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PLoS Biology

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https://www.readbyqxmd.com/read/30231016/anthropoid-primate-specific-retroviral-element-the1b-controls-expression-of-crh-in-placenta-and-alters-gestation-length
#1
Caitlin E Dunn-Fletcher, Lisa M Muglia, Mihaela Pavlicev, Gernot Wolf, Ming-An Sun, Yueh-Chiang Hu, Elizabeth Huffman, Shivani Tumukuntala, Katri Thiele, Amrita Mukherjee, Sandra Zoubovsky, Xuzhe Zhang, Kayleigh A Swaggart, Katherine Y Bezold Lamm, Helen Jones, Todd S Macfarlan, Louis J Muglia
Pregnancy and parturition are intricately regulated to ensure successful reproductive outcomes. However, the factors that control gestational length in humans and other anthropoid primates remain poorly defined. Here, we show the endogenous retroviral long terminal repeat transposon-like human element 1B (THE1B) selectively controls placental expression of corticotropin-releasing hormone (CRH) that, in turn, influences gestational length and birth timing. Placental expression of CRH and subsequently prolonged gestational length were found in two independent strains of transgenic mice carrying a 180-kb human bacterial artificial chromosome (BAC) DNA that contained the full length of CRH and extended flanking regions, including THE1B...
September 19, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30226866/jagged1-notch2-controls-kidney-fibrosis-via-tfam-mediated-metabolic-reprogramming
#2
Shizheng Huang, Jihwan Park, Chengxiang Qiu, Kiwung Chung, Szu-Yuan Li, Yasemin Sirin, Seung Hyeok Han, Verdon Taylor, Ursula Zimber-Strobl, Katalin Susztak
While Notch signaling has been proposed to play a key role in fibrosis, the direct molecular pathways targeted by Notch signaling and the precise ligand and receptor pair that are responsible for kidney disease remain poorly defined. In this study, we found that JAG1 and NOTCH2 showed the strongest correlation with the degree of interstitial fibrosis in a genome-wide expression analysis of a large cohort of human kidney samples. Transcript analysis of mouse kidney disease models, including folic-acid (FA)-induced nephropathy, unilateral ureteral obstruction (UUO), or apolipoprotein L1 (APOL1)-associated kidney disease, indicated that Jag1 and Notch2 levels were higher in all analyzed kidney fibrosis models...
September 18, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30222734/eukref-phylogenetic-curation-of-ribosomal-rna-to-enhance-understanding-of-eukaryotic-diversity-and-distribution
#3
Javier Del Campo, Martin Kolisko, Vittorio Boscaro, Luciana F Santoferrara, Serafim Nenarokov, Ramon Massana, Laure Guillou, Alastair Simpson, Cedric Berney, Colomban de Vargas, Matthew W Brown, Patrick J Keeling, Laura Wegener Parfrey
Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity...
September 17, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30222731/destabilized-adaptive-influenza-variants-critical-for-innate-immune-system-escape-are-potentiated-by-host-chaperones
#4
Angela M Phillips, Anna I Ponomarenko, Kenny Chen, Orr Ashenberg, Jiayuan Miao, Sean M McHugh, Vincent L Butty, Charles A Whittaker, Christopher L Moore, Jesse D Bloom, Yu-Shan Lin, Matthew D Shoulders
The threat of viral pandemics demands a comprehensive understanding of evolution at the host-pathogen interface. Here, we show that the accessibility of adaptive mutations in influenza nucleoprotein at fever-like temperatures is mediated by host chaperones. Particularly noteworthy, we observe that the Pro283 nucleoprotein variant, which (1) is conserved across human influenza strains, (2) confers resistance to the Myxovirus resistance protein A (MxA) restriction factor, and (3) critically contributed to adaptation to humans in the 1918 pandemic influenza strain, is rendered unfit by heat shock factor 1 inhibition-mediated host chaperone depletion at febrile temperatures...
