bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single cell resolution: a focus on aging and cancer
Authors: O’Hara Ryan , Tedone Enzo , Ludlow Andrew , Huang Ejun , Arosio Beatrice , Mari Daniela , Shay Jerry W.
Published: March 2019

Mitochondria are involved in a number of diverse cellular functions, including energy production, metabolic regulation, apoptosis, calcium homeostasis, cell proliferation and motility as well as free radical generation. Mitochondrial DNA (mtDNA) is present at hundreds to thousands of copies per cell in a tissue-specific manner. Importantly, mtDNA copy number also varies during aging and disease progression and therefore might be considered as a biomarker that mirrors alterations within the human body. Here we present a new quantitative, highly sensitive droplet digital PCR (ddPCR) method (ddMDM; droplet digital mitochondrial DNA measurement) to measure mtDNA copy number not only from cell populations but also from single cells. Our developed assay can generate data in as little as 3 hours, is optimized for 96-well plates and also allows the direct use of cell lysates without the need for DNA purification or nuclear reference genes. Importantly, we show that ddMDM is able to detect differences between samples whose mtDNA copy number was close enough as to be indistinguishable by other commonly used mtDNA quantitation methods. By utilizing ddMDM, we show quantitative changes in mtDNA content per cell across a wide variety of physiological contexts including cancer progression, cell cycle progression, human T cell activation, and human aging.
Virtual reality for animal navigation with camera-based optical flow tracking
Authors: Vishniakou Ivan , Plöger Paul G. , Seelig Johannes D.
Published: March 2019

Background

Virtual reality combined with spherical treadmills is used across species for studying neural circuits underlying navigation.

New Method

We developed an optical flow-based method for tracking treadmil ball motion in real-time using a single high-resolution camera.

Results

Tracking accuracy and timing were determined using calibration data. Ball tracking was performed at 500 Hz and integrated with an open source game engine for virtual reality projection. The projection was updated at 120 Hz with a latency with respect to ball motion of 30 ± 8 ms.

Comparison with Existing Method(s)

Optical flow based tracking of treadmill motion is typically achieved using optical mice. The camera-based optical flow tracking system developed here is based on off-the-shelf components and offers control over the image acquisition and processing parameters. This results in flexibility with respect to tracking conditions – such as ball surface texture, lighting conditions, or ball size – as well as camera alignment and calibration.

Conclusions

A fast system for rotational ball motion tracking suitable for virtual reality animal behavior across different scales was developed and characterized.
Nitroxide functionalized antibiotics are promising eradication agents against Staphylococcus aureus biofilms
Authors: Verderosa Anthony D. , Dhouib Rabeb , Fairfull-Smith Kathryn E. , Totsika Makrina
Published: March 2019

Treatment of Staphylococcus aureus biofilm-related infections represents an important medical challenge worldwide, as biofilms, even of drug-susceptible S. aureus strains, are highly refectory to conventional antibiotic therapy. Nitroxides were recently shown to induce dispersal of Gram-negative biofilms in vitro, but their action against Gram-positive bacterial biofilms remains unknown. Here we demonstrate that the biofilm dispersal activity of nitroxides extends to S. aureus, a clinically important Gram-positive pathogen. Co-administration of the nitroxide CTEMPO with ciprofloxacin significantly improved the antibiotic’s biofilm-eradication activity against S. aureus. Moreover, covalently linking the nitroxide to the antibiotic moiety further reduced ciprofloxacin’s minimal biofilm eradication concentration. Microscopy analysis revealed that fluorescent nitroxide-antibiotic hybrids could penetrate S. aureus biofilms and enter into cells localising at the surface and base of the biofilm structure. No toxicity was observed for the nitroxide CTEMPO and the nitroxide-antibiotic hybrids against human cells. Taken together, our results show that nitroxides can mediate dispersal of Gram-positive biofilms and that dual-acting biofilm-eradication antibiotics could provide broad-spectrum therapies for the treatment of biofilm-related infections.
Dynamic changes in large-scale functional connectivity prior to stimulation determine performance in a multisensory task
Authors: Galindo-Leon Edgar E. , Hollensteiner Karl J. , Pieper Florian , Engler Gerhard , Nolte Guido , Engel Andreas K.
Published: March 2019

Complex behavior and task execution require fast changes of local activity and functional connectivity in cortical networks at multiple scales. The roles that changes of power and connectivity play during these processes are still not well understood. Here, we study how fluctuations of functional cortical coupling across different brain areas determine performance in an audiovisual, lateralized detection task in the ferret. We hypothesized that dynamic variations in the network’s state determine the animals’ performance. We evaluated these by quantifying changes of local power and of phase coupling across visual, auditory and parietal regions. While power for hit and miss trials showed significant differences only during stimulus and response onset, phase coupling already differed before stimulus onset. An analysis of principal components in coupling at the single-trial level during this period allowed us to reveal the subnetworks that most strongly determined performance. Whereas higher global phase coupling of visual and auditory regions to parietal cortex was predictive of task performance, a second component revealed a reduction in coupling between subnetworks of different sensory modalities, probably to allow a better detection of the unimodal signals. Furthermore, we observed that long-range coupling became more predominant during the task period compared to the pre-stimulus baseline. Taken together, our results show that fluctuations in the network state, as reflected in large-scale coupling, are key determinants of the animals’ behavior.
The interaction of compliance and activation on the force-length operating range and force generating capacity of skeletal muscle
Authors: Cox S.M. , Easton K.L. , Cromie Lear M. , Marsh R.L. , Delp S.L. , Rubenson J.
Published: March 2019

