bluuebunny/crossref_metadata_2025 huggingface dataset:
Lumpy skin disease virus does not replicate productively in insect cell lines
Authors: Cook Charlotte , Dietrich Isabelle , Greaves David , Darpel Karin , Beard Pip
Published: December 2019

Lumpy skin disease virus (LSDV) is a capripoxvirus of cattle causing a severe disease that results in substantial economic impact to affected communities. The virus is endemic across sub-Saharan Africa, and has recently entered Europe and the Balkans. The virus is thought to be transmitted by an insect vector, but little is known about the role of the vector in the LSDV cycle.

In order to investigate interactions between LSDV and insect vectors this work studied the permissivity of insect cell lines for LSDV. Insect cell lines were inoculated with LSDV strain Cameroon at a multiplicity of infection (MOI) of 5. The mammalian cell line MDBK was infected as a positive control. Samples were collected up to a week after infection and virus amounts measured using titrated plaque assays in order to construct a growth curve.

Lumpy skin disease virus replicated in the MDBK mammalian cell line, increasing by 3log10 over the 7 day incubation from 2×104 pfu/ml to 2×107 pfu/ml. In contrast, no replication of LSDV was detected in the insect cell lines.

This work shows that LSDV does not productively replicate in insect cell lines and supports the current hypothesis that the insects act as mechanical rather than biological vectors of the virus.
Interrogation of the CHIKV nsP-host interactome in human and mosquito cells
Authors: Bartholomeeusen Koen , Groof Susan De , Hoffmann Chris , Agombin Terence , Caluwé Lien De , Coppens Sandra , Daled Simon , Deforce Dieter , Ariën Kevin
Published: December 2019

Chikungunya virus is a human pathogen transmitted by mosquitos. After a genetic adaptation of the virus that allows increased spreading by Aedes albopictus mosquitos, the past decade, Chikungunya virus has spread across the globe. In a significant number of patients, Chikungunya virus causes a chronic, debilitating, arthritic joint pain.

Chikungunya virus replicates in cells of both its vertebrate host and insect vector. To identify cellular pathways that the virus engages to allow optimal replication in these evolutionary distinct organisms we performed AP-MS to identify interaction partners of the viral non-structural proteins (nsPs) in both human and mosquito cells. Mass spectrometric analysis of on-bead-digestions of affinity purifications coupled to MiST analysis allowed sensitive and reproducible identification of a significant number of cellular protein interaction partners of nsP1, -3 and -4. The retrieval of well-established nsP3 interactors, G3BP and Bin1, in both human and mosquito cells validated our approach. Separate nsPs were associated with both shared and unique interaction partners, the latter belonging to different cellular pathways. Comparison of high-confidence interactors of nsP3 in human and mosquito cells identified 25 proteins that associate with nsP3 in both organisms. Functional classification of these shared nsP3 interactors using GO annotation showed engagement of cell-cell adhesion-, Hippo signaling-, ribosomal function- and innate immune signaling pathways by nsP3 in both human and mosquito cells. Interaction of members of each functional group with nsP3 were validated in AP-WB experiments. Functional roles in viral replication of several of these interactors are evaluated using knockouts.
The Using of Serum Free Media for the Production of J93-463-1-16-10 Monoclonal Antibody against Japanese encephalitis virus
Authors: Tangkananond Wipa , Petchin Nattha
Published: December 2019

The development of J93-463-1-16-10 cell culture by sequential adaptation method in serum-free media of Hybridoma-SFM medium and CD Hybridoma medium to produce the monoclonal antibody specific to Japanese encephalitis virus was shown that the viabilities of J93-463-1-16-10 were more than 70%. Then the supernatant from the cell culture was purified after precipitation with ammonium sulfate until the final concentration was 50% in order to separate the IgG. After that, the protein concentrations were measured by using the Bradford assay. Next, the proteins were separated, which made each protein purer with SDS-PAGE method in order to find the molecular weights of the separated proteins. The putative IgG and its heavy chains and light chains were divided in two sizes which were approximate 23-25 kDa and 50-53 kDa respectively. Later, the type of immunoglobulin will be identified by the Matrix-assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) method and its antibody characteristic to Japanese encephalitis virus which will be done further.

In the future, a monoclonal antibody in this research could be used to study the expression of the envelope protein of Japanese encephalitis virus in green cos and red cos, and to develop the vaccine for Japanese encephalitis virus in swine.

Keywords: Japanese encephalitis virus, J93-463-1-16-10, serum-free media, MALDI-TOF
AurKB activity is necessary for Dengue virus release
Authors: Olais Jose Humberto Perez , Jimenez Fernando Ruiz , García Esther Joquebeb Calderón , Rivas Rosaura Hernández , Angel Rosa Maria Del
Published: December 2019

Flaviviruses, such as Dengue (DENV), Zika and Yellow Fever are pathogens with high morbidity and mortality. Around 390 million people per year are infected with DENV, and almost 90 million develop the clinical forms of the infection. In the present work, we analyzed the role of Aurora Kinase B (AurKB) in the replicative cycle of DENV. This Kinase regulates the activation of ESCRT-III complex, which has an essential role in the viral morphogenesis and/or budding from RE to Golgi apparatus. The compound ZM 447439 (ZM) was used to inhibit specifically AurKB, and the viral progeny, viral RNA/protein synthesis efficiency and NS1 secretion were evaluated. The kinase inhibition did not alter the viral protein production/secretion or genome replication but impaired the viral yield without altering the percentage of infected cells.

