156 Works

Data from: PCB126 inhibits the activation of AMPK-CREB signal transduction required for energy sensing in liver

Gopi S. Gadupudi, Benjamin A. Elser, Fabian A. Sandgruber, Xueshu Li, Katherine N. Gibson-Corley & Larry W. Robertson
3,3’,4,4’,5-pentachlorobiphenyl (PCB126), a dioxin-like PCB, elicits toxicity through a wide array of non-carcinogenic effects, including metabolic syndrome, wasting, and non-alcoholic fatty-liver disease (NAFLD). Previously, we reported decreases in the transcription of several enzymes involved in gluconeogenesis, before the early onset of lipid accumulation. Hence, this study was aimed at understanding the impact of resultant decreases gluconeogenic enzymes on growth, weight and metabolism in the liver, upon extended exposure. Male Sprague-Dawley rats (75-100 g), fed a...

Data from: Contemporaneous radiations of fungi and plants linked to symbiosis

François Lutzoni, Michael D. Nowak, Michael E. Alfaro, Valérie Reeb, Jolanta Miadlikowska, Michael Krug, A. Elizabeth Arnold, Louise A. Lewis, David L. Swofford, David Hibbett, Khidir Hilu, Timothy Y. James, Dietmar Quandt & Susana Magallón
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma),...

Data from: Recalibrating timing behavior via expected covariance between temporal cues

Benjamin J. De Corte, Rebecca R. Della Valle & Matthew S. Matell
Individuals must predict future events to proactively guide their behavior. Predicting when events will occur is a critical component of these expectations. Temporal expectations are often generated based on individual cue-duration relationships. However, the durations associated with different environmental cues will often co-vary due to a common cause. We show that timing behavior may be calibrated based on this expected covariance, which we refer to as the 'common cause hypothesis'. In five experiments using rats,...

Limits of quantification for individual PCB congeners obtained from 6 blank LDPEs analyzed as samples

Andres Martinez, Andrew M Awad, Nicholas J Herkert & Keri C Hornbuckle
Determination of LOQ for individual PCB congeners obtained from 6 blank LDPEs analyzed as samples. LOQ calculated from the upper 95% confidence interval.

Fraction of equilibrium for individual PCB congener between LDPE and water

Andres Martinez, Andrew M Awad, Nicholas J Herkert & Keri C Hornbuckle

PCB fugacity water-air ratio obtained using passive samplers in IHSC

Andres Martinez, Andrew M Awad, Nicholas J Herkert & Keri C Hornbuckle

Data from: Postconvulsive central apnea as a biomarker for sudden unexpected death in epilepsy (SUDEP)

Laura Vilella, Nuria Lacuey, Johnson P. Hampson, M.R. Sandhya Rani, Rup K. Sanju, Daniel Friedman, Maromi Nei, Kingman Strohl, Catherine Scott, Brian K. Gehlbach, Bilal Zony, Norma J. Hupp, Anita Zaremba, Nassim Shafiabadi, Xihue Zhao, Victoria Reick-Mitrisin, Stephan Schuele, Jennifer Ogren, Ronald M. Harper, Beate Diehl, Lisa Bateman, Orrin Devinsky, George B. Richerson, Philippe Ryvlin & Samden D. Lhatoo
Objective: To characterize peri-ictal apnea and post-ictal asystole in generalized convulsive seizures (GCS) of intractable epilepsy. Methods: Prospective, multi-center epilepsy monitoring study of autonomic and breathing biomarkers of SUDEP in patient’s ≥18 years old with intractable epilepsy and monitored GCS. Video EEG, thoraco-abdominal excursions, nasal airflow, capillary oxygen saturation and electrocardiography were analyzed. Results: We studied 148 GCS in 87 patients. Nineteen patients had generalized epilepsy, 65 had focal, one had both and in two,...

Data from: Camponotus floridanus ants incur a trade-off between phenotypic development and pathogen susceptibility from their mutualistic Endosymbiont Blochmannia

Veronica M. Sinotte, Samantha N. Freedman, Line V. Ugelvig, Marc A. Seid, Line Ugelvig, Samantha Freedman, Veronica Sinotte & Marc Seid
Various insects engage in microbial mutualisms in which the reciprocal benefits exceed the costs. Ants of the genus Camponotus benefit from nutrient supplementation by their mutualistic endosymbiotic bacteria, Blochmannia, but suffer a cost in tolerating and regulating the symbiont. This cost suggests that the ants face secondary consequences such as susceptibility to pathogenic infection and transmission. In order to elucidate the symbiont’s effects on development and disease defence, Blochmannia floridanus was reduced in colonies of...

