386 Works

Effects of primary seed dormancy on life-time fitness of Arabidopsis thaliana in the field

Jon Ågren
Background and Aims Seed dormancy determines the environmental niche of plants in seasonal environments, and has consequences for plant performance that potentially go far beyond the seed and seedling stages. In this study, we examined the cascading effects of seed dormancy on the expression of subsequent life-history traits and fitness in the annual herb Arabidopsis thaliana. Methods We planted seeds of >200 recombinant inbred lines (RIL) derived from a cross between two locally adapted populations...

Upstream stimulatory factor 2 (USF2) induced upregulation of triggering receptor expressed on myeloid cells 1 (TREM1) promotes endometritis by regulating toll-like receptor (TLR) 2/4-nuclear factor-kappaB (NF-κB) signaling pathway

Miao Zhang, Chengkun Yin, Yan Chen, Juan Wang & Jing Jiang
Triggering receptor expressed on myeloid cells 1 (TREM1) participates in the development of endometritis. This study aims at identifying the effects and interaction of TREM1 and upstream stimulatory factor 2 (USF2) in endometritis by using a model of lipopolysaccharide (LPS)-induced human endometrial epithelial cells (HEnEpCs). ELISA was performed to determine the levels of interleukin (IL)-6, IL-1β, and tumor necrosis factor (TNF-α) after LPS stimulation. TREM1 and USF2 expression was examined with RT-qPCR and Western blot....

Context dependent variation in corticosterone and phenotypic divergence of Rana arvalis populations along an acidification gradient

Katja Räsänen, Jelena Mausbach & Anssi Laurila
Background Physiological processes, as immediate responses to the environment, are important mechanisms of phenotypic plasticity and can influence evolution at ecological time scales. In stressful environments, physiological stress responses of individuals are initiated and integrated via the release of hormones, such as corticosterone (CORT). In vertebrates, CORT influences energy metabolism and resource allocation to multiple fitness traits (e.g. growth and morphology) and can be an important mediator of rapid adaptation to environmental stress, such as...

Circular RNA protein tyrosine kinase 2 (circPTK2) promotes colorectal cancer proliferation, migration, invasion and chemoresistance

Zhipeng Jiang, Zehui Hou, Wei Liu, Zhuomin Yu, Zhiqiang Liang & Shuang Chen
The dysregulated circular RNAs (circRNAs) are linked to progression and chemoresistance in colorectal cancer (CRC). However, the role of circRNA protein tyrosine kinase 2 (circPTK2) in CRC progression and chemoresistance is uncertain. The circPTK2, microRNA (miR)-136-5p, m6A ‘reader’ protein YTH domain family protein 1 (YTHDF1), β-catenin and cyclin D1 abundances were examined via quantitative reverse transcription PCR or Western blotting. The progression was investigated by cell counting kit-8 (CCK-8), colony formation, transwell and xenograft analysis....

Habitat shapes diversity of gut microbiomes in a wild population of blue tits Cyanistes caeruleus

Szymon Drobniak, Mariusz Cichoń, Katarzyna Janas, Julia Barczyk, Lars Gustafsson, Magdalena Zagalska-Neubauer, Szymon M. Drobniak & Magdalena Zagalska‐Neubauer
Microbiome constitutes and important axis of individual variation that, together with genes and the environment, influences an individual’s physiology and fitness. Microbiomes are dependent not only on an individual’s body condition but also on external factors, such as diet or stress levels, and as such can be involved into feedbacks between the external ecological factors and internal physiology. In our study we used a wild population of blue tits (Cyanistes caeruleus) to investigate the impact...

Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Hollis Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa Komoroske, Tanya Lama, Andrew Crawford, Robert Murphy, Samara Brown, Alan Scott, Phillip Morin, Erich Jarvis & Olivier Fedrigo
Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different...

Acetylation of SCFD1 regulates SNARE complex formation and autophagosome-lysosome fusion

Hong Huang, Qinqin Ouyang, Kunrong Mei, Ting Liu, Qiming Sun, Wei Liu & Rong Liu
SCFD1 (sec1 family domain containing 1) was recently shown to function in autophagosome-lysosome fusion, and multiple studies have demonstrated the regulatory impacts of acetylation (a post-translational modification) on macroautophagy/autophagy. Here, we demonstrate that both acetylation- and phosphorylation-dependent mechanisms control SCFD1ʹs function in autophagosome-lysosome fusion. After detecting a decrease in the extent of SCFD1 acetylation under autophagy-stimulated conditions, we found that KAT2B/PCAF catalyzes the acetylation of residues K126 and K515 of SCFD1; we also showed that...

Experimental sexual selection affects the evolution of physiological and life history traits

Martin D. Garlovsky, Luke Holman, Andrew L. Brooks, Rhonda R. Snook & Zorana K. Novicic
Sexual selection and sexual conflict are expected to affect all aspects of the phenotype, not only traits that are directly involved in reproduction. Here, we show coordinated evolution of multiple physiological and life history traits in response to long-term experimental manipulation of the mating system in populations of Drosophila pseudoobscura. Development time was extended under polyandry relative to monogamy in both sexes, potentially due to higher investment in traits linked to sexual selection and sexual...