Moreover, confocal microscopy analysis of DENV-infected ZM447439-treated cells shows a delocalization of viral components from the replicative complexes. In summary, these observations indicate that AurKB participates in DENV viral morphogenesis or release. Together, our results suggest possible participation of AurKB in the viral release of budding through activation of the ESCRT-III complex and suggest a new role for AurKB on flavivirus viral cycle.
Zika virus infection of glia leads to secondary injury to axons and dendrites
Authors: Schultz Verena , Crawford Colin , Barrie Jennifer , Cumberworth Stephanie , Donald Claire , Barnett Susan , Linington Christopher , Kohl Alain , Willison Hugh , Edgar Julia
Published: December 2019

Zika virus infection was recently linked to microcephaly and peripheral neuropathy (GBS) in Zika virus epidemic areas. Building on our previous work (Cumberworth et al, 2017) we investigated, in a time-course study, how the viral infection and the injury of cell processes of oligodendrocytes and neurons are related to each other in the same in vitro model.

We generated CNS myelinating cultures from a reporter mouse (Thy1-YFP) on the Ifnar1 -/-background. A proportion of neurons and their processes are positive for YFP in those cultures, which enabled us to visualise single neurons. Cultures were infected with the Brazilian Zika virus strain (PE243) at an MOI of 0.3 and cultured for up to 6 days post infection. We observed that the neuronal cell processes were affected as early as the appearance of the first clusters of infected glial cells.

To analyse the interrelation of neurons and myelin further, cultures were labeled with an antibody recognising proteolipid protein. We found that the myelin got injured as early as neuronal processes. These results suggest that the injury to neuronal processes might be a consequence of the infection of the primary target of Zika virus: oligodendroglia.

These data help us to understand disease pathogenesis of Zika virus infection of the CNS, and whether there is a time-window to intervene therapeutically. Furthermore, this gives an insight as to how viral infection of glial cells can affect neuronal processes such as axons.
Of Mice and Monkeys: Determining Protective Serological Titres in Model Zika Virus Infections
Authors: Ferguson Debbie , Kempster Sarah , Dowall Stuart , Ham Claire , Hall Jo , Mattiuzzo Giada , Graham Victoria , Findlay-Wilson Stephen , Berry Neil , Page Mark , Hewson Roger , Almond Neil
Published: December 2019

Developmental vaccines against emerging pathogens face many hurdles including determining what protective level of serological responses must be generated. Knowledge of a likely protective titre is critical where human challenge studies are not possible.

We have used an anti-zika plasma pool from convalescent patients (candidate serological reference reagent NIBSC16/320-14), infused into cynomolgus macaques and Type-1 IFN deficient mice to determine likely protective neutralising titres.

Anti-zika plasma was administered to a group of 4 macaques (single concentration) and groups of 8 A129 mice (4 group titration series) 24 hours prior to sub-cutaneous challenge with Zika virus PRVABC59. Plasma/sera samples were collected at regular intervals to track peripheral viremia and anti-zika antibody responses. FFPE tissues were collected at termination for histological analysis.

Immediately prior to challenge, human IgG was detectable in all infused animals. Within macaques the NT50 at this time was 250. All macaques that received plasma were protected against zika virus infection as determined by plasma/tissue qRT-PCR and IgM responses.

Titration within A129 mice gave a neutralisation titre of 110, above which mice were generally protected against zika infection. However this was not absolute as a small number of mice with high neutralisation levels were infected.

A protective NT50 of 250 has been identified for macaques and this further titrated in A129 mice to give a guide protective neutralisation titre of 110. The lack of protection in some mice with higher titres is currently unclear and studies are underway to compare their infection pathology with that of controls.
Zika virus utilises the ubiquitin-proteasome pathway during infection of mosquito and human cells
Authors: Gestuveo Rommel , Varjak Margus , Royle Jamie , Donald Claire , Kohl Alain
Published: December 2019

Arthropod-borne viruses are able to infect vertebrate and invertebrate hosts. One such arbovirus is Zika virus (family Flaviviridae) that is mainly transmitted to humans by Aedes mosquitoes causing febrile illness and congenital Zika syndrome in infants. An interplay between host and virus proteins enables ZIKV to manipulate its host's cellular machineries in order to facilitate infection and evade antiviral responses. A possible mechanism it utilises is the ubiquitin-proteasome pathway (UPP) where target proteins are ubiquitinated and subsequently degraded by the proteasome. Results of proteomics analysis of Ae. aegypti cell lines (AF5) stably expressing V5-tagged ZIKV capsid (C), anchored capsid (AC) or non-structural 3 (NS3) proteins revealed that these viral proteins interact with effector proteins of the UPP. One of these proteins is TER94 an AAA-ATPase that acts as a chaperone segregating ubiquitinated proteins to the proteasome complex. Knockdown experiments of TER94 or its human ortholog VCP using dsRNA or siRNAs showed reduced virus replication in AF5 or A549 cells. Using small molecule inhibitors of UPP proteins also diminished ZIKV replication. Inhibiting different stages of the pathway have identified critical steps during early stages of infection. The ubiquitination of lysine-rich ZIKV C and its interaction with TER94/VCP could be one of the many universal strategies that the virus employs when it switches between mosquito and human hosts. Understanding how ZIKV is able to infect both human and insect species could provide novel strategies for prevention and therapeutics.