Selected polychlorinated biphenyl congener in sediment Standard Reference Material 1994

Andres Martinez, Karin Norström, Kai Wang & Keri C Hornbuckle
Selected PCB congener in sediment Standard Reference Material 1994 using GC-MS/MS

Data from: Parasite resistance predicts fitness better than fecundity in a natural population of the freshwater snail Potamopyrgus antipodarum

Dorota Paczesniak, Kirsten Klappert, Kirstin Kopp, Maurine Neiman, Katri Seppälä, Curtis M. Lively & Jukka Jokela
The cost of males should give asexual females an advantage when in competition with sexual females. In addition, high-fecundity asexual genotypes should have an advantage over low-fecundity clones, leading to reduction in clonal diversity over time. To evaluate fitness components in a natural population, we measured the annual reproductive rate of individual sexual and asexual female Potamopyrgus antipodarum, a New Zealand freshwater snail, in field enclosures that excluded competitors and predators. We used allozyme genotyping...

MicroRNA quantitative RT-PCR analysis of CMT1A Plasma

John Svaren, Hongge Wang, Matthew Davison & Michael Shy
Objective: To determine if microRNA’s (miR) are elevated in the plasma of individuals affected by the inherited peripheral neuropathy Charcot-Marie-Tooth Disease, type 1A (CMT1A), miR profiling was employed to compare control and CMT1A plasma. Methods: We undertook a screen of CMT1A and control plasma samples to identify miRs that are elevated in CMT1A using a pilot screen of plasma miR by next generation sequencing, followed by validation of selected miRs by quantitative PCR, and correlation...

Distances, climatic differences, and vegetation similarities of alpine grasslands in Europe

George Malanson & Borja Jiménez-Alfaro
The importance of environmental difference among sites and dispersal limitations of species to the explanation of diversity differs among biological systems and geographical regions. We hypothesized that climate and then dispersal limitation will predominantly explain the similarity of alpine vegetation at increasing distances between pairs of regions at sub-continental extent. We computed the similarity of all pairs of 23 European mountain regions below 50°N after dividing the species lists of each region by calcareous or...

Individual PCB congener masses measured in 180 samples using polyurethane foam passive air samplers (PUF-PAS) in Chicago, Il

Andres Martinez, Nicholas J Herkert, Jacob C Jahnke & Keri C Hornbuckle
Individual PCB congener mass in PUF using passive air sampler (i.e., PUF-PAS) * Quantification and determination of individual PCB congeners using GC-MS/MS * Values = 0 indicates non-detected * No blank correction performed

Concentrations of individual polychlorinated biphenyl congeners in soils from East Chicago, Indiana, USA in 2017/2018

Andres Martinez, Jason Hua, Ezazul Haque, Peter Thorne & Keri C Hornbuckle
Individual polychlorinated biphenyls (PCBs) in surficial urban soil from East Chicago, Indiana, USA, were measured and reported here from thirty-three sites. Gas chromatography (GC) in tandem with Mass Spectrometry GC-MS/MS (Agilent 7000) in multiple reaction monitoring (MRM) mode was used to quantify all 209 congeners in 171 individual or coeluting congener peaks. The GC was equipped with a Supelco SBP-Octyl capillary column (30 m × 0.25 mm ID, 0.25 mm film thicknesses) with helium as...

Total organic carbon in soils from East Chicago, Indiana, USA in 2017/2018

Andres Martinez, Jason Hua, Ezazul Haque, Peter Thorne & Keri C Hornbuckle
The total organic carbon (TOC) content was analyzed for each sample, with the exception of 5 samples. A ceramic sample boat was filled with about 0.2 g of soil and combusted at 900 °C with a Shimadzu Total Organic Carbon Analyzer (TOC-V Series) and Solid Sample Module (SSM-5000A). The measured TOC was divided by the initial sample mass and reported as a percentage.

Additional file 1 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 1. Table S1: Patient demography.