Muscle performance is influenced by where it operates on its force-length curve. Here we explore how activation and tendon compliance interact to influence muscle operating lengths and force-generating capacity. To study this, we built a musculoskeletal model of the lower limb of the guinea fowl and simulated the force-length operating range during fixed-end fixed-posture contractions for 39 actuators under thousands of combinations of activation and posture using three different muscle models: Muscles with non-compliant tendons, muscles with compliant tendons but no activation dependent shift in optimal fiber length (L0), and muscles with both compliant tendons and activation-dependent shifts in L0. We found that activation dependent effects altered muscle fiber lengths up to 40% and increased or decreased force capacity by up to 50% during fixed-end contractions. Typically, activation-compliance effects reduce muscle force and are dominated by the effects of tendon compliance at high activations. At low activation, however, activation-dependent shifts in L0 are equally important and can result in relative force changes for low compliance muscles of up to 60%. There are regions of the force-length curve in which muscles are most sensitive to compliance and there are troughs of influence where these factors have little effect. These regions are hard to predict, though, because the magnitude and location of these areas of high and low sensitivity shift with compliance level. Here we provide a map for when these effects will meaningfully influence force capacity and an example of their contributions to force production during a static task, namely standing.
Toxic Benthic Filamentous Cyanobacteria in Lakes and Rivers of South-Central Quebec, Canada
Authors: Husk Barry , Nieuwenhuis Debra
Published: March 2019

Toxic cyanobacteria are a present and growing threat to ecosystems and public health worldwide. However, most research and regulatory measures have focussed on the planktonic forms of cyanobacteria, with consequently little information available concerning potentially toxic benthic filamentous forms. Through a regional study of ten lake and river sites, including some which are sources of municipal drinking water, this investigation confirms for the first time the widespread presence of potentially toxic benthic filamentous cyanobacteria in south-central Quebec. These findings indicate that water quality monitoring programs in this region need to consider benthic cyanobacteria as a potential source of toxins.
Direct interaction of PIWI and DEPS-1 is essential for piRNA function and condensate ultrastructure inCaenorhabditis elegans
Authors: Suen KM , Braukmann F , Butler R , Bensaddek D , Akay A , Lin C. -C , Doshi N , Sapetschnig A , Lamond A , Ladbury JE , Miska EA
Published: March 2019

Membraneless organelles are platforms for many aspects of RNA biology including small non-coding RNA (ncRNA) mediated gene silencing. How small ncRNAs utilise phase separated environments for their function is unclear. To address this question, we investigated how the PIWI-interacting RNA (piRNA) pathway engages with the membraneless organelle P granule inCaenorhabditis elegans. Proteomic analysis of the PIWI protein PRG-1 revealed an interaction with the constitutive P granule protein DEPS-1. Furthermore we identified a novel motif on DEPS-1, PBS, which interacts directly with the Piwi domain of PRG-1. This protein complex forms intertwining ultrastructures to build elongated condensatesin vivo. These sub-organelle ultrastructures depend on the Piwi-interacting motif of DEPS-1 and mediate piRNA function. Additionally, we identify a novel interactor of DEPS-1, EDG-1, which is required for DEPS-1 condensates to form correctly. We show that DEPS-1 is not required for piRNA biogenesis but piRNA function:deps-1mutants fail to produce the secondary endo-siRNAs required for the silencing of piRNA targets. Our study reveals how specific protein-protein interactions drive the spatial organisation and function of small RNA pathways within membraneless organelles.
Adenovirus serotype 26 utilises sialic acid bearing glycans as a primary cell entry receptor
Authors: Baker Alexander T. , Mundy Rosie , Davies James , Rizkallah Pierre J. , Parker Alan L
Published: March 2019

Adenoviruses are clinically important agents. They cause respiratory distress, gastroenteritis, and epidemic keratoconjunctivitis (EKC). As non-enveloped, double stranded DNA viruses, they are easily manipulated, making them popular vectors for therapeutic applications, including vaccines. Species D adenovirus serotype 26 (HAdV-D26) is both a cause of EKC and other disease, and a promising vaccine vector. HAdV-D26 derived vaccines are under investigation as protective platforms against HIV, Zika, RSV infections and are in Phase-III clinical trials for Ebola.

We recently demonstrated that HAdV-D26 does not utilise CD46 or desmoglein 2 as entry receptors, whilst the putative interaction with Coxsackie and Adenovirus Receptor (CAR) is low affinity and unlikely to represent the primary cell receptor.

