bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrasting signatures of introgression in North American box turtle (Terrapenespp.) contact zones
Authors: Martin Bradley T. , Douglas Marlis R. , Chafin Tyler K. , Placyk John S. , Birkhead Roger D. , Phillips Christopher A. , Douglas Michael E. 
Published: September 2019

ABSTRACTHybridization occurs differentially across the genome in a balancing act between selection and migration. With the unprecedented resolution of contemporary sequencing technologies, selection and migration can now be effectively quantified such that researchers can identify genetic elements involved in introgression. Furthermore, genomic patterns can now be associated with ecologically relevant phenotypes, given availability of annotated reference genomes. We do so in North American box turtles (Terrapene) by deciphering how selection affects hybrid zones at the interface of species boundaries and identifying genetic regions potentially under selection that may relate to thermal adaptations. Such genes may impact physiological pathways involved in temperature-dependent sex determination, immune system functioning, and hypoxia tolerance. We contrasted these patterns across inter- and intra-specific hybrid zones that differ temporally and biogeographically. We demonstrate hybridization is broadly apparent inTerrapene, but with observed genomic cline patterns corresponding to species boundaries at loci potentially associated with thermal adaptation. These loci display signatures of directional introgression within intra-specific boundaries, despite a genome-wide selective trend against intergrades. In contrast, outlier loci for inter-specific comparisons exhibited evidence of being under selection against hybrids. Importantly, adaptations coinciding with species boundaries inTerrapeneoverlap with climatic boundaries and highlight the vulnerability of these terrestrial ectotherms to anthropogenic pressures.
A novel weight lifting task for investigating effort and persistence in rats
Authors: Porter Blake , Hillman Kristin L. 
Published: September 2019

AbstractHere we present a novel effort-based task for laboratory rats: the weight lifting task (WLT). Studies of effort expenditure in rodents have typically involved climbing barriers within T-mazes or operant lever pressing paradigms. These task designs have been successful for neuropharmacological and neurophysiological investigations, but both tasks involve simple action patterns prone to automatization. Furthermore, high climbing barriers present risk of injury to animals and/or tethered recording equipment. In the WLT, a rat is placed in a large rectangular arena and tasked with pulling a rope 30 cm to trigger food delivery at a nearby spout; weights can be added to the rope in 45 g increments to increase the intensity of effort. As compared to lever pressing and barrier jumping, 30 cm of rope pulling is a multi-step action sequence requiring sustained effort. The actions are carried out on the single plane of the arena floor, making it safer for the animal and more suitable for tethered equipment and video tracking. A microcontroller and associated sensors enable precise timestamping of specific behaviors to synchronize with electrophysiological recordings. The rope and reward spout are spatially segregated to allow for spatial discrimination of the effort zone and the reward zone. We validated the task across five cohorts of rats (total n=35) and report consistent behavioral metrics. The WLT is well-suited for neuropharmacological and/or in vivo neurophysiological investigations surrounding effortful behaviors, particularly when wanting to probe different aspects of effort expenditure (intensity vs. duration).
Genetic Control of Radical Crosslinking in a Semi-Synthetic Hydrogel
Authors: Graham Austin J. , Dundas Christopher M. , Hillsley Alexander , Kasprak Dain S. , Rosales Adrianne M. , Keitz Benjamin K. 
Published: September 2019

AbstractEnhancing materials with the qualities of living systems, including sensing, computation, and adaptation, is an important challenge in designing next-generation technologies. Living materials seek to address this challenge by incorporating live cells as actuating components that control material function. For abiotic materials, this requires new methods that couple genetic and metabolic processes to material properties. Toward this goal, we demonstrate that extracellular electron transfer (EET) fromShewanella oneidensiscan be leveraged to control radical crosslinking of a methacrylate-functionalized hyaluronic acid hydrogel. Crosslinking rates and hydrogel mechanics, specifically storage modulus, were dependent on a variety of chemical and biological factors, includingS. oneidensisgenotype. Bacteria remained viable and metabolically active in the crosslinked network for a least one week, while cell tracking revealed that EET genes also encode control over hydrogel microstructure. Moreover, construction of an inducible gene circuit allowed transcriptional control of storage modulus and crosslinking rate via the tailored expression of a key electron transfer protein, MtrC. Finally, we quantitatively modeled dependence of hydrogel stiffness on steady-state gene expression, and generalized this result by demonstrating the strong relationship between relative gene expression and material properties. This general mechanism for radical crosslinking provides a foundation for programming the form and function of synthetic materials through genetic control over extracellular electron transfer.Significance StatementNext-generation materials will require coupling the advantages of engineered and natural systems to solve complex challenges in energy, health, and the environment. Living cells, such as bacteria, naturally possess many of the qualities essential to addressing these challenges, including sensing, computation, and actuation, using their genetic and metabolic machinery. In addition, bacteria are attractive for incorporation into materials due to their durability, ease-of-use, and programmability. Here, we develop a platform for controlling hydrogel properties (e.g., stiffness, crosslinking rate) using extracellular electron transfer from the bacteriumShewanella oneidensis.In our system, metabolic electron flux fromS. oneidensisto a metal catalyst generates radical species that crosslink an acrylate-based macromer to form the gel. This synthetic reaction is under direct control of bacterial genetics and metabolism, which we demonstrate through inducible circuits and quantitative modeling of gene expression and resultant hydrogel properties. Developing methods that capitalize on the programmability of biological systems to control synthetic material properties will enable hybrid material designs with unprecedented functions.
Differential Striatal Axonal Arborizations of the Intratelencephalic and Pyramidal-Tract Neurons: Analysis of the Data in the MouseLight Database
Authors: Morita Kenji , Im Sanghun , Kawaguchi Yasuo 
Published: September 2019

