bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractDistilled 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

AbstractString-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 statementMouse 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

AbstractCognitive 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

ABSTRACTThe 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

AbstractIn 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

AbstractAlthough 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

AbstractMelanoides 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

AbstractGraph 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.