins of sociality, can further clarify the genomic causes and consequences of social life.
A space-saving visual screening method, Glycine max FAST, for generating transgenic soybean
Authors: Iwabuchi Kosei , Shimada Takashi L. , Yamada Tetsuya , Hara-Nishimura Ikuko 
Published: October 2019

AbstractSoybean is an important crop plant for food and biofuel production, and there have been considerable efforts to develop transgenic soybean lines with higher seed oil contents and/or seed yields. However, the process of screening transgenic lines is laborious and requires a large amount of space. Here, we describe a powerful screening method, Glycine max Fluorescence-Accumulating Seed Technology (GmFAST), which is based on a seed-specific fluorescent marker. The marker is composed of a soybean seed-specific promoter coupled to the OLE1-GFP gene, which encodes GFP fused to the oil-body membrane protein OLEOSIN1 of Arabidopsis thaliana. We introduced the marker gene into cotyledonary nodes of G. max Kariyutaka via Agrobacterium-mediated transformation and regenerated heterozygous transgenic plants. OLE1-GFP-expressing soybean seeds can be selected nondestructively using a fluorescence stereomicroscope. Among T2 seeds, the most strongly fluorescent seeds were homozygous. GmFAST uses one-tenth of the growing space required for the conventional method. This space-saving method will contribute to facilitating transformation of soybean. OLE1-GFP was localized specifically to oil bodies in the cotyledon cells of seeds, but it did not affect oil content per seed, the size and density of the oil bodies, or oil composition. One of the homozygous lines (line #8) showed a 44% increase in the seed pod number, which resulted in 41% and 30% increases in seed yield and total oil production, respectively, compared with the wild type. In line #8, OLE1-GFP was inserted into the intron of Glyma13g30950, causing its overexpression. An increase in seed pod number was confirmed in Arabidopsis thaliana plants that overexpressed the Arabidopsis ortholog of Glyma13g30950, E6L1. These results suggest that line #8 is a valuable resource for agricultural and industrial applications. Taken together, GmFAST provides a space-saving visual and non-destructive screening method for soybean transformation, thereby increasing the chance of developing useful soybean lines.
Detection of antibodies against a conserved capsid epitope as the basis of a novel universal serological test for foot-and-mouth disease
Authors: Asfor A , Howe N , Grazioli S , Berryman S , Parekh K , Wilsden G , Ludi A , King DP , Parida S , Brocchi E , Tuthill TJ 
Published: October 2019

AbstractDiagnostic tests for foot-and-mouth disease (FMD) include the detection of antibodies against either the viral non-structural proteins or the capsid. The detection of antibodies against the structural proteins (SP) of the capsid can be used to monitor seroconversion in both infected and vaccinated animals. However, SP tests need to be tailored to the individual FMD virus serotype and their sensitivity performances may be affected by antigenic variability within each serotype and mismatching between tests reagents. As a consequence, FMD Reference Laboratories need to maintain contingency to employ multiple type-specific assays for large-scale serological surveillance and post-vaccination monitoring in the event of FMD outbreaks. In this study, a highly conserved region in the N terminus of FMDV capsid protein VP2 (VP2N) was characterised using a panel of intertypic-reactive monoclonal antibodies. This revealed a universal epitope in VP2N which could be used as a peptide antigen to detect FMDV-specific antibodies against all types of the virus. A VP2-peptide ELISA (VP2-ELISA) was optimised using experimental and reference antisera from immunized, convalescent and negative animals (n=172). The VP2-ELISA is universal, simple and provided sensitive (98.6 %) and specific (93%) detection of antibodies to all FMDV strains used in this study. We anticipate that this SP test could have utility for sero-surveillance during virus incursions in FMD-free countries and as an additional screening tool to assess FMD virus circulation in endemic countries.
Light-mediated decreases in cyclic di-GMP levels are potentiated by pyocyanin and inhibit structure formation inPseudomonas aeruginosabiofilms
Authors: Kahl Lisa Juliane , Price-Whelan Alexa , Dietrich Lars E. P. 
Published: October 2019