Here, we definitively establish sialic acid as the primary entry receptor utilised by HAdV-D26. We demonstrate removal of cell surface sialic acid inhibits HAdV-D26 infection and provide a high-resolution crystal structure of HAdV-D26 fiber-knob in complex with sialic acid.
Male recombination produced multiple geographically restricted neo-Y chromosome haplotypes of varying ages that correlate with onset of neo-Y decay inDrosophila albomicans
Authors: Wei Kevin H-C. , Bachtrog Doris
Published: March 2019

Male Drosophila typically have achiasmatic meiosis, and fusions between autosomes and the Y have repeatedly created non-recombining neo-Y chromosomes that degenerate. Intriguingly,Drosophila nasutamales recombine, but their close relativeD. albomicansreverted back to achiasmy after evolving neo-sex chromosomes. Here we use genome-wide polymorphism data to reconstruct the complex evolutionary history of neo-sex chromosomes inD. albomicansand examine the effect of recombination and its cessation on the initiation of neo-Y decay. Population and phylogenomic analyses reveal three distinct neo-Y types that are geographically restricted. Due to meiotic exchange with the neo-X, overall nucleotide diversity on the neo-Y is similar to the neo-X but severely reduced within neo-Y types. Consistently, outside of the region proximal to the fusion, the neo-Ys fail to form a monophyletic clade in sliding window trees. Based on tree topology changes, we inferred the recombinant breakpoints that produced haplotypes specific to each neo-Y type and estimated their ages revealing that recombination became suppressed at different time points for the different neo-Y haplotypes. Although there are no evidence of chromosome-wide differentiation between the neo-sex chromosomes, haplotype age correlates with onset of neo-Y decay. Older neo-Y haplotypes show more fixed gene disruption via frameshift indels and down-regulation of neo-Y alleles. Genes are downregulated independently on the different neo-Ys, but are depleted of testes-biased genes across all haplotypes, indicating that genes important for male function are shielded from degeneration. Our results offer a time course of the early progression of Y chromosome evolution, showing how the suppression of recombination, through the reversal to achiasmy inD. albomicansmales, initiates the process of degeneration.
Vps34/PIK3C3 deletion in thyroid impairs thyroid hormonogenesis and autophagic flux
Authors: Grieco Giuseppina , Wang Tongsong , Delcorte Ophélie , Janssens Virginie , Spourquet Catherine , Strickaert Aurélie , Gaide Chevronnay Héloïse P. , Liao Xiao-Hui , Bilanges Benoît , Refetoff Samuel , Vanhaesebroeck Bart , Maenhaut Carine , Courtoy Pierre J. , Pierreux Christophe E.
Published: March 2019

BACKGROUND

The production of thyroid hormones (T3, T4) depends on thyroid organization in follicles, lined by a monolayer of thyrocytes with strict apico-basal polarity. Polarization supports vectorial transport of thyroglobulin for storage into, and recapture from, the colloid. It also allows selective addressing of channels, transporters, pumps and enzymes to their appropriate basolateral (NIS and Na+/K+-ATPase) or apical membrane domain (pendrin, anoctamin, DUOX2, DUOXA2 and TPO). How these actors of T3/T4synthesis reach their final destination remains poorly understood. Vps34/PIK3C3 is now recognized as a main component in the general control of vesicular trafficking and of cell homeostasis via autophagy. We recently reported that conditional Vps34 inactivation in kidney proximal tubular cells by Pax8-driven excision prevents normal addressing of apical membrane proteins and causes abortive macroautophagy.

METHODS

Vps34 was inactivated using a Pax8-driven Cre recombinase system. The impact of Vps34 inactivation in thyrocytes was analyzed by histological, immunolocalization and mRNA expression profiling. Thyroid hormone synthesis was assayed by125I injection and by serum plasma analysis.

RESULTS

Vps34cKOmice were born at the expected Mendelian ratio and showed normal growth until postnatal day 14, then stopped growing and died at around 1 month of age. We therefore analyzed thyroid Vps34cKObefore postnatal day 14. We found that loss of Vps34 in thyrocytes causes: (i) disorganization of thyroid parenchyma with abnormal thyrocyte and follicular shape and reduced PAS+colloidal spaces; (ii) impaired125I organification at comparable uptake and frequent occurrence of follicles with luminal thyroglobulin but non-detectable T4-bearing thyroglobulin; (iii) severe non-compensated hypothyroidism with extremely low T4levels (<0.25 ± 1.5 μg/dL) and huge TSH plasma levels (19,300 ± 10,500 mU/L); (iv) intense signal in thyrocytes for the lysosomal membrane marker, LAMP-1, as well as thyroglobulin and the autophagy marker, p62, indicating defective proteolysis.

CONCLUSIONS

We conclude that Vps34 is crucial for thyroid hormonogenesis, at least by controlling delivery of apical actors responsible for biogenesis of thyroid hormones on Tg as well as defective proteolytic T3/T4excision in lysosomes.
The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function
Authors: Storz Jay F. , Natarajan Chandrasekhar , Signore Anthony V. , Witt Christopher C. , McCandlish David M. , Stoltzfus Arlin
Published: March 2019

An underexplored question in evolutionary genetics concerns the extent to which mutational bias in the production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG dinucleotides: If the DNA nucleotide cytosine (C) is immediately 5’ to guanine (G) on the same coding strand, then – depending on methylation status – point mutations at both sites occur at an elevated rate relative to mutations at non-CpG sites. Here we examine experimental data from case studies in which it has been possible to identify the causative substitutions that are responsible for adaptive changes in the functional properties of vertebrate hemoglobin (Hb). Specifically, we examine the molecular basis of convergent increases in Hb-O2affinity in high-altitude birds. Using a data set of experimentally verified, affinity-enhancing mutations in the Hbs of highland avian taxa, we tested whether causative changes are enriched for mutations at CpG dinucleotides relative to the frequency of CpG mutations among all possible missense mutations. The tests revealed that a disproportionate number of causative amino acid replacements were attributable to CpG mutations, suggesting that mutation bias can influence outcomes of molecular adaptation.
The actin-capping protein alpha-adducin is required for T-cell costimulation
Authors: Thauland Timothy J. , Butte Manish J.
Published: March 2019