September 17, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30222729/morphology-of-mitochondria-in-spatially-restricted-axons-revealed-by-cryo-electron-tomography
#5
Tara D Fischer, Pramod K Dash, Jun Liu, M Neal Waxham
Neurons project axons to local and distal sites and can display heterogeneous morphologies with limited physical dimensions that may influence the structure of large organelles such as mitochondria. Using cryo-electron tomography (cryo-ET), we characterized native environments within axons and presynaptic varicosities to examine whether spatial restrictions within these compartments influence the morphology of mitochondria. Segmented tomographic reconstructions revealed distinctive morphological characteristics of mitochondria residing at the narrowed boundary between presynaptic varicosities and axons with limited physical dimensions (approximately 80 nm), compared to mitochondria in nonspatially restricted environments...
September 17, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30212465/integrative-proteomics-and-bioinformatic-prediction-enable-a-high-confidence-apicoplast-proteome-in-malaria-parasites
#6
Michael J Boucher, Sreejoyee Ghosh, Lichao Zhang, Avantika Lal, Se Won Jang, An Ju, Shuying Zhang, Xinzi Wang, Stuart A Ralph, James Zou, Joshua E Elias, Ellen Yeh
Malaria parasites (Plasmodium spp.) and related apicomplexan pathogens contain a nonphotosynthetic plastid called the apicoplast. Derived from an unusual secondary eukaryote-eukaryote endosymbiosis, the apicoplast is a fascinating organelle whose function and biogenesis rely on a complex amalgamation of bacterial and algal pathways. Because these pathways are distinct from the human host, the apicoplast is an excellent source of novel antimalarial targets. Despite its biomedical importance and evolutionary significance, the absence of a reliable apicoplast proteome has limited most studies to the handful of pathways identified by homology to bacteria or primary chloroplasts, precluding our ability to study the most novel apicoplast pathways...
September 13, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30208028/vocal-practice-regulates-singing-activity-dependent-genes-underlying-age-independent-vocal-learning-in-songbirds
#7
Shin Hayase, Hongdi Wang, Eri Ohgushi, Masahiko Kobayashi, Chihiro Mori, Haruhito Horita, Katsuhiko Mineta, Wan-Chun Liu, Kazuhiro Wada
The development of highly complex vocal skill, like human language and bird songs, is underlain by learning. Vocal learning, even when occurring in adulthood, is thought to largely depend on a sensitive/critical period during postnatal development, and learned vocal patterns emerge gradually as the long-term consequence of vocal practice during this critical period. In this scenario, it is presumed that the effect of vocal practice is thus mainly limited by the intrinsic timing of age-dependent maturation factors that close the critical period and reduce neural plasticity...
September 12, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30208022/protein-kinase-a-negatively-regulates-ca2-signalling-in-toxoplasma-gondii
#8
Alessandro D Uboldi, Mary-Louise Wilde, Emi A McRae, Rebecca J Stewart, Laura F Dagley, Luning Yang, Nicholas J Katris, Sanduni V Hapuarachchi, Michael J Coffey, Adele M Lehane, Cyrille Y Botte, Ross F Waller, Andrew I Webb, Malcolm J McConville, Christopher J Tonkin
The phylum Apicomplexa comprises a group of obligate intracellular parasites that alternate between intracellular replicating stages and actively motile extracellular forms that move through tissue. Parasite cytosolic Ca2+ signalling activates motility, but how this is switched off after invasion is complete to allow for replication to begin is not understood. Here, we show that the cyclic adenosine monophosphate (cAMP)-dependent protein kinase A catalytic subunit 1 (PKAc1) of Toxoplasma is responsible for suppression of Ca2+ signalling upon host cell invasion...
September 12, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30199532/transcriptional-outcomes-and-kinetic-patterning-of-gene-expression-in-response-to-nf-%C3%AE%C2%BAb-activation
#9
Mingming Zhao, Jaimy Joy, Weiqiang Zhou, Supriyo De, William H Wood, Kevin G Becker, Hongkai Ji, Ranjan Sen
Transcription factor nuclear factor kappa B (NF-κB) regulates cellular responses to environmental cues. Many stimuli induce NF-κB transiently, making time-dependent transcriptional outputs a fundamental feature of NF-κB activation. Here we show that NF-κB target genes have distinct kinetic patterns in activated B lymphoma cells. By combining RELA binding, RNA polymerase II (Pol II) recruitment, and perturbation of NF-κB activation, we demonstrate that kinetic differences amongst early- and late-activated RELA target genes can be understood based on chromatin configuration prior to cell activation and RELA-dependent priming, respectively...