Depletion, Density, and Deposits through the mantle transition zone (MTZ)

Thorsten Joachim Nagel , Anders Vesterholt & Christian Schiffer
We present phase diagrams of variously enriched and depleted mantle rocks down to 800 kilometers depth and explore density as the parameter governing convection and compositional stratification. Some results are surprising and not all are included in present concepts and models: (1) Primitive and enriched mantle compositions are buoyant in the uppermost lower mantle compared to depleted mantle, especially, when they are warmer, but also at identical temperatures. Hence, if the upper mantle is depleted...

ISIMIP2b Simulation Data from the Local Lakes Sector

Rafael Marcé, Donald Pierson, Daniel Mercado-Bettin, Wim Thiery, Sebastiano Piccolroaz, Bronwyn Woodward, Richard Iestyn Woolway, Zeli Tan, Georgiy Kirillin, Tom Shatwell, Raoul-Marie Couture, Marianne Côté, Damien Bouffard, Carl Love Mikael Råman Vinnå, Martin Schmid & Jacob Schewe
The Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) provides a framework for the collation of a set of consistent, multi-sector, multi-scale climate-impact simulations, based on scientifically and politically relevant historical and future scenarios. This framework serves as a basis for robust projections of climate impacts, as well as facilitating model evaluation and improvement, allowing for advanced estimates of the biophysical and socio-economic impacts of climate change at different levels of global warming. It also provides a...

ESR2 expression in subcutaneous adipose tissue is related to body fat distribution in women, and knockdown impairs preadipocyte differentiation

Fozia Ahmed, Susanne Hetty, Milica Vranic, Giovanni Fanni, Joel Kullberg, Maria João Pereira & Jan W Eriksson
Oestrogen receptor 2 (ESR2) expression has been shown to be higher in subcutaneous adipose tissue (SAT) from postmenopausal compared to premenopausal women. The functional significance of altered ESR2 expression is not fully known. This study investigates the role of ESR2 for adipose tissue lipid and glucose metabolism. SAT biopsies were obtained from 44 female subjects with or without T2D. Gene expression of ESR2 and markers of adipose function and metabolism was assessed. ESR2 knockdown was...

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Bilena L.B. Almeida, Mohamed N.M. Bahrudeen, Vatsala Chauhan, Suchintak Dash, Vinodh Kandavalli, Antti Häkkinen, Jason Lloyd-Price, Cristina S.D. Palma, Ines S.C. Baptista, Abhishekh Gupta, Juha Kesseli, Eric Dufour, Olli-Pekka Smolander, Matti Nykter, Petri Auvinen, Howard T. Jacobs, Samuel M.D. Oliveira & Andre S. Ribeiro
The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the...

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)

Stefan Prost, Ana Paula Machado, Julia Zumbroich, Lisa Preier, Sarita Mahtani-Williams, René Meißner, Katerina Guschanski, Jaelle C. Braeley, Carlos Rodriguez Fernandes, Paul Vercammen, Luke T. B. Hunter, Alexei V. Abramov, Martin Plasil, Petr Horin, Lena Godsall-Botriell, Paul Bottriell, Desire Lee Dalton, Antoinette Kotze & Pamela Burger
We live in a world characterised by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict, and illegal trafficking, there are only approximately...

Additional file 4 of Oxidative stress genes in patients with esophageal squamous cell carcinoma: construction of a novel prognostic signature and characterization of tumor microenvironment infiltration

Wei Liu, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng & Yi-Yan Lei
Additional file 4: Table S3. The results of univariate Cox proportional hazards regression analyses between clinical features and risk score in the training, testing, and entire sets.

Additional file 5 of Oxidative stress genes in patients with esophageal squamous cell carcinoma: construction of a novel prognostic signature and characterization of tumor microenvironment infiltration

Wei Liu, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng & Yi-Yan Lei
Additional file 5: Table S4. The results of univariate Cox proportional hazards regression analyses between clinical features and risk score in the training, testing, and entire sets.

Oxidative stress genes in patients with esophageal squamous cell carcinoma: construction of a novel prognostic signature and characterization of tumor microenvironment infiltration

Wei Liu, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng & Yi-Yan Lei
Abstract Background Oxidative stress plays an important role in the progression of various types of tumors. However, its role in esophageal squamous cell carcinoma (ESCC) has seldom been explored. This study aimed to discover prognostic markers associated with oxidative stress in ESCC to improve the prediction of prognosis and help in the selection of effective immunotherapy for patients. Results A consensus cluster was constructed using 14 prognostic differentially expressed oxidative stress-related genes (DEOSGs) that were...

Additional file 3 of Oxidative stress genes in patients with esophageal squamous cell carcinoma: construction of a novel prognostic signature and characterization of tumor microenvironment infiltration

Wei Liu, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng & Yi-Yan Lei
Additional file 3: Figure S1. (A, D, G) The heat map of 10 prognostic DEOSG expressions in the train (A), testing (D), and entire sets (G), respectively. (B, E, H) The comparison of 10 prognostic DEOSG expressions between high- and low-risk groups in the training (B), testing (E), and entire sets (H), respectively. (C, F, I) The correlations among 10 prognostic DEOSG between high- and low-risk groups in the training (C), testing (F), and entire...