AbstractThere exist two major types of striatum-targeting neocortical neurons, specifically, intratelencephalic (IT) neurons and pyramidal-tract (PT) neurons. Regarding their striatal projections, it was once suggested that IT axons are extended whereas PT axons are primarily focal. However, subsequent study with an increased number of well-stained extended axons concluded that such an apparent distinction was spurious due to limited sample size. Recent work using genetically labeled neurons reintroduced the differential spatial extent of the striatal projections of IT and PT neurons through population-level analyses, complemented by observations of single axons. However, quantitative analysis of a large number of axons remained to be conducted. We analyzed the data of axonal end-points of 161 IT neurons and 33 PT neurons in the MouseLight database (http://ml-neuronbrowser.janelia.org/). The number of axonal end-points in the ipsilateral striatum exhibits roughly monotonically decreasing distributions in both neuron types. However, the proportion of neurons having >50 ipsilateral end-points is larger in IT neurons than in PT neurons. Moreover, distinguishing IT subpopulations in the secondary motor area (MOs), layer 5 neurons and bilateral striatum-targeting layer 2/3 neurons, but not contralateral striatum-non-targeting layer 2/3 neurons, have a larger number of ipsilateral end-points than MOs PT neurons. We also found that IT ipsilateral striatal axonal end-points are on average more widely distributed than PT end-points, especially in the medial-lateral direction. These results indicate that IT and PT striatal axons differ in the frequency of having numerous end-points and the spatial extent of end-points while there are wide varieties within each neuron type.
The Influence of Blood Collection Tubes in Biomarkers Screening by Mass Spectrometry
Authors: Zhang Siyuan , Zhao Zixuan , Duan Wenjing , li Zhaoxin , Nan Zhuhui , Du Hanzhi , Wang Mengchang , Yang Juan , Huang Chen 
Published: September 2019

AbstractBackgroundMass spectrometry (MS) is one of the rapidly developing bio-analytical techniques in recent years and have found many biomarkers of variety of disease. Whereas pre-analytical process is one of most crucial procedure which would significantly influence the results of biomarkers screening. In the current study, we conducted a pilot analysis of serum to determine the effects of blood collection tubes in biomarkers screening.MethodsMagnetic bead separation and matrix-assisted laser desorption ionization time-of-flight mass spectrometry were used for qualitative analysis of healthy control and serum cancer patients. A total of 24 serum samples were analyzed in this study, of which were collected from patients or healthy control using non-additive tubes or coagulant activator tubes respectively. ClinProTools were used to compare the difference among the different groups.ResultsThe results demonstrated that no matter for patients or normal people, the serum protein profile changed significantly when using coagulant tubes. We also found that the effect of coagulant on serum protein of patients was smaller than that of control group. There were significant differences among 27 peaks which were obtained in the control group and the control coagulant group. However, between patient group and patient coagulant group, only 1 differential peak were obtained. Coagulant changed the protein expression difference in the original serum, and the difference expanded, narrowed even reversed, most of which are small polypeptides (Mass<3000 Da), which significantly changed the results of biomarkers screening. The results showed that 19 potential biomarkers could be found with non-additive tubes and 16 potential biomarkers could be found with coagulate activator tubes, among which only 6 were the same.ConclusionsThe choice of blood collection tube significantly influence the results of biomarkers screening by MS.
Stimulus-Specific Information Flow Across the Canonical Cortical Microcircuit
Authors: Tovar David A. , Westerberg Jacob A. , Cox Michele A. , Dougherty Kacie , Carlson Thomas , Wallace Mark T. , Maier Alexander 
Published: September 2019

