bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of copy number assays for detection and surveillance of piperaquine resistance associated plasmepsin 2/3 copy number variation in Plasmodium falciparum
Authors: Jacob Christopher G , Ansbro Megan R , Amato Roberto , Kekre Mihir , Vongpromek Ranitha , Dhorda Mehul , Amaratunga Chanaki , Sreng Sokunthea , Suon Seila , Miotto Olivo , Fairhurst Rick M , Wellems Thomas E , Kwiatkowski Dominic P 
Published: May 2019

AbstractLong regarded as an epicenter of drug-resistant malaria, Southeast Asia continues to provide new challenges to the control of Plasmodium falciparum malaria. Recently, resistance to the artemisinin combination therapy partner drug piperaquine has been observed in multiple locations across Southeast Asia. Genetic studies have identified a single nucleotide polymorphism as well as a copy number variation molecular marker that associate with clinical and in vitro resistance. The copy number polymorphism is a duplication of a region containing members of the plasmepsin multi-gene family of proteases. To accurately and quickly determine the presence of copy number variation in the plasmepsin 2/3 duplication in field isolates, we developed a quantitative PCR assay using TaqMan probes. We validated copy number estimates using a separate SYBR green-based quantitative PCR assay as well as a novel breakpoint assay to detect the hybrid gene product. Field samples from 2012 – 2015 across 3 sites in Cambodia were tested using DNA extracted from dried blood spots and whole blood to monitor the extent of plasmepsin 2/3 gene duplications, as well as pfmdr1. We found high concordance across all methods of copy number detection. For samples derived from dried blood spots we found a greater than 80% success rate in each assay, with more recent samples performing better. We found evidence of extensive plasmepsin 2/3 copy number amplifications in Pursat (94%, 2015) and Preah Vihear (87%, 2014), and lower levels in Ratanakiri (16%, 2014) in eastern Cambodia. We also see evidence of a shift from two copies of plasmepsin 2/3 in Pursat 2013 to three copies in 2014-15 (25% to 64%). Pfmdr1 duplications are absent from all samples in 2014 from Preah Vihear and Ratanakiri and 2015 from Pursat. This study shows increasing levels of plasmepsin 2/3 gene amplifications across Cambodia from 2012 – 2015 and a complete reversion of pfmdr1 mutant parasites in all study locations. The multiplex TaqMan assay is a robust tool for monitoring both plasmepsin and pfmdr1 copy number variations in field isolates, and the SYBR-green and breakpoint assays are useful for monitoring plasmepsin 2/3 duplications.
Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila
Authors: Ullastres Anna , Merenciano Miriam , González Josefa 
Published: May 2019

ABSTRACTBackgroundVariation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remain largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements.ResultsIn this work, we used a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identified 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validated three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions was consistent with an increased survival to infection. Indeed, for one of the insertions, we showed that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion was deleted from its native genomic context.ConclusionsWe showed that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, TEs are likely to play a role in immune response in other organisms as well.
Recombination detected in the Heat Shock Protein 90 (HSP90) of theBemisia tabacispecies complex
Authors: Kinene Tonny , De Marchi Bruno Rossito , Alicai Titus , Luboobi Livingstone S. , Omongo Christopher Abu , Savill Anders , Boykin Laura M. 
Published: May 2019