Additional file 1 of Identification of HMGB2 associated with proliferation, invasion and prognosis in lung adenocarcinoma via weighted gene co-expression network analysis

Xie Qiu, Wei Liu, Yifan Zheng, Kai Zeng, Hao Wang, Haijun Sun & Jianhua Dai
Additional file 1: Table S1. Clinical informations and IHC score of patients with LUAD.

Additional file 2 of Identification of HMGB2 associated with proliferation, invasion and prognosis in lung adenocarcinoma via weighted gene co-expression network analysis

Xie Qiu, Wei Liu, Yifan Zheng, Kai Zeng, Hao Wang, Haijun Sun & Jianhua Dai
Additional file 2: Figure S1. Original blot and images. Figure S2. HMGB2 expression is not correlated with survival of patients with LUSC.

The Death Spiral of T Pyxidis

Joseph Patterson, Arto Oksanen, Berto Monard, Robert Rea, Franz-Josef Hambsch, Jennie McCormick, Peter Nelson, Jonathan Kemp, William Allen, Thomas Krajci, Simon Lowther, Shawn Dvorak, Thomas Richards, Gordon Myers & Greg Bolt
We report a long campaign to track the 1.8 hr photometric wave in the recurrent nova T Pyxidis, using the global telescope network of the Center for Backyard Astrophysics. During 1996-2011, that wave was highly stable in amplitude and waveform, resembling the orbital wave commonly seen in supersoft binaries. The period, however, was found to increase on a timescale P/P-dot=3x10^5 yr. This suggests a mass transfer rate of ~10^-7 M_sol/yr in quiescence. The orbital signal...

sj-pdf-1-cpj-10.1177_00099228221134441 – Supplemental material for Electrocardiographic QTc as a Surrogate Measure of Cardiac Risk in Children, Adolescents, and Young Adults With Eating Disorders

Perry B. Dinardo, Ellen S. Rome, Ira B. Taub, Wei Liu, Kenneth Zahka & Peter F. Aziz
Supplemental material, sj-pdf-1-cpj-10.1177_00099228221134441 for Electrocardiographic QTc as a Surrogate Measure of Cardiac Risk in Children, Adolescents, and Young Adults With Eating Disorders by Perry B. Dinardo, Ellen S. Rome, Ira B. Taub, Wei Liu, Kenneth Zahka and Peter F. Aziz in Clinical Pediatrics

Development of a theoretical model for the inhibition of nsP3 of Chikungunya virus using pyranooxazoles

Durgesh Kumar, Kamlesh Kumari, Abhilash Jayaraj & Prashant Singh
Chikungunya virus (CHIKV) causes Chikungunya fever (CHIKF) and till date no effective medicine for its cure is available in market. Different research groups find various possible interactions between small molecules and non-structural proteins, viz. nsP3, one of the most important viral elements in CHIKV. In this work, authors have studied the interactions of nsP3 of CHIKV with pyranooxazoles. Initially, a one-pot three-component reaction was designed using oxazolidine-2,4-dione, benzaldehyde and cyanoethylacetate to get a proposed biological...

Additional file 1 of MED12 mutation as a potential predictive biomarker for immune checkpoint inhibitors in pan-cancer

Yong Zhou, Yuan Tan, Qin Zhang, Qianqian Duan & Jun Chen
Additional file 1: Fig. S1. Flowchart of the study design. A. Merge of WES cohorts from five published studies (Hellman et al. [10], Rizvi et al. [11], Miao et al [12, 13], Allen et al. [14], Liu et al. [15]). B. MSKCC cohort from the published study (Samstein et al [16]). C. The TCGA dataset was used to perform DDR-related gene mutation, tumor-infiltrating immune cells and prognostic analyses.

Additional file 3 of MED12 mutation as a potential predictive biomarker for immune checkpoint inhibitors in pan-cancer

Yong Zhou, Yuan Tan, Qin Zhang, Qianqian Duan & Jun Chen
Additional file 3: Fig. S3. Kaplan–Meier curves of OS between the MED12-Mut and wildtype groups in the TCGA cohort.

Additional file 3 of MED12 mutation as a potential predictive biomarker for immune checkpoint inhibitors in pan-cancer

Yong Zhou, Yuan Tan, Qin Zhang, Qianqian Duan & Jun Chen
Additional file 3: Fig. S3. Kaplan–Meier curves of OS between the MED12-Mut and wildtype groups in the TCGA cohort.

Registration Year

  • 2022
    386

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Affiliations

  • Uppsala University
    386
  • Zhengzhou University
    130
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    122
  • Army Medical University
    119
  • Tongji University
    116
  • Central South University
    114
  • Capital Medical University
    114
  • Shandong Academy of Agricultural Sciences
    113
  • Fudan University
    112
  • Peking University
    99