AbstractThe vast majority of mammalian neocortex consists of a stereotypical microcircuit, the canonical cortical microcircuit (CCM), consisting of a granular input layer, positioned between superficial and deep layers. Due to this uniform layout, neuronal activation tends to follow a similar laminar sequence, with unique information extracted at each step. For example, the primate primary visual cortex (V1) combines the two eyes’ signals, extracts stimulus orientation and modulates its activity depending on stimulus history. Several theories have been proposed on when and where these processes happen within the CCM’s laminar activation sequence, but it has been methodologically challenging to test these hypotheses. Here, we use time-resolved multivariate pattern analysis (MVPA) to decode information regarding the eye-of-origin, stimulus orientation and stimulus repetition from simultaneously measured spiking responses across V1’s laminar microcircuit. We find that eye-of-origin information was decodable for the entire duration of stimulus presentation, but diminished in the deepest layers of V1, consistent with the notion that two eyes’ signals are combined within the upper layers. Conversely, orientation information was transient and equally pronounced across the microcircuit, in line with the idea that this information is relayed to other areas for further processing. Moreover, when stimuli were repeated, information regarding orientation was enhanced at the expense of eye-of origin information, suggesting that V1 modulates information flow to optimize specific stimulus dimensions. Taken together, these findings provide empirical evidence that adjudicates between long-standing hypotheses and reveals how information transfer within the CCM supports unique cortical functions.Significance StatementDespite the brain’s daunting complexity, there are common organizing principles across brain areas. For example, neocortical activation follows a stereotypical pattern that spreads from input layers towards layers above and below. While this activation pattern is well known, it has been challenging to ascertain how unique types of information are extracted within this common sequence in different brain areas. Here we use machine learning to track the flow of stimulus-specific information across the layers of visual cortex. We found that information regarding several separate stimulus dimensions was routed uniquely within the common activation sequence in a manner that confirmed prior model predictions. This finding demonstrates how differences in information flow within the stereotypical neocortical activation sequence shape area-specific functions.
Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau
Authors: Queiroz Luciano Lopes , Gonçalves Bendia Amanda , Duarte Rubens Tadeu Delgado , das Graças Diego Assis , Costa da Silva Artur Luiz da , Nakayama Cristina Rossi , Sumida Paulo Yukio , Lima Andre O. S. , Nagano Yuriko , Fujikura Katsunori , Kitazato Hiroshi , Pellizari Vivian Helena 
Published: September 2019

AbstractHere we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing (NGS) method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2,456-2,728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaprotebacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.
Chronic pain alters microvascular architectural organization of somatosensory cortex
Authors: Zippo A.G. , Del Grosso V. , Patera A. , Riccardi M. P. , Tredici I. G. , Bertoli G. , Mittone A. , Valente M. , Stampanoni M. , Coan P. , Bravin A. , Biella G.E.M. 
Published: September 2019

AbstractChronic pain (CP) represents a complex pathology profoundly involving both neural and glial compartments of the central nervous system. While most CP studies have also investigated the macroscopic brain vascular system, its microstructural architecture still remains largely unexplored. Further, the adaptive modifications of the vascular microstructure as consequence of diseases or pathological insults, did not receive adequate attention. Here we show microtomographic signs of diffuse and conspicuous microvascular neogenesis in somatosensory cortex of CP animal models already peaking at 15 days from the model instantiation. Progressive fading of this microvessel neogenesis then ensued in the next six months yet maintaining higher vascular density with a preserved small fraction of them. Due to the important consequences on the neuron-glial-vessel arrangements and on the resulting metabolic and functional disorders of the local networks, novel additional scenarios of CP are thus conceivable with profound consequences of potential future CP diagnostic and therapeutic appraisals.
Sorting for CCR7-positivity enriches for a dendritic cell population with enhanced antigen-presenting capacity and anti-tumour potency
Authors: Burgoyne Paul , Hayes Alan J , Cooper Rachel S , Le Brocq Michelle L , Hansell Christopher A.H. , Campbell John DM , Graham Gerard J 
Published: September 2019

AbstractDendritic cell therapy has been a promising addition to the current armoury of therapeutic options in cancer for more than 20 years but has not yet achieved break-through success. To successfully initiate immunity, dendritic cells have to enter the lymph nodes. However, previous experience of therapeutic dendritic cell administration indicates that this is frequently an extremely inefficient process. The major regulator of dendritic cell migration to the lymph nodes is the chemokine receptor CCR7 and in vitro generated dendritic cells typically display heterogenous expression of this receptor. Here we demonstrate that positive-selection for the dendritic cell subpopulation expressing CCR7 enriches for cells with enhanced lymph node migration and antigen presentation competence as well as a chemokine expression profile indicative of improved interactions with T cells. In models of both subcutaneous and metastatic melanoma we demonstrate that the dendritic cells sorted for CCR7 expression trigger enhanced CD8 T-cell driven antitumour immune responses which correlate with reduced tumour burden and increased survival. Finally we demonstrate that this approach is directly translatable to human dendritic cell therapy using clinical-grade cell sorting.SynopsisTherapeutic dendritic cells drive anti-cancer immune responses but they migrate inefficiently to lymph nodes. We show that enriching for CCR7 expression yields a dendritic cellular product with enhanced ability to generate immune responses to localised and disseminated tumours.
Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5
Authors: Rahman Nusrat , Shamsuzzaman Md , Lindahl Lasse 
Published: September 2019