AbstractBackgroundBemisia tabaci(whiteflies) are a global insect pest causing billions of dollars in damage each year, leaving farmers with low yields. In East Africa, whiteflies are superabundant and present on cassava plants throughout the year. Whiteflies do not decrease in number in the hot dry seasons in East Africa, therefore, it has been suggested that the synthesis of Heat Shock Protein (HSP) may protect the whitefly from heat stress and other biotic factors. In this study we used data sequence generated from individual whiteflies to assess variability and recombination of the HSP90 gene in members of theB. tabacispecies complex.ResultsA total of 21 samples were sequenced on Illumina Hiseq 2500 and Hiseq 4000. These included eight genetic groups ofB. tabaci: 7 SSA1, 5 SSA2, 2 Australia I (AUSI), 2 New World Africa (NWAfrica),B. afer, Uganda, Mediterranean (MED), and Middle East Asia Minor 1 (MEAM1). An alignment of 21 HSP90 sequences was generated after mapping andde novoassembly. Recombination analysis was performed on an alignment of 27 HSP90 sequences (we added an additional 6 sequences from GenBank). There were 18 recombination events detected in the HSP90 gene of theB. tabacispecies complex, 7 of which were regarded as events that could be caused by evolutionary mechanisms such as gene duplication other than recombination. The phylogenetic analysis carried out on dataset without recombination events revealed a tree pattern with short terminal branches.ConclusionRecombination events were detected for members of theB. tabacispecies complex in the HSP90 gene. This could explain the variability in the HSP90 gene of theB. tabacispecies complex and highlight the phenomenon of the increased chance of survival and reproductive abundance of whiteflies in hot conditions in East Africa, since recombination is a major driving force of evolution.
Amyloid-β induced membrane damage instigates tunneling nanotubes by exploiting p21-activated kinase dependent actin remodulation
Authors: Dilna Aysha , K.V Deepak , Damodaran Nandini , Kielkopf Claudia S. , Kagedal Katarina , Ollinger Karin , Nath Sangeeta 
Published: May 2019

AbstractAlzheimer’s disease (AD) pathology progresses gradually via anatomically connected brain regions. Earlier studies have shown that amyloid-β1-42 oligomers (oAβ) can be directly transferred between connected neurons. However, the mechanism of transfer is not fully revealed. We observed formation of oAβ induced tunneling nanotubes (TNTs), nanoscaled f-actin containing membrane conduit, in differentially differentiated SH-SY5Y neuronal models. Time-lapse images showed that TNTs propagate oligomers from one cell to another. Preceding the TNT-formation, we detected oAβ induced plasma membrane (PM) damage and calcium-dependent repair through lysosomal-exocytosis and significant membrane surface expansion, followed by massive endocytosis to re-establish the PM. Massive endocytosis was monitored by an influx of the membrane-impermeable dye TMA-DPH and PM damage was quantified by propidium iodide influx in the absence of calcium. The massive endocytosis eventually caused accumulation of internalized oAβ in Lamp1 positive multi vesicular bodies/lysosomes via the actin cytoskeleton remodulating p21-activated kinase1 (PAK1) dependent endocytic pathway. Three dimensional quantitative and qualitative confocal imaging, structured illumination superresolution microscopy (SIM) and flowcytometry data revealed that oAβ induces activated phospho-PAK1, which modulates the formation of long stretched f-actin extensions between cells. Moreover, formation of TNTs can be inhibited by preventing PAK1 dependent internalization of oAβ using small-molecule inhibitor IPA-3, a highly selective cell permeable auto-regulatory inhibitor of PAK1. The present study gives insight that the TNTs are probably instigated as a consequence of oAβ induced PM damage and repair process, followed by PAK1 dependent endocytosis and actin remodeling, probably to maintain cell surface expansion and/or membrane tension in equilibrium.
Glutathione is Required for Efficient Post-Golgi Trafficking of Incoming HPV16 Genome
Authors: Li Shuaizhi , Bronnimann Matthew P. , Williams Spencer J. , Campos Samuel K. 
Published: May 2019

AbstractHuman papillomavirus (HPV) is the most common sexually transmitted pathogen in the United States, causing 99% of cervical cancers and 5% of all human cancers worldwide. HPV infection requires transport of the viral genome (vDNA) into the nucleus of basal keratinocytes. During this process, minor capsid protein L2 facilitates subcellular retrograde trafficking of the vDNA from endosomes to the Golgi, and accumulation at host chromosomes during mitosis for nuclear retention and localization during interphase. Here we investigated the relationship between cytosolic GSH and HPV16 infection. siRNA knockdown of GSH biosynthetic enzymes results in a partial decrease of HPV16 infection. Likewise, infection of HPV16 in GSH depleted keratinocytes is inefficient, an effect that was not seen with adenoviral vectors. Analysis of trafficking revealed no defects in cellular binding, entry, furin cleavage of L2, or retrograde trafficking of HPV16, but GSH depletion hindered post-Golgi trafficking and translocation, decreasing nuclear accumulation of vDNA. Although precise mechanisms have yet to be defined, this work suggests that GSH is required for a specific post-Golgi trafficking step in HPV16 infection.
VGLUT2/ Cdk5/p25 Signaling Pathway Contributed to Inflammatory Pain By CFA
Authors: Tang YuWen , Peng ZhiYou , Tao ShouJun , Sun Jianliang , Wang WenYuan , Guo XueJiao , Liu GongLu , Luo XianZhe , Chen Yuan , Shen Yue , Ma HaiXiang , Xu Peng , Li Qing Hua , Zhang HongHai , Feng ZhiYing 
Published: May 2019