Keywords: Zika virus, Aedes aegypti, ubiquitin-proteasome pathway, mosquito, virus-host interaction
The use of ‘artificial saliva’ as a neutral control condition in gustatory research
Authors: Hensels Imca S. , Talmi Deborah , Baines Stephanie
Published: December 2019

Distilled water with NaHCO3and KCl, a solution often referred to as ‘artificial saliva’ because its chemical composition mimics human saliva, is the control liquid of choice in gustatory research, because it is believed to be entirely affectively neutral. Yet evidence that human research volunteers perceive this liquid as emotionally neutral is lacking. Unpublished data from our lab suggested that this solution might be perceived as aversive. This study set out to systematically test the parameters influencing taste neutrality. We used two different concentrations of distilled water with NaHCO3and KCl, as well as bottled water as a control taste. Healthy adults rated all tastes on two separate scales to rule out an interpretation based on the specifics of a single scale. Our participants rated artificial saliva as aversive on both scales. The bottled water was rated as neutral on both scales, and as significantly less intense in sensation than both concentrations of the distilled water solution. This is the first study to have directly tested the subjective feelings that accompany the ingestion of these oft-used solutions. We found that these liquids, which were previously assumed to be neutral, may not be perceived as such by research participants. Therefore, future gustatory studies should take care when using this solution as a neutral baseline. It is advised that trial-by-trial ratings are collected. Also, depending on the nature of future studies, bottled water may be considered as a preferable neutral baseline.
A toolbox for automated video analysis of rodents engaged in string-pulling: Phenotyping motor behavior of mice for sensory, whole-body and bimanual skilled hand function
Authors: Inayat Samsoon , Singh Surjeet , Ghasroddashti Arashk , Qandeel  , Egodage Pramuka , Whishaw Ian Q. , Mohajerani Majid H.
Published: December 2019

String-pulling in rodents (rats and mice) is a task in which animals make hand-over-hand movements to spontaneously reel in a string with or without a food reward attached to its end. The task elicits bilateral skilled hand movements for which rodents require little training. The task is suitable for phenotyping physiology and pathophysiology of sensorimotor integration in rodent models of neurological and motor disorders. Because a rodent stands in the same location and its movements are repetitive, the task lends itself to quantification of topographical and kinematic parameters for on-line tactile tracking of the string, skilled hand movements for grasping, and rhythmical bilateral forearm movements to advance the string. Here we describe a Matlab®based software with a graphical user interface to assist researchers in analyzing the video record of string pulling. The software allows global characterization of position and motion using optical flow estimation, descriptive statistics, principal component, and independent component analyses as well as temporal measures of Fano factor, entropy, and Higuchi fractal dimension. Based on image segmentation and object tracking heuristic algorithms, the software also allows independent tracking of the body, ears, nose, and forehands for estimation of kinematic parameters such as body length, body angle, head roll, head yaw, head pitch, movement paths and speed of hand movement. The utility of the task and that of the software is presented by describing mouse strain characteristics in string-pulling behavior of two strains of mice, C57BL/6 and Swiss Webster. Postural and skilled hand kinematic differences that characterize the strains highlight the utility of the task and assessment methods for phenotypic and neurological analysis of healthy and rodent models of diseases such as Parkinson’s, Huntington’s, Alzheimer’s and other neurological and motor disorders.

Significance statement

Mouse models are used to investigate the physiology and pathophysiology of motor deficits observed in human neurological conditions, for testing substances for therapeutic drug development, and to investigate the role of neural systems and their genetic basis in the expression of behavior. Behavioral tasks involving unconditioned and natural behavior can provide rich insights into motor performance in animal models and analyses can be aided by the automated processing of video data for reliable quantification and high throughput.
Cognitive control of behavior and hippocampal information processing without medial prefrontal cortex
Authors: Park Eun Hye , O’Reilly Sparks Kally C. , Grubbs Griffin , Taborga David , Nicholas Kyndall , Ahmed Armaan S , Ruiz-Pérez Natalie , Kim Natalie , Segura-Carrillo Simon , Fenton André A.
Published: December 2019