Alpha-adducin (Add1) is a critical component of the actin-spectrin network in erythrocytes, acting to cap the fast-growing, barbed ends of actin filaments, and recruiting spectrin to these junctions. Add1 is highly expressed in T cells, but its role in T-cell activation has not been examined. Using a conditional knockout model, we show that Add1 is necessary for complete activation of CD4+ T cells in response to low levels of antigen but is dispensable for CD8+ T cell activation and response to infection. Surprisingly, costimulatory signals through CD28 were completely abrogated in the absence of Add1. This study is the first to examine the role of actin-capping in T cells, and it reveals a previously unappreciated role for the actin cytoskeleton in regulating costimulation.
Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention
Authors: Grembi Jessica A , Nguyen Lan H , Haggerty Thomas D , Gardner Christopher D , Holmes Susan P , Parsonnet Julie
Published: March 2019

Background

Obesity is a complex global health challenge. Although both low-carbohydrate (low-carb) and low-fat diets can lead to weight loss, there is typically substantial variability in weight and related outcomes for both diet approaches among obese but otherwise healthy adults. Elucidating individual characteristics that might contribute to sustained weight loss is critical to developing effective dietary intervention strategies. We hypothesized that structural differences in the gut microbiota explained some portion of the weight loss variability among people randomized to either a low-carb or low-fat diet, possibly related to its effects on dietary compliance.

Results

Our study included two staggered cohorts of obese adults enrolled in the Diet Intervention Examining The Factors Interacting with Treatment Success (DIETFITS) study - a randomized clinical trial of either a low-fat or low-carb diet. In the discovery cohort (n=66), 161 pre-diet fecal samples were sequenced in addition to 157 samples collected after 10-weeks of dietary intervention. In the validation cohort (n = 56), 106 pre-diet fecal samples were sequenced. Pre-diet taxonomic features, such as the Prevotella/Bacteroides ratio, correlated to weight loss in the discovery cohort were not confirmed in the validation cohort. The most robust finding in the discovery cohort indicated that gut microbiota plasticity was linked to 12-month weight loss in a diet-dependent manner; subjects with higher sustained weight loss on a low-fat diet had higher pre-diet daily plasticity, whereas those most successful on the low-carb diet had greater microbiota plasticity over 10 weeks of dietary intervention. Unfortunately, because sample frequency and timing was quite different in the validation cohort, the relationship between plasticity and weight loss could not be studied in this group.

Conclusions

These findings suggest the potential importance of gut microbiota plasticity in sustained weight loss. We highlight the importance of evaluating kinetic trends and in assessing reproducibility in studies of the gut microbiota.
Molecular signatures of the rediae, cercariae and adult worm stages in the complex life cycles of parasitic flatworms (Psilostomatidae, Trematoda)
Authors: Nesterenko Maksim A. , Starunov Viktor V. , Shchenkov Sergei V. , Maslova Anna R. , Denisova Sofia A. , Granovich Andrey I. , Dobrovolskij Andrey A. , Khalturin Konstantin V.
Published: March 2019

Trematodes are one of the most remarkable animals with complex life cycles with several generations. Life histories of a parasitic flatworms include several stages with disparate morphological and physiological characteristics follow each other and infect hosts ranging from mollusks to higher vertebrates. How does one genome regulate the development of various life forms and how many genes are needed to the functioning of each stages? How similar are molecular signatures of life stages in closely related species of parasitic flatworms? Here we present the comparative analysis of transcriptomic signatures of the rediae, cercaria and adult worm stages in two representatives of the family Psilostomatidae (Echinostomata, Trematoda) -Psilotrema simillimumandSphaeridiotrema pseudoglobulus. Our results indicate that the transitions between the stages of the complex life cycle are associated with massive changes in gene expression with thousands of genes being stage-specific. In terms of expression dynamics, the adult worm is the most similar stage betweenPsilotremaandSpaeridiotrema, while expression patterns of genes in the rediae and cercariae stages are much more different. This study provides transcriptomic evidences not only for similarities and differences between life stages of two related species, but also for cryptic species inSphaeridiotrema.
Separations-encoded microparticles for single-cell western blotting
Authors: Gumuscu Burcu , Herr Amy Elizabeth
Published: March 2019

Direct measurement of proteins from single cells has been realized at the microscale using microfluidic channels, capillaries, and semi-enclosed microwell arrays. Although powerful, these formats are constrained, with the enclosed geometries proving cumbersome for multistage assays, including electrophoresis followed by immunoprobing. We introduce a hybrid microfluidic format that toggles between a planar microwell array and a suspension of microparticles. The planar array is stippled in a thin sheet of polyacrylamide gel, for efficient single-cell isolation and protein electrophoresis of hundreds-to-thousands of cells. Upon mechanical release, array elements become a suspension of separations-encoded microparticles for more efficient immunoprobing due to enhanced mass transfer. Dehydrating microparticles offer improved analytical sensitivity owing to in-gel concentration of fluorescence signal for high-throughput single-cell targeted proteomics.
The Work Performed By Biological Motors
Authors: Baker Josh E.
Published: March 2019