AbstractVesicular glutamate transporter type 2 (VGLUT2) is known to play an important role in mediating the heat hyperalgesia induced by inflammation. However, the underlying mechanism for this activity is poorly understood. Cyclin-dependent kinase 5 (Cdk5), serving as a key regulator in mediating release of glutamate, contributed to the inflammatory heat. It remains unknown whether there is a bridge between Cdk5 and VGLUT2 for mediating inflammatory pain. Therefore, we designed the experiment to determine whether VGLUT2 signaling pathway is involved in Inflammatory pain mediated by Cdk5 and the heat hyperalgesia induced by complete Freund’s adjuvant (CFA) can be reversed by roscovitine, a selective inhibitor for Cdk5 through inhibition of VGLUT2 expression. Immunohistochemistry results suggest that when compared with rats in a control group, rats in an experimental group showed significant coexpression of Cdk5/VGLUT2 in small and medium-sized neuronal cells of the dorsal root ganglion (DRG) and spinal cord between days 1 and 3 following subcutaneous injection of CFA. Moreover, our study revealed that the expression of VGLUT2 protein in DRG and spinal cord was remarkably increased between days 1 and 3 following CFA injection. Additionally, p25 but not p35, a activator of Cdk5, protein was significantly increased and reduced by roscovitine. The increased expressions of VGLUT2 protein was significantly reduced by roscovitine as well. Our study showed that VGLUT2/Cdk5 signaling pathway contributed to the inflammatory pain medicated by Cdk5/p25.
A slight decrease in serum albumin level is associated with rapid progression of kidney dysfunction even within the normal range: The Yuport Health Checkup Center Cohort Study
Authors: Amano Hoichi , Yoshimura Kazunobu , Iijima Ryutaro , Waki Kaito , Matsumoto Keisei , Ueda Hitomi , Ito Yasuko , Miyamoto Ken , Akimoto Kimihiko , Yokoo Takashi , Inoue Kazuo , Terawaki Hiroyuki 
Published: May 2019

AbstractObjectiveA low-normal albumin level is associated with a high risk of cardiovascular disease and mortality in the general population. However, the relationship between serum albumin level and future decline of kidney function is unclear. We aimed to clarify the effect of serum albumin level on the decline of kidney function in the general population.MethodsThe data used were from 11,000 participants of a voluntary health checkup program between 1998 and 2006 conducted in Japan. The primary outcome for kidney function was a difference in estimated glomerular filtration rate (ΔeGFR) of ≥3 mL/min/1.73 m2/year. The association of the risk of decreased kidney function with albumin level was determined using a logistic regression analysis. We fit separate multivariable logistic regressions for serum albumin levels (g/dL) as a continuous variable and as categorical data, classified as ≤4.3 (n=2,530), 4.4– 4.6 (n=5,427), and ≥4.7 (n=3,043).ResultsOf 11,000 participants, 346 had a ΔeGFR/year of ≥3. As compared with the participants with albumin levels of ≥4.7 g/dL, the risk of decline in kidney function was higher not only in those with albumin levels of ≤4.3 g/dL (adjusted OR = 2,29, 95% CI: 1.65–3.18) but also in 4.4-4.6 g/dL (adjusted OR = 1.60, 95% CI: 1.20–2.14).ConclusionDecreased albumin level is an independent risk factor for rapid decline in kidney function even within the normal range.
Accuracy of somatic variant detection in multiregional tumor sequencing data
Authors: Detering Harald , Tomás Laura , Prieto Tamara , Posada David 
Published: May 2019