September 10, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30169503/symptoms-of-systemic-lupus-erythematosus-are-diagnosed-in-leptin-transgenic-pigs
#10
Junchen Chen, Weiqi Zeng, Weirong Pan, Cong Peng, Jianglin Zhang, Juan Su, Weihu Long, Heng Zhao, Xiaoxia Zuo, Xiaoyun Xie, Jing Wu, Ling Nie, Hong-Ye Zhao, Hong-Jiang Wei, Xiang Chen
Leptin is a well-known adipokine that plays a critical role in immune responses. To further explore the immunological roles of leptin, we developed a transgenic leptin pig controlled by the pig leptin (pleptin) promoter to overexpress leptin. Symptoms typically associated with systemic lupus erythematosus (SLE) were evident in this transgenic pig strain, including anemia, leukopenia, and thrombocytopenia as well as kidney and liver impairment. Histologically, there were increased immunoglobulin G (IgG) levels, elevated antiplatelet antibody (APA) levels, and deposition of immune complexes in the kidney and liver...
August 31, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30231017/correction-comparative-genomics-and-the-nature-of-placozoan-species
#11
Michael Eitel, Warren R Francis, Frédérique Varoqueaux, Jean Daraspe, Hans-Jürgen Osigus, Stefan Krebs, Sergio Vargas, Helmut Blum, Gray A Williams, Bernd Schierwater, Gert Wörheide
[This corrects the article DOI: 10.1371/journal.pbio.2005359.].
September 2018: PLoS Biology
https://www.readbyqxmd.com/read/30226872/carnivore-conservation-needs-evidence-based-livestock-protection
#12
Lily M van Eeden, Ann Eklund, Jennifer R B Miller, José Vicente López-Bao, Guillaume Chapron, Mikael R Cejtin, Mathew S Crowther, Christopher R Dickman, Jens Frank, Miha Krofel, David W Macdonald, Jeannine McManus, Tara K Meyer, Arthur D Middleton, Thomas M Newsome, William J Ripple, Euan G Ritchie, Oswald J Schmitz, Kelly J Stoner, Mahdieh Tourani, Adrian Treves
Carnivore predation on livestock often leads people to retaliate. Persecution by humans has contributed strongly to global endangerment of carnivores. Preventing livestock losses would help to achieve three goals common to many human societies: preserve nature, protect animal welfare, and safeguard human livelihoods. Between 2016 and 2018, four independent reviews evaluated >40 years of research on lethal and nonlethal interventions for reducing predation on livestock. From 114 studies, we find a striking conclusion: scarce quantitative comparisons of interventions and scarce comparisons against experimental controls preclude strong inference about the effectiveness of methods...
September 2018: PLoS Biology
https://www.readbyqxmd.com/read/30226837/large-scale-investigation-of-the-reasons-why-potentially-important-genes-are-ignored
#13
Thomas Stoeger, Martin Gerlach, Richard I Morimoto, Luís A Nunes Amaral
Biomedical research has been previously reported to primarily focus on a minority of all known genes. Here, we demonstrate that these differences in attention can be explained, to a large extent, exclusively from a small set of identifiable chemical, physical, and biological properties of genes. Together with knowledge about homologous genes from model organisms, these features allow us to accurately predict the number of publications on individual human genes, the year of their first report, the levels of funding awarded by the National Institutes of Health (NIH), and the development of drugs against disease-associated genes...