Molecular motors are enzymes that perform work (F · x) when they move along a track a distance x against a constant force F. This work is performed through intermediate chemical steps in a motor’s ATPase reaction cycle, each step having a free energy change associated with it that is a sum of chemical, Δµchem, and mechanical, Δµext, potentials. Defining Δµext is fundamental to our understanding of how molecular motors work, yet after decades of study the definition of Δµext remains disputed. Some postulate that Δµext is a function of both F and x, while others assume that Δµext is a function of neither F nor x, and still others argue that Δµext is a function of F but not x. Here we evaluate these models and conclude that only the latter – a mechanochemical model proposed by A.V. Hill in the 1930’s – describes molecular motor mechanochemistry.
A candidate causal variant underlying both enhanced cognitive performance and increased risk of bipolar disorder
Authors: Shen Susan Q. , Kim-Han Jeong Sook , Cheng Lin , Xu Duo , Gokcumen Omer , Hughes Andrew E.O. , Myers Connie A. , Corbo Joseph C.
Published: March 2019

Bipolar disorder is a highly heritable mental illness, but the relevant genetic variants and molecular mechanisms are largely unknown. Recent GWASs have identified an intergenic region associated with both cognitive performance and bipolar disorder. This region contains dozens of putative fetal brain-specific enhancers and is located ∼0.7 Mb upstream of the neuronal transcription factor POU3F2. We identified a candidate causal variant, rs77910749, that falls within a highly conserved putative enhancer, LC1. This human-specific variant is a single-base deletion in a PAX6 binding site and is predicted to be functional. We hypothesized that rs77910749 alters LC1 activity and hence POU3F2 expression during neurodevelopment. Indeed, transgenic reporter mice demonstrated LC1 activity in the developing cerebral cortex and amygdala. Furthermore, ex vivo reporter assays in embryonic mouse brain and human iPSC-derived cerebral organoids revealed increased enhancer activity conferred by the variant. To probe the in vivo function of LC1, we deleted the orthologous mouse region, which resulted in amygdala-specific changes in Pou3f2 expression. Lastly, ‘humanized’ rs77910749 knock-in mice displayed behavioral defects in sensory gating, an amygdala-dependent endophenotype seen in patients with bipolar disorder. Our study suggests a molecular mechanism underlying the long-speculated link between enhanced cognitive performance and neuropsychiatric disease.
Proteomic Analysis ofPlasmodiumMerosomes: The Link Between Liver and Blood Stages in Malaria
Authors: Shears Melanie J , Nirujogi Raja Sekhar , Swearingen Kristian E , Renuse Santosh , Mishra Satish , Reddy Panga Jaipal , Moritz Robert L , Pandey Akhilesh , Sinnis Photini
Published: March 2019

The pre-erythrocytic liver stage of the malaria parasite, comprising sporozoites and the liver stages into which they develop, remains one of the least understood parts of the lifecycle, in part owing to the low numbers of parasites. Nonetheless, it is recognized as an important target for anti-malarial drugs and vaccines. Here we provide the first proteomic analysis of merosomes, which define the final phase of the liver stage and are responsible for initiating the blood stage of infection. We identify a total of 1879 parasite proteins, and a core set of 1188 proteins quantitatively detected in every biological replicate, providing an extensive picture of the protein repertoire of this stage. This unique dataset will allow us to explore key questions about the biology of merosomes and hepatic merozoites.

Highlights

First proteome of the merosome stage of malaria parasites

Quantitative detection of 1188 parasite proteins across 3 biological replicates

Comparison to blood stage proteomes identifies shared and unique proteins

Discovery of cleaved PEXEL motifs highlights liver stage protein export

In Brief

The merosome stage that links malaria liver and blood stage infection is poorly understood. Here we provide the first proteome of this life cycle stage using thePlasmodium bergheirodent malaria model.

Graphical Abstract
The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology
Authors: Chen Jonathan L. , Moss Walter N. , Spencer Adam , Zhang Peiyuan , Childs-Disney Jessica L. , Disney Matthew D.
Published: March 2019

Tauopathies are neurodegenerative diseases that affect millions of people worldwide including those with Alzheimer’s disease. While many efforts have focused on understanding the role of tau protein in neurodegeneration, there has been little done to systematically analyze and study the structures within tau’s encoding RNA and their connection to disease pathology. Knowledge of RNA structure can provide insights into disease mechanisms and how to affect protein production for therapeutic benefit. Using computational methods based on thermodynamic stability and evolutionary conservation, we identified structures throughout the tau pre-mRNA, especially at exon-intron junctions and within the 5′ and 3′ untranslated regions (UTRs). In particular, structures were identified at twenty exon-intron junctions. The 5′ UTR contains one structured region, which lies within a known internal ribosome entry site. The 3′ UTR contains eight structured regions, including one that contains a polyadenylation signal. A series of functional experiments were carried out to assess the effects of mutations associated with mis-regulation of alternative splicing of exon 10 and to identify regions of the 3′ UTR that contain cis-regulatory elements. These studies defined novel structural regions within the mRNA that affect stability and pre-mRNA splicing and may lead to new therapeutic targets for treating tau-associated diseases.
Morphine analgesia and μ opioid receptor signaling require programed death protein 1
Authors: Wang Zilong , Jiang Changyu , He Qianru , Matsuda Megumi , Han Qingjian , Wang Kaiyuan , Bang Sangsu , Ji Ru-Rong
Published: March 2019