AbstractMultiregional bulk sequencing data is necessary to characterize intratumor genetic heterogeneity. Novel somatic variant calling approaches aim to address the particular characteristics of multiregional data, but it remains unclear to which extent they improve compared to single-sample strategies. Here we compared the performance of 16 single-nucleotide variant calling approaches on multiregional sequencing data under different scenarios with in-silico and real sequencing reads, including varying sequencing coverage and increasing levels of spatial clonal admixture. Under the conditions simulated, methods that use information across multiple samples do not necessarily perform better than some of the standard calling methods that work sample by sample. Nonetheless, our results indicate that under difficult conditions, Mutect2 in multisample mode, in combination with a correction step, seems to perform best. Our analysis provides data-driven guidance for users and developers of somatic variant calling tools.
Metronomic capecitabine as an immune modulator in glioblastoma patients reduces myeloid-derived suppressor cells
Authors: Peereboom David M. , Alban Tyler J. , Grabowski Matthew M. , Alvarado Alvaro G. , Otvos Balint , Bayik Defne , Roversi Gustavo , McGraw Mary , Huang Pengjing , Mohammadi Alireza M. , Kornblum Harley I. , Ahluwalia Manmeet S. , Vogelbaum Michael A. , Lathia Justin D. 
Published: May 2019

AbstractBackgroundMyeloid-derived suppressor cells (MDSCs) are elevated in glioblastoma (GBM) patient circulation, present in tumor tissue, and associated with poor prognosis. While low-dose chemotherapy reduces MDSCs in preclinical models, the use of this strategy to reduce MDSCs in GBM patients has yet to be evaluated.MethodsA phase 0/1 dose-escalation clinical trial was conducted in recurrent glioblastoma patients treated 5-7 days prior to surgery with low-dose chemotherapy via capecitabine followed by concomitant low-dose capecitabine and bevacizumab. Clinical outcomes, including progression-free and overall survival, were measured, along with safety and toxicity profiles. Over the treatment time course, circulating MDSC levels were measured by multi-parameter flow cytometry, and tumor tissue immune profiles were assessed via mass cytometry time-of-flight.ResultsA total of 11 patients were enrolled across escalating dose cohorts of 150, 300, and 450 mg bid, with a progression-free survival of 5.8 months (range of 1.8-27.8 months) and an overall survival of 11.5 months (range of 3->28.0 months) from trial enrollment. No serious adverse events related to the drug combination were observed. Compared to pre-treatment baseline, circulating MDSCs were found to be higher after surgery in the 150 mg treatment arm and lower in the 300 mg and 450 mg treatment arms. Increased cytotoxic immune infiltration was observed after low-dose capecitabine compared to untreated GBM patients in the 300 mg and 450 mg treatment arms.ConclusionsLow-dose, metronomic capecitabine in combination with bevacizumab is well tolerated in GBM patients and was associated with a reduction in circulating MDSC levels and an increase in cytotoxic immune infiltration into the tumor microenvironment.Trial registrationNCT02669173FundingThis research was funded by the Cleveland Clinic, Case Comprehensive Cancer Center, Musella Foundation, and B*CURED. Capecitabine was provided in kind by Mylan Pharmaceuticals.
IF3 licenses newly made 30S subunits for translation during stress
Authors: Sharma Indra Mani , Woodson Sarah A. 
Published: May 2019

SUMMARYBacterial ribosome biogenesis and translation occur in the same cellular compartment. Therefore, a biochemical gate-keeping step is required to prevent immature ribosomes from engaging in protein synthesis. Here, we show that the abundant ribosome assembly factor, RbfA, creates this checkpoint by suppressing protein synthesis by immatureE. coli30S subunits. After 30S maturation, RbfA is released by initiation factor 3 (IF3), which remains bound to 30S subunits to promote translation initiation. Genetic interactions between RbfA and IF3 show that IF3 is important for RbfA release during logarithmic growth. Moreover, IF3 is the main pathway for RbfA release in stationary phase when the activity of a less abundant RbfA-release factor, RsgA GTPase, is inhibited by the alarmone (p)ppGpp. By gating the transition from 30S biogenesis to translation initiation, RbfA and IF3 maintain the integrity of bacterial protein synthesis under a range of growth conditions and especially under stress.
Modeling pupil responses to rapid sequential events
Authors: Denison Rachel N. , Parker Jacob A. , Carrasco Marisa 
Published: May 2019