Cognitive control tasks require using one class of information while ignoring competing classes of information. The central role of the medial prefrontal cortex (mPFC) in cognitive control is well established in the primate literature, and largely accepted in the rodent literature because mPFC damage causes deficits in tasks that may require cognitive control, as inferred, typically from the task design. In prior work, we used an active place avoidance task where a rat or mouse on a rotating arena is required to avoid the stationary task-relevant locations of a mild shock and ignore the rotating task-irrelevant locations of those shocks. The task is impaired by hippocampal manipulations, and the discharge of hippocampal place cell populations judiciously alternates between representing stationary locations near the shock zone and rotating locations far from the shock zone, demonstrating cognitive control concurrently in behavior and the hippocampal representation of spatial information. Here we test whether rat mPFC lesion impairs the active place avoidance task to evaluate two competing hypotheses, a “central-computation” hypothesis that the mPFC is essential for the computations required for cognitive control and an alternative “local-computation” hypothesis that other brain areas can perform the computations required for cognitive control, independent of mPFC. Ibotenic acid lesion of the mPFC was effective, damaging the cingulate, prelimbic and infralimbic cortices. The lesion also altered the normal coordination of metabolic activity across remaining structures. The lesion did not impair learning to avoid the initial location of shock or long-term place avoidance memory, but impaired avoidance after the shock was relocated. The lesion also did not impair the alternation between task-relevant and task-irrelevant hippocampal representations of place information. These findings support the local-computation hypothesis that computations required for cognitive control can occur locally in brain networks independently of the mPFC.
Age and life expectancy clocks based on machine learning analysis of mouse frailty
Authors: Schultz Michael B , Kane Alice E , Mitchell Sarah J , MacArthur Michael R , Warner Elisa , Mitchell James R. , Howlett Susan E , Bonkowski Michael S , Sinclair David A
Published: December 2019

The identification of genes and interventions that slow or reverse aging is hampered by the lack of non-invasive metrics that can predict life expectancy of pre-clinical models. Frailty Indices (FIs) in mice are composite measures of health that are cost-effective and non-invasive, but whether they can accurately predict health and lifespan is not known. Here, mouse FIs were scored longitudinally until death and machine learning was employed to develop two clocks. A random forest regression was trained on FI components for chronological age to generate the FRIGHT (Frailty InferredGeriatricHealthTimeline) clock, a strong predictor of chronological age. A second model was trained on remaining lifespan to generate the AFRAID (Analysis ofFrailty andDeath) clock, which accurately predicts life expectancy and the efficacy of a lifespan-extending intervention up to a year in advance. Adoption of these clocks should accelerate the identification of novel longevity genes and aging interventions.
DeepLabStream: Closing the loop using deep learning-based markerless, real-time posture detection
Authors: Schweihoff Jens F. , Loshakov Matvey , Pavlova Irina , Kück Laura , Ewell Laura A. , Schwarz Martin K.
Published: December 2019

In general, animal behavior can be described as the neuronal-driven sequence of reoccurring postures through time. Current technologies enable offline pose estimation with high spatio-temporal resolution, however to understand complex behaviors, it is necessary to correlate the behavior with neuronal activity in real-time. Here we present DeepLabStream, a highly versatile, closed-loop solution for freely moving mice that can autonomously conduct behavioral experiments ranging from behavior-based learning tasks to posture-dependent optogenetic stimulation. DeepLabStream has a temporal resolution in the millisecond range, can operate with multiple devices and can be easily tailored to a wide range of species and experimental designs. We employ DeepLabStream to autonomously run a second-order olfactory conditioning task for freely moving mice and to deliver optogenetic stimuli based on mouse head-direction.
MGMM: An R Package for fitting Gaussian Mixture Models on Incomplete Data
Authors: McCaw Zachary R. , Julienne Hanna , Aschard Hugues
Published: December 2019

Although missing data are prevalent in applications, existing implementations of Gaussian mixture models (GMMs) require complete data. Standard practice is to perform complete case analysis or imputation prior to model fitting. Both approaches have serious drawbacks, potentially resulting in biased and unstable parameter estimates. Here we presentMGMM, anRpackage for fitting GMMs in the presence of missing data. Using three case studies on real and simulated data sets, we demonstrate that, when the underlying distribution is near-to a GMM,MGMMis more effective at recovering the true cluster assignments than state of the art imputation followed by standard GMM. Moreover,MGMMprovides an accurate assessment of cluster assignment uncertainty even when the generative distribution is not a GMM. This assessment may be used to identify unassignable observations.MGMMis available as anRpackage on CRAN:https://CRAN.R-project.org/package=MGMM.
Genetic and morphological variation is associated with differences in cold-water tolerance and geographic expansion among invasive snails (Melanoides tuberculata) in central Texas
Authors: Harding Stephen , Rodriguez David , Jackson Jacob , Huffman David
Published: December 2019

Melanoides tuberculata(Thiaridae) is an old-world freshwater snail that is and now circumtropical. After being introduced in the 1960s via the aquarium trade, populations ofM. tuberculataare thriving in spring systems of Texas (USA). Field surveys and experimental investigations of temperature tolerance suggestM. tuberculatais stenothermal, and thus range expansions outside of aquatic habitats with water temperatures between 18° and 32°C should be unlikely. However, in 2012 snails were detected in natural aquatic habitats with seasonal temperatures below the experimentally determined lethal thermal minimum. To test whether genetic and phenotypic variation might be associated with cold-water tolerance and range expansion, we sequenced the 16S ribosomal rRNA gene and measured qualitative conch morphology of 170 snails collected at 26 sites in three central Texas rivers. We also conducted phylogenetic analyses ofM. tuberculatacollected globally and in Texas to determine potential source populations and estimate the number of invasion events. Our results show snails detected in variable temperature habitats are genetically divergent and morphologically distinct from snails collected in habitats with stable temperatures. These data are consistent with at least three introduction events into Texas ofM. tuberculata sensu latothat are characterized by distinct habitat preferences, physiological tolerances, and/or adaptive behaviors.
Distance Indexing and Seed Clustering in Sequence Graphs
Authors: Chang Xian , Eizenga Jordan , Novak Adam M. , Sirén Jouni , Paten Benedict
Published: December 2019