September 2018: PLoS Biology
https://www.readbyqxmd.com/read/30226835/science-in-the-fight-to-uphold-the-rights-of-children
#14
Arthur L Caplan, Peter J Hotez
The United States is the only major nation to not yet have ratified the United Nations Convention on the Rights of the Child (UNCRC). Recently, there has been an erosion of the rights of children across America, Europe, and elsewhere, but through science, we may have an opportunity to counter some of this alarming trend. In the area of vaccines, the scientific community can raise its voice on the dangers that nonmedical exemptions and delays pose to children at risk for measles, influenza, and other childhood illnesses...
September 2018: PLoS Biology
https://www.readbyqxmd.com/read/30212454/correction-genome-sequence-of-the-pea-aphid-acyrthosiphon-pisum
#15
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pbio.1000313.].
September 2018: PLoS Biology
https://www.readbyqxmd.com/read/30212448/refined-rip-seq-protocol-for-epitranscriptome-analysis-with-low-input-materials
#16
Yong Zeng, Shiyan Wang, Shanshan Gao, Fraser Soares, Musadeqque Ahmed, Haiyang Guo, Miranda Wang, Junjie Tony Hua, Jiansheng Guan, Michael F Moran, Ming Sound Tsao, Housheng Hansen He
N6-Methyladenosine (m6A) accounts for approximately 0.2% to 0.6% of all adenosine in mammalian mRNA, representing the most abundant internal mRNA modifications. m6A RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-seq) is a powerful technique to map the m6A location transcriptome-wide. However, this method typically requires 300 μg of total RNA, which limits its application to patient tumors. In this study, we present a refined m6A MeRIP-seq protocol and analysis pipeline that can be applied to profile low-input RNA samples from patient tumors...
September 2018: PLoS Biology
https://www.readbyqxmd.com/read/30208026/lso2-is-a-conserved-ribosome-bound-protein-required-for-translational-recovery-in-yeast
#17
Yinuo J Wang, Pavanapuresan P Vaidyanathan, Maria F Rojas-Duran, Namrata D Udeshi, Kristen M Bartoli, Steven A Carr, Wendy V Gilbert
Ribosome-binding proteins function broadly in protein synthesis, gene regulation, and cellular homeostasis, but the complete complement of functional ribosome-bound proteins remains unknown. Using quantitative mass spectrometry, we identified late-annotated short open reading frame 2 (Lso2) as a ribosome-associated protein that is broadly conserved in eukaryotes. Genome-wide crosslinking and immunoprecipitation of Lso2 and its human ortholog coiled-coil domain containing 124 (CCDC124) recovered 25S ribosomal RNA in a region near the A site that overlaps the GTPase activation center...
September 2018: PLoS Biology
https://www.readbyqxmd.com/read/30208025/the-microbiome-and-the-human-a-reply-to-parke-and-colleagues
#18
Tobias Rees, Thomas Bosch, Angela E Douglas
No abstract text is available yet for this article.
September 2018: PLoS Biology
https://www.readbyqxmd.com/read/30208018/a-cautionary-note-for-claims-about-the-microbiome-s-impact-on-the-self
#19
Emily C Parke, Brett Calcott, Maureen A O'Malley
No abstract text is available yet for this article.
September 2018: PLoS Biology
https://www.readbyqxmd.com/read/30199530/copper-dependent-amino-oxidase-3-governs-selection-of-metabolic-fuels-in-adipocytes
#20
Haojun Yang, Martina Ralle, Michael J Wolfgang, Neha Dhawan, Jason L Burkhead, Susana Rodriguez, Jack H Kaplan, G William Wong, Norman Haughey, Svetlana Lutsenko
Copper (Cu) has emerged as an important modifier of body lipid metabolism. However, how Cu contributes to the physiology of fat cells remains largely unknown. We found that adipocytes require Cu to establish a balance between main metabolic fuels. Differentiating adipocytes increase their Cu uptake along with the ATP7A-dependent transport of Cu into the secretory pathway to activate a highly up-regulated amino-oxidase copper-containing 3 (AOC3)/semicarbazide-sensitive amine oxidase (SSAO); in vivo, the activity of SSAO depends on the organism's Cu status...
September 2018: PLoS Biology
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