AbstractLight is known to trigger regulatory responses in diverse organisms including slime molds, animals, plants, and phototrophic bacteria. However, light-dependent processes in non-phototrophic bacteria, and those of pathogens in particular, have received comparatively little research attention. In this study, we examined the impact of light on multicellular development inPseudomonas aeruginosa, a leading cause of biofilm-based bacterial infections, using a colony morphology assay. In this assay,P. aeruginosastrain PA14 grown in the dark forms vertical structures (i.e., “wrinkles”) on the third day of incubation. We found that growth in blue light inhibited wrinkle formation until the fifth day and that this required the phenazine pyocyanin, a redox-active metabolite produced by PA14. Light-dependent inhibition of wrinkling was also correlated with low levels of cyclic di-GMP (c-di-GMP), consistent with the role of this signal in stimulating biofilm matrix production. Though phenazine-null biofilms also showed lower levels of c-di-GMP and subtle effects on wrinkling when grown in the light, their overall levels of c-di-GMP were higher than those of the wild type. This indicates that phenazines and light simultaneously promote c-di-GMP degradation such that c-di-GMP is pushed to a minimum level, yielding a pronounced macroscopic phenotype. A screen of enzymes with the potential to catalyze c-di-GMP synthesis or degradation identified four proteins that contribute to light-dependent inhibition of biofilm wrinkling. Together, these results provide a foundation for understanding the significance of light-dependent regulation inP. aeruginosa.ImportanceThe response to light in non-phototrophic bacteria (i.e., chemotrophs) is relatively understudied in comparison to light-mediated behavior in eukaryotes and phototrophic bacteria. Though they do not depend on light for growth, chemotrophic bacteria could benefit from sensing this cue when it correlates with other parameters that are important for metabolism. In this paper, we describe light-dependent effects on a cellular signal that controls the development of multicellular assemblages, called biofilms, inPseudomonas aeruginosa. We found that light at intensities that are not harmful to human cells inhibited biofilm maturation.P. aeruginosais a leading cause of chronic lung infections in people with cystic fibrosis and of hospital-acquired infections. AsP. aeruginosa’s recalcitrance to treatment is attributed in part to its facile formation of biofilms, this study provides insight into a mechanism that could be inhibited via new therapeutic tools, such as photodynamic therapy.
Sugars dominate the seagrass rhizosphere
Authors: Maggie Sogin E. , Michellod Dolma , Gruber-Vodicka Harald , Bourceau Patric , Geier Benedikt , Meier Dimitri V. , Seidel Michael , Ahmerkamp Soeren , Schorn Sina , D’Angelo Grace , Procaccini Gabriele , Dubilier Nicole , Liebeke Manuel 
Published: October 2019

SummarySeagrasses are one of the most efficient sinks of carbon dioxide on Earth1: They bury carbon 35 times faster than tropical rainforests on a per unit area basis2. While we know that carbon sequestration in terrestrial plants is intimately linked to the microorganisms living in their soils3–6, the interactions of seagrasses with their rhizospheres are poorly understood. We show that three seagrass species from two oceans excrete simple sugars, mainly sucrose, into their rhizosphere that accumulate to over 200 µM. Such high concentrations are at least 80 times higher than previously observed in the ocean, and surprising, as sugars are quickly consumed by microorganisms. In situ analyses and incubation experiments indicated that phenolic compounds from the seagrass inhibited microbial consumption of sucrose. Metagenomic and metatranscriptomic analyses of the microbial communities in the seagrass rhizosphere revealed that many members had the genes for degrading sucrose, but these were only expressed by a few specialists that also expressed genes for degrading phenolics. Our results explain why sucrose accumulates under seagrass meadows, where it comprises as much as 40% of the dissolved organic carbon. Destruction of extant seagrass canopies would allow sediment microorganisms to consume the tremendous deposits of sucrose buried underneath their meadows, thereby releasing large amounts of CO2 into the oceans and atmosphere.
Potent and lasting seizure suppression by systemic delivery of antagomirs targeting miR-134 timed with blood-brain barrier disruption
Authors: Reschke C. R. , Silva L. F. A. , Vangoor V. R. , Rosso M. , David B. , Cavanagh B. L. , Connolly N. M. C. , Brennan G. P. , Sanz-Rodriguez A. , Mooney C. , Batool A. , Greene C. , Brennan M. , Conroy R. M. , Rüber T. , Prehn J. H. M. , Campbell M. , Pasterkamp R. J. , Henshall D. C. 
Published: October 2019

AbstractRNA therapies such as oligonucleotides (OGNs) offer precision treatments for a variety of neurological diseases, including epilepsy but their deployment is hampered by the blood brain barrier (BBB). Here we used brain imaging and assays of serum proteins and tracer extravasation, to determine that BBB disruption occurring after status epilepticus in mice was sufficient to permit passage of systemically-injected antisense OGNs targeting microRNA-134 (Ant-134) into the brain parenchyma. A single intraperitoneal injection of Ant-134 two hours after status epilepticus in mice resulted in potent suppression of spontaneous recurrent seizures, reaching a 99.5% reduction during recordings at three months. The duration of spontaneous seizures, when they occurred, was also reduced in Ant-134-treated mice. These studies indicate that systemic delivery of Ant-134 reaches the brain and produces disease-modifying effects after systemic injection in mice when timed with BBB disruption and may be a clinically-viable approach for this and other disease-modifying microRNA therapies.
Coordination during group departures and group progressions in the tolerant multilevel society of wild Guinea baboons (Papio papio)
Authors: Montanari Davide , Hambuckers Julien , Fischer Julia , Zinner Dietmar 
Published: October 2019