AbstractPupil size is an easily accessible, noninvasive online indicator of various perceptual and cognitive processes. Pupil measurements have the potential to reveal continuous processing dynamics throughout an experimental trial, including anticipatory responses. However, the relatively sluggish (∼2 s) response dynamics of pupil dilation make it challenging to connect changes in pupil size to events occurring close together in time. Researchers have used models to link changes in pupil size to specific trial events, but such methods have not been systematically evaluated. Here we developed and evaluated a general linear model (GLM) pipeline that estimates pupillary responses to multiple rapid events within an experimental trial. We evaluated the modeling approach using a sample dataset in which multiple sequential stimuli were presented within 2-s trials. We found: (1) Model fits improved when the pupil impulse response function (puRF) was fit for each observer. PuRFs varied substantially across individuals but were consistent for each individual. (2) Model fits also improved when pupil responses were not assumed to occur simultaneously with their associated trial events, but could have non-zero latencies. For example, pupil responses could anticipate predictable trial events. (3) Parameter recovery confirmed the validity of the fitting procedures, and we quantified the reliability of the parameter estimates for our sample dataset. (4) A cognitive task manipulation modulated pupil response amplitude. We provide our pupil analysis pipeline as open-source software (Pupil Response Estimation Toolbox: PRET) to facilitate the estimation of pupil responses and the evaluation of the estimates in other datasets.
The human gut virome database
Authors: Gregory Ann C. , Zablocki Olivier , Howell Allison , Bolduc Benjamin , Sullivan Matthew B. 
Published: May 2019

ABSTRACTThe gut microbiome profoundly impacts human health and disease, but viruses that infect these microbes are likely also important. Problematically, viral sequences are often missed due to insufficient reference viral genomes. Here we (i) built a human gut virome database, GVD, from 648 viral particle metagenomes or microbial metagenomes from 572 individuals previously searched for viruses, (ii) assessed its effectiveness, and (iii) conducted meta-analyses. GVD contains 13,203 unique viral populations (approximately species-level taxa) organized into 702 novel genera, which roughly doubles known phage genera and improves viral detection rates over NCBI viral RefSeq nearly 60-fold. Applying GVD, we assessed and rejected the idea of a ‘core’ gut virome in healthy individuals, and found through meta-analyses that technical artifacts are more impactful than any ‘treatment’ effect across the entire meta-study dataset. Together, this foundational resource and these findings will help human microbiome researchers better identify viral roles in health and disease.
Cocaine experience abolishes the motivation suppressing effect of CRF in the ventral midbrain
Authors: Oliva Idaira , Donate Melissa M. , Lefner Merridee J. , Wanat Matthew J. 
Published: May 2019

AbstractStress affects dopamine-dependent behaviors in part through the actions of corticotropin releasing factor (CRF) in the ventral tegmental area (VTA). For example, acute stress engages CRF signaling in the VTA to suppress the motivation to work for food rewards and promote drug seeking behavior. These diverging behavioral effects in food- and drug-based tasks could indicate that CRF modulates goal-directed actions in a reinforcer-specific manner. Alternatively, prior drug experience could functionally alter how CRF in the VTA regulates dopamine-dependent behavior. To address these possibilities, we examined how intra-VTA injections of CRF influenced cocaine intake and whether prior drug experience alters how CRF modulates the motivation for food rewards. Our results demonstrate that intra-VTA injections of CRF had no effect on drug intake when self-administering cocaine under a progressive ratio reinforcement schedule. We also found that a prior history of either contingent or non-contingent cocaine infusions abolished the capacity for CRF to reduce the motivation for food rewards. Furthermore, voltammetry recordings in the nucleus accumbens illustrate that CRF in the VTA had no effect on cocaine-evoked dopamine release. These results collectively illustrate that exposure to abused substances functionally alters how neuropeptides act within the VTA to influence motivated behavior.