Graph representations of genomes are capable of expressing more genetic variation and can therefore better represent a population than standard linear genomes. However, due to the greater complexity of genome graphs relative to linear genomes, some functions that are trivial on linear genomes become more difficult in genome graphs. Calculating distance is one such function that is simple in a linear genome but much more complicated in a graph context. In read mapping algorithms, distance calculations are commonly used in a clustering step to determine if seed alignments could belong to the same mapping. Clustering algorithms are a bottleneck for some mapping algorithms due to the cost of repeated distance calculations. We have developed an algorithm for quickly calculating the minimum distance between positions on a sequence graph using a minimum distance index. We have also developed an algorithm that uses the distance index to cluster seeds on a graph. We demonstrate that our implementations of these algorithms are efficient and practical to use for mapping algorithms.
Transfer Learning for Predicting Conversion from Mild Cognitive Impairment to Dementia of Alzheimer’s Type based on 3D-Convolutional Neural Network
Authors: Bae Jinhyeong , Stocks Jane , Heywood Ashley , Jung Youngmoon , Jenkins Lisanne , Katsaggelos Aggelos , Popuri Karteek , Beg M. Faisal , Wang Lei ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: December 2019

Dementia of Alzheimer’s Type (DAT) is associated with a devastating and irreversible cognitive decline. As a pharmacological intervention has not yet been developed to reverse disease progression, preventive medicine will play a crucial role for patient care and treatment planning. However, predicting which patients will progress to DAT is difficult as patients with Mild Cognitive Impairment (MCI) could either convert to DAT (MCI-C) or not (MCI-NC). In this paper, we develop a deep learning model to address the heterogeneous nature of DAT development. Structural magnetic resonance imaging was utilized as a single biomarker, and a three-dimensional convolutional neural network (3D-CNN) was developed. The 3D-CNN was trained using transfer learning from the classification of Normal Control and DAT scans at the source task. This was applied to the target task of classifying MCI-C and MCI-NC scans. The model results in 82.4% classification accuracy, which outperforms current models in the field. Furthermore, by implementing an occlusion map approach, we visualize key brain regions that significantly contribute to the prediction of MCI-C and MCI-NC. Results show the hippocampus, amygdala, cerebellum, and pons regions as significant to prediction, which are consistent with current understanding of disease. Finally, the model’s prediction value is significantly correlated with rates of change in clinical assessment scores, indicating the model is able to predict an individual patient’s future cognitive decline. This information, in conjunction with the identified anatomical features, will aid in building a personalized therapeutic strategy for individuals with MCI. This model could also be useful for selection of participants for clinical trials.
Metastasis-specific gene expression in autochthonous and allograft mouse mammary tumor models: stratification and identification of targetable signatures
Authors: Ross Christina , Szczepanek Karol , lee Maxwell , Yang Howard , Peer Cody J. , Kindrick Jessica , Shankarappa Priya , Lin Zhi-Wei , Sanford Jack , Figg William D. , Hunter Kent
Published: December 2019

Breast cancer is a leading cause of cancer-related death of women in the U.S., which is ultimately due to metastasis rather than primary tumor burden. Therefore, increased understanding of metastasis to develop novel therapies is critical in reducing breast cancer-related mortality. Indeed, a major hurdle in advancing metastasis-targeted intervention is the genotypic and phenotypic heterogeneity that exists between primary and secondary lesions. To identify targetable metastasis-specific gene expression profiles we performed RNA sequencing of breast cancer metastasis mouse models. We analyzed metastases from models of various oncogenic drivers and routes, including orthotopic injection, tail vein injection, intracardiac injection, and genetically engineered mouse models (GEMMs). Herein, we analyzed samples from 176 mice and tissue culture samples, resulting in 338 samples total. Using these data, we contrasted the different breast cancer metastasis models, and also identified common, targetable metastasis specific gene expression signatures.

Principal component analysis revealed that mouse model (Allograft v. GEMM) rather than tissue source (PT v metastatic nodule) shaped the transcriptomes of our samples. Allograft models exhibited more mesenchymal-like gene expression than GEMM models, and primary culturing of GEMM-derived metastatic tissue induced more mesenchymal-like gene expression. Furthermore, metastasis-specific gene expression differed between tail vein and orthotopic injection models of the same cell line, the degree of which was cell line dependent. Finally, we examined metastasis-specific gene expression common to models of spontaneous metastasis (orthotopic injection and GEMMs). Pathway analysis identified upregulation of the sildenafil response, and nicotine degradation pathways. The influence of these pathways on metastatic spread was assessed by treatment of allograft models with clinically relevant dosing of sildenafil or nicotine. Sildenafil significantly reduced pulmonary metastasis while nicotine administration significantly increased metastasis, and neither regimen altered primary tumor mass. Taken together our data reveals critical differences between pre-clinical models of metastatic breast cancer. Additionally, this strategy has identified clinically targetable metastasis-specific pathways integral to metastatic spread.
Real-time spectroscopic photoacoustic/ultrasound (PAUS) scanning with simultaneous fluence compensation and motion correction for quantitative molecular imaging
Authors: Jeng Geng-Shi , Li Meng-Lin , Kim MinWoo , Yoon Soon Joon , Pitre John J. , Li David S. , Pelivanov Ivan , O’Donnell Matthew
Published: December 2019