Opioids such as morphine produce analgesia via mu opioid receptor (MOR), but opioid receptor signaling is not fully understood. Here we report that morphine analgesia and MOR signaling require neuronal Programmed cell death protein-1 (PD-1). We found that morphine-induced antinociception following systemic or intrathecal injection was compromised in Pd1-/- mice. Morphine analgesia was also abrogated in wild-type mice after treatment with Nivolumab, a clinically used anti-PD-1 monoclonal antibody. Morphine produced analgesia by suppressing calcium currents in DRG neurons and excitatory synaptic transmission in spinal cord neurons, but strikingly, both actions were impaired by PD-1 blockade. In a mouse model of bone cancer, the antinociceptive action of systemic morphine was compromised in Pd1-/- mice. Finally, PD-L1 and morphine produce synergistic analgesia. Our findings demonstrate that PD-1 also acts as a neuro checkpoint inhibitor and mediates opioid-induced analgesia and MOR signaling in neurons.
Ancestral range reconstruction of remote oceanic island species of Plantago (Plantaginaceae) reveals differing scales and modes of dispersal
Authors: Iwanycki Ahlstrand N. , Verstraete B. , Hassemer G. , Dunbar‐Co S. , Hoggard R. , Meudt H. M. , Rønsted N.
Published: March 2019

Aim

The aim of this study was to resolve the phylogenetic placement of island taxa, reconstruct ancestral origins and resolve competing hypotheses of dispersal patterns and biogeographical histories for oceanic island endemic taxa within subgenus Plantago (Plantaginaceae).

Location

Juan Fernández Islands, the Auckland Islands, Lord Howe Island, New Amsterdam Island, New Zealand, Tasmania, Falkland Islands, Rapa Iti and the Hawaiian Islands.

Taxon

Island endemics within Plantago (Plantaginaceae), a globally distributed taxonomic group comprising approximately 250 species.

Methods

We use Bayesian phylogenetic and divergence time analyses and historical biogeographical analysis of molecular sequence data to infer the ancestral origins of the oceanic island species in Plantago.

Results

Taxa within subgenus Plantago form clades based on geographic proximities and challenge previous phylogenetic relationships and classification based on morphology. We infer that biogeographic histories of oceanic island taxa from multiple islands were shaped by dispersal at different scales and possibly by different types of birds. The highly remote Hawaiian Islands and Rapa Iti were colonized from North American taxa in a pattern corresponding to known migration routes of large marine birds, rather than from New Zealand as previously hypothesized. The island endemics of Juan Fernández, the Falkland Islands, Lord Howe, Auckland Islands and New Zealand are found to have sources in the nearest continental areas. The analyses confirm recent speciation within subgenus Plantago – which is particularly heightened in island lineages in Hawaii and Rapa Iti – but show slightly older divergence times than previous molecular dating studies.

Main conclusions

Using molecular data to infer ancestral ranges for plants with uncertain taxonomic relationships can greatly improve our understanding of biogeographical histories and help elucidate origins, dispersal modes and routes in widespread lineages with complex distribution patterns such as Plantago. We improve understanding of important floristic exchange areas between continents and islands as a result of long‐distance dispersal. We infer that a combination of both stepping stone dispersal and extreme long‐distance dispersal can shape insular floras, and that multiple floristic areas can be the sources of closely related island taxa. However, despite the successful dispersal of Plantago, radiation in island archipelagos is generally limited suggesting specific traits may limit diversification.
Laser Forming of Metal Foam Sandwich Panels: Effect of Panel Manufacturing Method
Authors: Bucher Tizian , Zhang Min , Chen Chang Jun , Verma Ravi , Li Wayne , Yao Y. Lawrence
Published: March 2019

Sandwich panels with metal foam cores have a tremendous potential in various industrial applications due to their outstanding strength-to-weight ratio, stiffness, and shock absorption capacity. A recent study paved the road toward a more economical implementation of sandwich panels, by showing that the material can be successfully bent up to large angles using laser forming. The study also developed a fundamental understanding of the underlying bending mechanisms and established accurate numerical models. In this study, these efforts were carried further, and the impact of the foam core structure, the facesheet and foam core compositions, and the adhesion method on the bending efficiency and the bending limit was investigated. These factors were studied individually and collectively by comparing two fundamentally different sandwich panel types. Thermally induced stresses at the facesheet/core interface were thoroughly considered. Numerical modeling was carried out under different levels of geometric accuracy to complement bending experiments under a wide range of process conditions. Interactions between panel properties and process conditions were demonstrated and discussed.
How does 6 months of active bike commuting or leisure-time exercise affect insulin sensitivity, cardiorespiratory fitness and intra-abdominal fat? A randomised controlled trial in individuals with overweight and obesity
Authors: Blond Martin Bæk , Rosenkilde Mads , Gram Anne Sofie , Tindborg Marie , Christensen Anders Nymark , Quist Jonas Salling , Stallknecht Bente Merete
Published: March 2019

Objectives

To evaluate effects of active bike commuting or leisure-time exercise of two intensities on peripheral insulin sensitivity (primary outcome), cardiorespiratory fitness and intra-abdominal adipose tissue mass (secondary outcomes).