Cannabidiol attenuates methamphetamine-induced conditioned place preference in male rats and viability in PC12 cells through the Sigma1R/AKT/GSK3β/CREB signaling pathway

Liu Liu, Juan Li, Chan Wang, Yue Xu, Chi-Kwan Leung, Genmeng Yang, Shucheng Lin, Shuwei Zhang, Yi Tan, Huijie Zhang, Haowei Wang, Jianxing Liu, Ming Li & Xiaofeng Zeng
Background: Methamphetamine use is associated with several negative consequences, including neurotoxicity and greater probability of exhibiting a substance use disorder. Sigma1 receptor is involved in the neurobiological basis of several drug use disorders. Cannabidiol has received attention in the treatment of drug use disorders and neurotoxicity. Objectives: To investigate the effects of cannabidiol on methamphetamine-induced conditioned place preference (CPP) and the viability of PC12 cells. Methods: Adult male rats (n = 70) underwent methamphetamine (2...

Additional file 2 of Vikrahraun—the 1961 basaltic lava flow eruption at Askja, Iceland: morphology, geochemistry, and planetary analogs

Aline Y. Blasizzo, Ingrid A. Ukstins, Stephen P. Scheidt, Alison H. Graettinger, David W. Peate, Tamara L. Carley, Adam J. Moritz & Jennifer E. Thines
Additional file 2: Textural data presented in this paper, including crystallinity, vesicularity, density, and viscosity calculations

Additional file 5 of Carbohydrates and ginsenosides in shenmai injection jointly improve hematopoietic function during chemotherapy-induced myelosuppression in mice

Shiyu Zhang, Yinxiao Mi, Tingting Ye, Xiaoyan Lu, Li Liu, Jing Qian & Xiaohui Fan
Additional file 5: Table S2. DEGs in Model, S+Rg, S, and Rg groups.

Additional file 6 of Carbohydrates and ginsenosides in shenmai injection jointly improve hematopoietic function during chemotherapy-induced myelosuppression in mice

Shiyu Zhang, Yinxiao Mi, Tingting Ye, Xiaoyan Lu, Li Liu, Jing Qian & Xiaohui Fan
Additional file 6: Table S3. Co-regulated DEGs among the three-treatment group and Model group.

Additional file 15 of A comprehensive pan-cancer analysis of necroptosis molecules in four gynecologic cancers

Jianfeng Zheng, Xintong Cai, Yu Zhang, Huihui Wang, Li Liu, Fengling Tang, Linying Liu & Yang Sun
Additional file 15: Supplementary Table 3. The results of Univariate Cox regression analysis for pan-cancer.

Silencing circular RNA circ_0054537 and upregulating microRNA-640 suppress malignant progression of renal cell carcinoma via regulating neuronal pentraxin-2 (NPTX2)

Long Pei, Xianqiang Lv, Gaopei Jia, Xiaoliang Tan, Ming Li & Aili Zhang
Hsa_circ_0054537 (circ_0054537) is a novel tumor-related circular RNA in renal cell carcinoma (RCC), and we intended to ascertain its dysregulation and functions in RCC malignant progression, as well as the underlying mechanism via serving as competing endogenous RNA (ceRNA). In this research, using real-time quantitative PCR, we found circ_0054537 was upregulated in RCC tissues and cells, and distributed throughout the cytoplasm. Then, functional effects of circ_0054537 in RCC were detected using cell counting kit-8, transwell,...

Data from: Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and D. santomea

Ana Llopart, Danielle Herrig, Evgeny Brud & Zachary Stecklein
Interspecific hybridization provides the unique opportunity for species to tap into genetic variation present in a closely related species and potentially take advantage of beneficial alleles. It has become increasingly clear that when hybridization occurs, mitochondrial DNA (mtDNA) often crosses species boundaries, raising the possibility that it could serve as a recurrent target of natural selection and source of species’ adaptations. Here we report the sequences of 46 complete mitochondrial genomes of Drosophila yakuba and...

Data from: Wide variation in ploidy level and genome size in a New Zealand freshwater snail with coexisting sexual and asexual lineages

Maurine Neiman, Dorota Paczesniak, Deanna M Soper, Austin T Baldwin & Gery Hehman
Natural animal populations are rarely screened for ploidy-level variation at a scale that allows detection of potentially important aberrations of common ploidy patterns. This type of screening can be especially important for the many mixed sexual/asexual systems where sexuals are presumed to be dioecious diploids and asexuals are assumed to be triploid and all-female. For example, elevation of ploidy level above triploidy can be a source of genetic variation and raises the possibility of gene...

Data from: The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.

David B Carlon, Ann F Budd, Catherine Lippé & Rose L Andrew
Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h²) in a suite of...

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