For over two decades photoacoustic (PA) imaging has been tested clinically, but successful human trials have been minimal. To enable quantitative clinical spectroscopy, the fundamental issues of wavelength-dependent fluence variations and inter-wavelength motion must be overcome. Here we propose a new real-time, spectroscopic photoacoustic/ultrasound (PAUS) imaging approach using a compact, 1-kHz rate wavelength-tunable laser. Instead of illuminating tissue over a large area, the fiber-optic delivery system surrounding an US array sequentially scans a narrow laser beam, with partial PA image reconstruction for each laser pulse. The final image is then formed by coherently summing partial images at a 50-Hz video rate. This scheme enables (i) automatic laser-fluence compensation in spectroscopic PA imaging and (ii) inter-wavelength motion correction using US speckle tracking, which have never been shown before in real-time systems. The 50-Hz video rate PAUS system is demonstratedin vivousing a murine model of drug delivery monitoring.
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
Authors: Liu Miao , Lu Yanfang , Yang Bing , Chen Yanbo , Radda Jonathan S.D. , Hu Mengwei , Katz Samuel G. , Wang Siyuan
Published: December 2019

The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and regions associated with nuclear lamina and nucleoli, have been discovered. However, how these structures are arranged in the same cell and how they are correlated with each other in different cell types in mammalian tissue are largely unknown. Here, we developed Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We applied this method in mouse fetal liver, and identifiedde novocell-type-specific chromatin architectures associated with gene expression, as well as chromatin organization principles independent of cell type. Polymer simulation showed that both intra-chromosomal phase-separating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our experiments and modeling provide a multiscale and multi-faceted picture of chromatin folding and nucleome architectures in mammalian tissue and illustrate physical principles for maintaining chromatin organization.
QuantifiableIn VivoImaging Biomarkers of Retinal Regeneration by Photoreceptor Cell Transplantation
Authors: Liu Ying V. , Sodhi Simrat , Xue Gilbert , Teng Derek , Agakishiev Dzhalal , McNally Minda M. , Harris-Bookman Sarah , McBride Caitlin , Konar Gregory , Singh Mandeep S.
Published: December 2019

Purpose

Short-term improvements in retinal anatomy are known to occur in preclinical models of photoreceptor transplantation. However, correlative changes over the long term are poorly understood. We aimed to develop a quantifiable imaging biomarker grading scheme, using non-invasive multimodal confocal scanning laser ophthalmoscopy (cSLO) imaging, to enable serial evaluation of photoreceptor transplantation over the long term.

Methods

Yellow-green fluorescent microspheres were transplanted into the vitreous cavity and/or subretinal space ofC57/BL6Jmice. Photoreceptor cell suspensions or sheets from rhodopsin-green fluorescent protein mice were transplanted subretinally, into eitherNOD.CB17-Prkdcscid/JorC3H/HeJ-Pde6brd1mice. Multimodal cSLO imaging was performed serially for up to three months after transplantation. Imaging biomarkers were scored, and a grade was defined for each eye by integrating the scores. Image grades were correlated with immunohistochemistry (IHC) data.

Results

Multimodal imaging enabled the extraction of quantitative imaging biomarkers including graft size, GFP intensity, graft length, on-target graft placement, intra-graft lamination, hemorrhage, retinal atrophy, and peri-retinal proliferation. Migration of transplanted material was observed. Changes in biomarker scores and grades were detected in 13/16 and 7/16 eyes, respectively. A high correlation was found between image grades and IHC parameters.

Conclusions

Serial evaluation of multiple imaging biomarkers, when integrated into a per-eye grading scheme, enabled comprehensive tracking of longitudinal changes in photoreceptor cell grafts over time. The application of systematic multimodalin vivoimaging could be useful in increasing the efficiency of preclinical retinal cell transplantation studies in rodents and other animal models.
The psychological correlates of distinct neural states occurring during wakeful rest
Authors: Karapanagiotidis Theodoros , Vidaurre Diego , Quinn Andrew J. , Vatansever Deniz , Poerio Giulia L. , Turnbull Adam , Ho Nerissa Siu Ping , Leech Robert , Bernhardt Boris C. , Jefferies Elizabeth , Margulies Daniel S. , Nichols Thomas E. , Woolrich Mark W. , Smallwood Jonathan
Published: December 2019