Methods

188 physically inactive, healthy women and men (20-45 years) with overweight or class 1 obesity were recruited. In the 6-month trial, 130 participants were randomised to either: no intervention (CON), active commuting (BIKE) or leisure-time exercise of moderate (MOD, 50% VO2peak) or vigorous (VIG, 70% VO2peak) intensity. 100 completed follow-up testing. Exercise prescription was 5 days/week with a weekly exercise energy expenditure of 1600 kcal for women and 2100 kcal for men. Testing was performed at baseline, 3 months and 6 months.

Results

Peripheral insulin sensitivity (ml/min/pmol insulin/L) increased (improved) by 24% (95% CI 6% to 46%, p=0.01) in VIG compared with CON at 3 months. Peripheral insulin sensitivity increased (improved) by 20% in BIKE (95% CI 1% to 43%, p=0.04) and 26% in VIG (95% CI 7% to 47%, p<0.01) compared with CON at 6 months. Cardiorespiratory fitness increased in all exercise groups compared with CON at 6 months; but the increase was higher in those that undertook vigorous exercise than those who did moderate exercise. Intra-abdominal adipose tissue mass diminished across all exercise groups in comparison to CON at 6 months.

Conclusions

Active bike commuting improved cardiometabolic health; as did leisure-time exercise. Leisure-time exercise of vigorous intensity conferred more rapid effects on peripheral insulin sensitivity as well as additional effects on cardiorespiratory fitness than did moderate intensity exercise.

Trial registration

NCT01962259
Does the withdrawal time affect adenoma detection in non-screening colonoscopies?
Authors: Al-Rifaie Ammar , El-Feki Mohammed , Al-Talib Ismaeel , Abdulwahid Maysam , Hopper Andrew , Thoufeeq Mo
Published: March 2019

Aims

There are no studies looking at the relationship between colonoscopy withdrawal time (CWT) and adenoma detection rate (ADR) in non-screening patients. Our aim is to explore the relationship between CWT and ADR, particularly in the proximal colon where colonoscopy is shown to be less protective for the development of cancers.

Methods

This is a retrospective study during November 2015 to December 2016 of non-screening colonoscopies done at a large teaching hospital. Incomplete and therapeutic procedures were excluded. The 39 endoscopists included were 15 gastroenterologists, 10 colorectal surgeons and 14 trainee colonoscopists. CWT was calculated by reviewing caecal intubation and rectal retroflexion images.

Results

783 colonoscopies were included, with mean patient age of 58.51 years (SD 15.5). The mean ADR was 21.45% in the study. The CWT could be calculated for 62.83% of the cases (n=492). 80% (393) of colonoscopies had CWT of ≥6 min. Mean CWT was 9.15 min (SD 4.4). The ADR positively correlated with longer CWT (r=0.31, p=0.0001). The ADR was significantly higher when CWT was ≥8 min compared with CWT <6 min or CWT of 6–8 min (p=0.0001). More polyps were detected in the proximal colon when CWT ≥8 min (p=0.078). Mean CWT of gastroenterologists was 9.8 min (SD 4.5), similar to the trainee group (10.3 min, SD 3.8), while mean CWT for colorectal surgeons was 5.7 min (SD 3.2). The ADR for gastroenterologists was 25.9% versus 17.5% for colorectal surgeons and 17.8% for trainees.

Conclusions

There is a moderately strong positive correlation between longer CWT and ADR in non-screening colonoscopies. CWT can differ between different endoscopists. Meticulous colonoscopy withdrawal may improve polyp detection in the proximal colon.
Serum-dependent and -independent regulation of PARP2
Authors: Sun Qizhi , Gatie Mohamed I. , Kelly Gregory M.
Published: March 2019

PARP2 belongs to a family of proteins involved in cell differentiation, DNA damage repair, cellular energy expenditure, and chromatin modeling. In addition to these overlapping functions with PARP1, PARP2 participates in spermatogenesis, T-cell maturation, extra-embryonic endoderm formation, adipogenesis, lipid metabolism, and cholesterol homeostasis. Knowledge of the functions of PARP2 is far from complete, and the mechanism(s) by which the gene and protein are regulated are unknown. In this study, we found that two different mechanisms are used in vitro to regulate PARP2 levels. In the presence of serum, PARP2 is degraded through the ubiquitin–proteasome pathway; however, when serum is removed or dialyzed with a 3.5 kDa molecular cut membrane, PARP2 rapidly becomes sodium dodecyl sulphate- and urea-insoluble. Despite the presence of a putative serum response element in the PARP2 gene, transcription is not affected by serum deprivation, and PARP2 levels are restored when serum is replaced. The loss of PARP2 affects cell differentiation and gene expression linked to cholesterol and lipid metabolism. These observations highlight the critical roles that PARP2 plays under different physiological conditions, and reveal that PARP2 is tightly regulated by distinct pathways.
State-space analysis of power to detect regional brook trout population trends over time
Authors: Pregler Kasey C. , Hanks R. Daniel , Childress Evan S. , Hitt Nathaniel P. , Hocking Daniel J. , Letcher Benjamin H. , Wagner Tyler , Kanno Yoichiro
Published: March 2019