AbstractObjectivesMost primate species live in groups, and temporal and spatial coordination of activities of individuals is essential for maintaining group cohesion, and there is still considerable debate to which degree social organization, the extent of despotism, and resource distribution shape group coordination processes. As different baboon species exhibit considerable variation in all of these factors, they constitute an excellent test case to resolve this debate.Materials and MethodsWe analyzed group departures and progressions of Guinea baboons,Papio papio, in the Niokolo Koba National Park in Senegal. Guinea baboons live in a multi-level society with strong male bonds and a lack of a clear dominance hierarchy between males.ResultsTwo-thirds of departures were initiated by adult males, and one third by adult females. Although initiators were more likely to signal than followers, signaling did not affect the initiation success. During group progression, males that were not affiliated with females were predominantly found in the front, while affiliated males, females and young were observed more frequently closer to the center of the group, and no preferences for rear positions. Overall, affiliated subjects were more likely to depart and travel together.DiscussionThe group departures in Guinea baboons differed strikingly from the elaborate ‘negotiation’ behaviors among male hamadryas baboons,Papio hamadryas. We did not observe that specific individuals dominated the group coordination. Neither social organization, variation in despotism, nor resource distribution alone explain variation between species. Future studies should test whether specific combinations of factors promote the occurrence of negotiation processes.Research HighlightsIn wild Guinea baboons, both adult males and females initiated group departuresInitiators signaled during departures, but this did not affect initiation successSolitary males were predominantly found at the front during group progression
Acute and repeated intranasal oxytocin differentially modulate brain-wide functional connectivity
Authors: Pagani Marco , De Felice Alessia , Montani Caterina , Galbusera Alberto , Papaleo Francesco , Gozzi Alessandro 
Published: October 2019

AbstractCentral release of the neuropeptide oxytocin (OXT) modulates neural substrates involved in socio-affective behavior. This property has prompted research into the use of intranasal OXT administration as an adjunctive therapy for brain conditions characterized by social impairment, such as autism spectrum disorders (ASD). However, the neural circuitry and brain-wide functional networks recruited by intranasal OXT administration remain elusive. Moreover, little is known of the neuroadaptive cascade triggered by long-term administration of this peptide at the network level. To address these questions, we applied fMRI-based circuit mapping in adult mice upon acute and repeated (seven-day) intranasal dosing of OXT. We report that acute and chronic OXT administration elicit comparable fMRI activity as assessed with cerebral blood volume mapping, but entail largely different patterns of brain-wide functional connectivity. Specifically, acute OXT administration focally boosted connectivity within key limbic components of the rodent social brain, whereas repeated dosing led to a prominent and widespread increase in functional connectivity, involving a strong coupling between the amygdala and extended cortical territories. Importantly, this connectional reconfiguration was accompanied by a paradoxical reduction in social interaction and communication in wild-type mice. Our results identify the network substrates engaged by exogenous OXT administration, and show that repeated OXT dosing leads to a substantial reconfiguration of brain-wide connectivity, entailing an aberrant functional coupling between cortico-limbic structures involved in socio-communicative and affective functions. Such divergent patterns of network connectivity might contribute to discrepant clinical findings involving acute or long-term OXT dosing in clinical populations.
Mammary epithelial cells have lineage-restricted metabolic identities
Authors: Mahendralingam Mathepan , Aliar Kazeera , Elisabeth Casey Alison , Pellacani Davide , Kim Hyeyeon , Ignatchenko Vladimir , Valero Mar Garcia , Palomero Luis , Sinha Ankit , Stambolic Vid , Alam Mina , Schimmer Aaron , Berman Hal , Angel Pujana Miquel , Eaves Connie , Kislinger Thomas , Khokha Rama 
Published: October 2019

ABSTRACTCancer metabolism adapts the metabolic network of its tissue-of-origin. However, breast cancer is not a disease of a singular origin. Multiple epithelial populations serve as the culprit cell-of-origin for specific breast cancer subtypes, yet knowledge surrounding the metabolic network of normal mammary epithelial cells is limited. Here, we show that mammary populations have cell type-specific metabolic programs. Primary human breast cell proteomes of basal, luminal progenitor, and mature luminal populations revealed their unique enrichment of metabolic proteins. Luminal progenitors had higher abundance of electron transport chain subunits and capacity for oxidative phosphorylation, whereas basal cells were more glycolytic. Targeting oxidative phosphorylation and glycolysis with inhibitors exposed distinct metabolic vulnerabilities of the mammary lineages. Computational analysis indicated that breast cancer subtypes retain metabolic features of their putative cell-of-origin. Lineage-restricted metabolic identities of normal mammary cells partly explain breast cancer metabolic heterogeneity and rationalize targeting subtype-specific metabolic vulnerabilities to advance breast cancer therapy.
A Single-Cell Atlas and Lineage Analysis of the Adult Drosophila Ovary
Authors: Rust Katja , Byrnes Lauren , Yu Kevin Shengyang , Park Jason S. , Sneddon Julie B. , Tward Aaron D. , Nystul Todd G. 
Published: October 2019

AbstractThe Drosophila ovary is a widely used model for germ cell and somatic tissue biology. We have used single-cell RNA-sequencing to build a comprehensive cell atlas of the adult Drosophila ovary containing unique transcriptional profiles for every major cell type in the ovary, including the germline and follicle stem cells. Using this atlas we identify novel tools for identification and manipulation of known and novel cell types and perform lineage tracing to test cellular relationships of previously unknown cell types. By this we discovered a new form of cellular plasticity in which inner germarial sheath cells convert to follicle stem cells in response to starvation.Graphical Abstract