When unoccupied by an explicit external task, humans engage in a wide range of different types of self-generated thinking. These are often unrelated to the immediate environment and have unique psychological features. Although contemporary perspectives on ongoing thought recognise the heterogeneity of these self-generated states, we lack both a clear understanding of how to classify the specific states, and how they can be mapped empirically. In the current study, we capitalise on advances in machine learning that allow continuous neural data to be divided into a set of distinct temporally re-occurring patterns, or states. We applied this technique to a large set of resting state data in which we also acquired retrospective descriptions of the participants’ experiences during the scan. We found that two of the identified states were predictive of patterns of thinking at rest. One state highlighted a pattern of neural activity commonly seen during demanding tasks, and the time individuals spent in this state was associated with descriptions of experience focused on problem solving in the future. A second state was associated with patterns of activity that are commonly seen under less demanding conditions, and the time spent in it was linked to reports of negative rumination. Finally, we found that these two neural states tended to fall at either end of a neural hierarchy that is thought to reflect the brain’s response to cognitive demands. Together, these results demonstrate that approaches which take advantage of time-varying changes in neural function can play an important role in understanding the repertoire of self-generated states. Moreover, they establish that important features of self-generated ongoing experience are related to variation along a similar vein to those seen when the brain responds to cognitive task demands.
Visual self-motion cues are impaired in Parkinson’s disease yet over-weighted during visual-vestibular integration
Authors: Yakubovich Sol , Israeli-Korn Simon , Halperin Orly , Yahalom Gilad , Hassin-Baer Sharon , Zaidel Adam
Published: December 2019

Background

Parkinson’s disease (PD) is prototypically a movement disorder. Although perceptual and motor functions are interdependent, much less is known about perceptual dysfunction in PD. Perceptual deficits can impact activities of daily living, and contribute to motor symptoms, but might go unnoticed if not tested directly. Posture, gait and balance, affected in PD, rely on veridical perception of one’s own motion in space. Yet it is unknown whether self-motion perception is impaired in PD.

Objectives

To test self-motion perception in PD, separately for visual and vestibular cues (unisensory), and multisensory integration thereof.

Methods

Participants (19 early stage PD, 23 age-matched and 20 young adult controls) experienced vestibular (motion platform), visual (optic flow), and combined visual-vestibular self-motion stimuli, and discriminated whether the stimulus headings were rightward or leftward of straight ahead. PD participants and age-matched controls were tested on two visits (PD on and off medication).

Results

PD participants had significantly impaired visual self-motion perception, both on and off medication. This deficit correlated significantly with clinical disease severity. By contrast, their vestibular performance was unimpaired. Remarkably, despite impaired visual self-motion perception, PD participants significantly over-weighted visual cues during multisensory (visual-vestibular) integration.

Conclusions

Self-motion perception is affected already in early stage PD, specifically by impaired visual (vs. vestibular) function, and by suboptimal visual-vestibular integration. This may contribute to impaired balance and gait control. Future investigation into this connection might open up new avenues for alternative therapies to better treat these symptoms. Furthermore, these results may also impact early PD diagnosis and subtyping.
Role of HP1β during spermatogenesis and DNA replication
Authors: Charaka Vijaya , Tiwari Anjana , Pandita Raj K , Hunt Clayton R , Pandita Tej K.
Published: December 2019

Maintaining genomic stability in a continually dividing cell population requires accurate DNA repair, especially in male germ cells. Repair and replication protein access to DNA, however, is complicated by chromatin compaction. The HP1β chromatin protein, encoded byCbx1, is associated with chromatin condensation but its role in meiosis is not clear. To investigate the role ofCbx1 in male germ cells, we generated testis specificCbx1 deficient transgenic mice by crossingCbx1flox/flox(Cbx1f/f) mice with Stra8Cre+/−mice. Loss ofCbx1 in testes adversely affected sperm maturation andCbx1 deletion increased seminiferous tubule degeneration and basal level DNA damage., We observed thatCbx1−/−MEF cells displayed reduced resolution of stalled DNA replication forks as well as decreased fork restart, indicating defective DNA synthesis. Taken together, these results suggest that loss ofCbx1 in growing cells leads to DNA replication defects and associated DNA damage that impact cell survival.
SCSA: a cell type annotation tool for single-cell RNA-seq data
Authors: Cao Yinghao , Wang Xiaoyue , Peng Gongxin
Published: December 2019

Currently most methods take manual strategies to annotate cell types after clustering the single-cell RNA sequencing (scRNA-seq) data. Such methods are labor-intensive and heavily rely on user expertise, which may lead to inconsistent results. We present SCSA, an automatic tool to annotate cell types from scRNA-seq data, based on a score annotation model combining differentially expressed genes (DEGs) and confidence levels of cell markers from both known and user-defined information. Evaluation on real scRNA-seq datasets from different sources with other methods shows that SCSA is able to assign the cells into the correct types at a fully automated mode with a desirable precision.
Multimodal Learning of Pheromone Locations
Authors: Pardasani Meenakshi , Marathe Shruti D. , Purnapatre Maitreyee Mandar , Dalvi Urvashi , Abraham Nixon M.
Published: December 2019