AbstractInhibition of the synthesis of a ribosomal protein (r-protein) abrogates the assembly of its cognate subunit, while assembly of the other subunit continues. Ribosomal components that are not stably incorporated into ribosomal particles due to the disrupted assembly are rapidly degraded. The 60S protein uL18/L5 is an exception, because this protein accumulates extra-ribosomally during inhibition of 60S assembly. Since the r-proteins in each ribosomal subunit are essential only for formation of their own subunit, it would be predicted that accumulation of extra-ribosomal uL18/5 only occurs during restriction of 60S assembly, and not during abolition of 40S assembly. Contrary to this prediction, we report here that repression of 40S r-protein genes does in fact lead to accumulation of uL18/L5 does outside the ribosome due modified 60S assembly. Furthermore, the effect varies depending on which 40S ribosomal protein is repressed. We propose that disruption of early steps in the 40S subunit assembly changes the kinetics of 60S subunit assembly resulting in a buildup of extra-ribosomal uL18/L5, even though 60S formation continues. Finally, our results show that maintenance of the pool of extra-ribosomal uL18/L5 requires continual protein synthesis showing that extra-ribosomal protein is not stable, but is slowly “consumed” by incorporation into 60S subunits and/or turnover.
Camelina (Camelina sativa L. Crantz) Crop Performance, Insect Pollinators, and Pollen Dispersal in the Northeastern US
Authors: Rizzitello Richard , Zhang Chuan-Jie , Auer Carol 
Published: September 2019

AbstractCamelina sativa (camelina) is an oilseed crop in the Brassicaceae that has been genetically engineered for the production of biofuels, dietary supplements, and other industrial compounds. Cultivation in North America is both recent and limited, so there are gaps in knowledge regarding yield, weed competition, and pollen-mediated gene flow. For these experiments, camelina ‘SO-40’ was grown for three years without weed control. Spring-sown camelina was harvested at 80-88 days with ∼1200 growing degree days (GDD) with yields of 425-508 kg/hectare. Camelina yields were the same with or without weeds, showing competitive ability in low-management conditions. Crop failure in 2015 was associated with delayed rainfall and above-average temperatures after seeding. Camelina flowers attracted pollinating insects from the Hymenoptera, Diptera, Lepidoptera, and Coleoptera. Hymenoptera included honey bees (Apis melifera), mining bees (Andrenidae), sweat bees (Halictidae), bumble bees (Bombus spp.) and leaf cutter bees (Megachilidae). Insect visitation on camelina flowers was associated with modest increases in seed yield. Honey bees comprised 28-33% of all pollinators and were shown to carry camelina pollen on their legs. Air sampling showed that wind-blown pollen was present at low concentrations at 9 m beyond the edges of the field. These experiments demonstrated for the first time that camelina pollen dispersal could occur through honey bees or wind, although bee activity would likely be more significant for long-distance gene flow.
A signalling axis involving CNOT3, Aurora B and ERK promotes differentiation and survival of mesendodermal progenitor cells
Authors: Sarkar Moumita , Martufi Matteo , Roman-Trufero Monica , Wang Yi-Fang , Whilding Chad , Dormann Dirk , Sabbattini Pierangela , Dillon Niall 
Published: September 2019

ABSTRACTMesendoderm cells are key intermediate progenitors that form at the early primitive streak (PrS) and give rise to mesoderm and endoderm in the gastrulating embryo. We have identified an interaction between CNOT3 and the cell cycle kinase Aurora B, which requires sequences in the NOT box domain of CNOT3, and regulates MAPK/ERK signalling during mesendoderm differentiation. Aurora B phosphorylates CNOT3 at two sites located close to a nuclear localization signal and promotes localization of CNOT3 to the nuclei of mouse ES cells (ESCs) and metastatic lung cancer cells. ESCs that have both sites mutated give rise to embryoid bodies that are largely devoid of mesoderm and endoderm and are composed mainly of ectoderm. The mutant ESCs are also compromised in their ability to differentiate into mesendoderm in response to FGF2, BMP4 and Wnt3. The double mutation affects interaction of CNOT3 with Aurora B and with ERK and reduces phosphorylation of ERK in response to FGF2, impacting on survival of the differentiated ME cells. Our results identify an adaptor function for CNOT3 that regulates a key pathway in embryogenesis and cancer.