Threats to aquatic biodiversity are expressed at broad spatial scales, but identifying regional trends in abundance is challenging owing to variable sampling designs and temporal and spatial variation in abundance. We compiled a regional data set of brook trout (Salvelinus fontinalis) counts across their southern range representing 326 sites from eight states between 1982 and 2014 and conducted a statistical power analysis using Bayesian state-space models to evaluate the ability to detect temporal trends by characterizing posterior distributions with three approaches. A combination of monitoring periods, number of sites and electrofishing passes, decline magnitude, and different revisit patterns were tested. Power increased with monitoring periods and decline magnitude. Trends in adults were better detected than young-of-the-year fish, which showed greater interannual variation in abundance. The addition of weather covariates to account for the temporal variation increased power only slightly. Single- and three-pass electrofishing methods were similar in power. Finally, power was higher for sampling designs with more frequent revisits over the duration of the monitoring program. Our results provide guidance for broad-scale monitoring designs for temporal trend detection.
A torsion-free background solution of the string theory
Authors: Park Eun Kyung , Kwon Pyung Seong
Published: March 2019

We find a background solution of the string theory which has a special property distinguished from the usual background solutions. This background solution does not produce the NS-NS two-form fields under T-duality and therefore the background vacua described by this solution essentially do not involve NS-NS type branes in their configurations, unlike the case of the ordinary Calabi–Yau ansatz. As a result the non-linear [Formula: see text]-models, whose target space metrics are given by these T-dual partners, can both be torsion-free.
Orthogonality spaces of finite rank and the complex Hilbert spaces
Authors: Vetterlein Thomas
Published: March 2019

An orthogonality space is a set endowed with a symmetric, irreflexive binary relation. By means of the usual orthogonality relation, each anisotropic quadratic space gives rise to such a structure. We investigate in this paper the question to which extent this strong abstraction suffices to characterize complex Hilbert spaces, which play a central role in quantum physics. To this end, we consider postulates concerning the nature and existence of symmetries. Together with a further postulate excluding the existence of nontrivial quotients, we establish a representation theorem for finite-dimensional orthomodular spaces over a dense subfield of [Formula: see text].
Lattice Boltzmann Method Simulations of High Reynolds Number Flows Past Porous Obstacles
Authors: Sangtani Lakhwani N. M. , Nicolleau F. C. G. A. , Brevis W.
Published: March 2019

Lattice Boltzmann Method (LBM) simulations for turbulent flows over fractal and non-fractal obstacles are presented. The wake hydrodynamics are compared and discussed in terms of flow relaxation, Strouhal numbers and wake length for different Reynolds numbers. Three obstacle topologies are studied, Solid (SS), Porous Regular (PR) and Porous Fractal (FR). In particular, we observe that the oscillation present in the case of the solid square can be annihilated or only pushed downstream depending on the topology of the porous obstacle. The LBM is implemented over a range of four Reynolds numbers from 12,352 to 49,410. The suitability of LBM for these high Reynolds number cases is studied. Its results are compared to available experimental data and published literature. Compelling agreements between all three tested obstacles show a significant validation of LBM as a tool to investigate high Reynolds number flows in complex geometries. This is particularly important as the LBM method is much less time consuming than a classical Navier–Stokes equation-based computing method and high Reynolds numbers need to be achieved with enough details (i.e., resolution) to predict for example canopy flows.
Optimal management adaptive of two crossroads by genetic algorithm
Authors: Merbah Amal , Makrizi Abdelilah
Published: March 2019

This paper addresses the issue of managing the traffic flow at traffic-light controlled junctions adopting a mixed, nonlinear programming model. More precisely, we adopt an adaptive, acyclic control system based on the genetic algorithm (GA), a system that allows to accurately decide in real time on the light switching pattern that minimizes the traffic waiting time. Equally importantly, the inherent crossroads constraints, namely, the security of their users and the structure thereof, also referred to as the antagonism principle, are considered in the proceeding of this method.

The implementation of this model on two crossroads significantly decreases the waiting time and regulates the traffic flow. Therefore, the adaptive control system based on the GA proves efficient compared to the nonadaptive system.
Agent-based dynamic simulation of an electricity market with multilateral bidding
Authors: Wu Jiahui , Wang Jidong , Yan Yuanyuan
Published: March 2019

The electricity market is a complex system in which participants interact and compete with each other, which makes description of them with mathematical models difficult. To solve these difficulties, computer simulation has become one of the main methods for studying electricity market problems. How to establish a reasonable electricity market has always been a major research issue in the electric power industry, for which a key point is the bidding mechanism. Agent-based modeling and a simulation (ABMS) method are used in this paper to study the imperfect competitive electricity market. An agent-based simulation method of multilateral bargaining game theory in the dynamics of the power bidding market is presented, and a multi-agent power market bidding dynamics simulation model based on game theory is established. The dynamic bidding game behavior among the government, power grid companies, power plant companies, and consumer parties is simulated in the market, and the simulation method is realized by Anylogic software. Finally, an agent-based four-party competitive dynamic game simulation in the electricity market is implemented, which provides a theoretical reference for further understanding resource optimization problems in the electricity market.