Memorizing pheromonal locations is critical for many mammalian species as it involves finding mates and avoiding competitors. In rodents, pheromonal information is perceived by the main and accessory olfactory systems. However, the role of somatosensation in context dependent learning and memorizing of pheromone locations remains unexplored. We addressed this problem by training female mice on a multimodal task to locate pheromones by sampling volatiles emanating from male urine through the orifices of varying dimensions or shapes that are sensed by their vibrissae. In this novel pheromone location assay, female mice’ preference towards male urine scent decayed over time when they were permitted to explore pheromones v/s neutral stimuli, water. On training them for the associations involving olfactory and whisker systems, it was established that they were able to memorize the location of opposite sex pheromones, when tested 15 days later. This memory was not formed either when the somatosensory inputs through whisker pad were blocked or when the pheromonal cues were replaced with that of same sex. The association between olfactory and somatosensory systems were further confirmed by the enhanced expression of the Activity regulated cytoskeleton protein. Further, the activation of main olfactory bulb circuitry by pheromone volatiles did not cause any modulation in learning and memorizing non-pheromonal volatiles. Our study thus provides the evidence for associations formed between different sensory modalities facilitating the long-term memory formation relevant to social and reproductive behaviors.
Exaptation of two ancient immune proteins into a new dimeric pore-forming toxin in snails
Authors: Giglio M.L. , Ituarte S. , Milesi V. , Dreon M.S. , Brola T.R. , Caramelo J. , Ip J.C.H. , Maté S. , Qiu J.W. , Otero L.H. , Heras H.
Published: December 2019

The Membrane Attack Complex-Perforin (MACPF) family is ubiquitously found in all kingdoms. They have diverse cellular roles but MACPF but pore-forming toxic function are very rare in animals. Here we present the structure of PmPV2, a MACPF toxin from the poisonous apple snail eggs, that can affect the digestive and nervous systems of potential predators. We report the three-dimensional structure of PmPV2, at 15 Å resolution determined by negative stain electron microscopy (NS-EM) and its solution structure by small angle X-ray scattering (SAXS). We found that PV2s differ from nearly all MACPFs in two respects: it is a dimer in solution and protomers combine two immune proteins into an AB toxin. MACPF chain is linked by a single disulfide bond to a tachylectin chain, and two heterodimers are arranged head-to-tail by non-covalent forces in the native protein. MACPF domain is fused with a putative new Ct-accessory domain exclusive to invertebrates. Tachylectin is a six-bladed β-propeller, similar to animal tectonins. We experimentally validated the predicted functions of both subunits and demonstrated for the first time that PV2s are true pore-forming toxins. The tachylectin..B..delivery subunit would bind to target membranes, and then its MACPF..A..toxic subunit disrupt lipid bilayers forming large pores altering the plasma membrane conductance. These results indicate that PV2s toxicity evolved by linking two immune proteins where their combined preexisting functions give rise to a new toxic entity with a novel role in defense against predation. This structure is an unparalleled example of protein exaptation.
Field evaluation of DNA amplification of human filarial and malaria parasites using mosquito excreta/feces
Authors: Minetti Corrado , Pilotte Nils , Zulch Michael , Canelas Tiago , Tettevi Edward J. , Veriegh Francis B. D. , Osei-Atweneboana Mike Yaw , Williams Steven A. , Reimer Lisa J.
Published: December 2019

Background

We recently developed a superhydrophobic cone-based method for the collection of mosquito excreta/feces (E/F) for the molecular xenomonitoring of vector-borne parasites showing higher throughput compared to the traditional approach. To test its field applicability, we used this platform to detect the presence of filarial and malaria parasites in two villages of Ghana and compared results to those for detection in mosquito carcasses and human blood.

Methodology and principal findings

We compared the molecular detection of three parasites (Wuchereria bancrofti, Plasmodium falciparumandMansonella perstans) in mosquito E/F, mosquito carcasses and human blood collected from the same households in two villages in the Savannah Region of the country. We successfully detected the parasite DNA in mosquito E/F from indoor resting mosquitoes, includingW. bancroftiwhich had a very low community prevalence (2.5-3.8%). Detection in the E/F samples was concordant with detection in insect whole carcasses and people, and laboratory tests showed that the risk of mosquito carcass cross-contamination with positive excreta when insects are held together in the device is minimal.

Conclusions

Our approach to collect and test mosquito E/F successfully detected a variety of parasites at varying prevalence in the human population under field conditions, including a pathogen (M. perstans) which is not transmitted by mosquitoes. The method shows promise for further development and applicability for the early detection and surveillance of a variety of pathogens carried in human blood.

Author summary

Molecular xenomonitoring of parasites or viruses using mosquitoes as “flying syringes” is a promising and non-invasive tool for early detection and surveillance of various pathogens, particularly in low prevalence settings, but there is a need for cost-effective and higher throughput alternatives. We recently developed a novel approach based on the collection of mosquito excreta/feces (E/F) using a superhydrophobic cone that directs the sample into a tube at the bottom of the collection cup. We tested this method’s ability to detect the presence of lymphatic filariasis, malaria, and mansonellosis from households in two endemic rural communities of Ghana and compared it to the molecular detection from blood and mosquito carcass samples from corresponding households. The detection of parasite DNA in mosquito E/F was successful for all three pathogens, and it showed good concordance with the detection in the insects’ whole carcasses. Given the successful detection ofMansonella perstans, which is not transmitted by mosquitoes, our tool shows promise for use as an alternative method for the early and non-invasive detection and surveillance of various pathogens in human blood, including those not strictly mosquito-borne, in endemic settings.