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BMC Biology

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https://www.readbyqxmd.com/read/28431535/ion-and-water-binding-sites-inside-an-occluded-hourglass-pore-of-a-trimeric-intracellular-cation-tric-channel
#1
Xiaomin Ou, Jianli Guo, Longfei Wang, Hanting Yang, Xiuying Liu, Jianyuan Sun, Zhenfeng Liu
BACKGROUND: Trimeric intracellular cation (TRIC) channels are crucial for Ca(2+) handling in eukaryotes and are involved in K(+) uptake in prokaryotes. Recent studies on the representative members of eukaryotic and prokaryotic TRIC channels demonstrated that they form homotrimeric units with the ion-conducting pores contained within each individual monomer. RESULTS: Here we report detailed insights into the ion- and water-binding sites inside the pore of a TRIC channel from Sulfolobus solfataricus (SsTRIC)...
April 22, 2017: BMC Biology
https://www.readbyqxmd.com/read/28395669/single-swim-sessions-in-c-elegans-induce-key-features-of-mammalian-exercise
#2
Ricardo Laranjeiro, Girish Harinath, Daniel Burke, Bart P Braeckman, Monica Driscoll
BACKGROUND: Exercise exerts remarkably powerful effects on metabolism and health, with anti-disease and anti-aging outcomes. Pharmacological manipulation of exercise benefit circuits might improve the health of the sedentary and the aging populations. Still, how exercised muscle signals to induce system-wide health improvement remains poorly understood. With a long-term interest in interventions that promote animal-wide health improvement, we sought to define exercise options for Caenorhabditis elegans...
April 10, 2017: BMC Biology
https://www.readbyqxmd.com/read/28385158/a-multi-animal-tracker-for-studying-complex-behaviors
#3
Eyal Itskovits, Amir Levine, Ehud Cohen, Alon Zaslaver
BACKGROUND: Animals exhibit astonishingly complex behaviors. Studying the subtle features of these behaviors requires quantitative, high-throughput, and accurate systems that can cope with the often rich perplexing data. RESULTS: Here, we present a Multi-Animal Tracker (MAT) that provides a user-friendly, end-to-end solution for imaging, tracking, and analyzing complex behaviors of multiple animals simultaneously. At the core of the tracker is a machine learning algorithm that provides immense flexibility to image various animals (e...
April 6, 2017: BMC Biology
https://www.readbyqxmd.com/read/28385155/oslg3-contributing-to-rice-grain-length-and-yield-was-mined-by-ho-lamap
#4
Jianping Yu, Haiyan Xiong, Xiaoyang Zhu, Hongliang Zhang, Huihui Li, Jinli Miao, Wensheng Wang, Zuoshun Tang, Zhanying Zhang, Guoxin Yao, Qiang Zhang, Yinghua Pan, Xin Wang, M A R Rashid, Jinjie Li, Yongming Gao, Zhikang Li, Weicai Yang, Xiangdong Fu, Zichao Li
BACKGROUND: Most agronomic traits in rice are complex and polygenic. The identification of quantitative trait loci (QTL) for grain length is an important objective of rice genetic research and breeding programs. RESULTS: Herein, we identified 99 QTL for grain length by GWAS based on approximately 10 million single nucleotide polymorphisms from 504 cultivated rice accessions (Oryza sativa L.), 13 of which were validated by four linkage populations and 92 were new loci for grain length...
April 6, 2017: BMC Biology
https://www.readbyqxmd.com/read/28372547/open-questions-tackling-darwin-s-instincts-the-genetic-basis-of-behavioral-evolution
#5
J Roman Arguello, Richard Benton
All of us have marveled at the remarkable diversity of animal behaviors in nature.None of us has much idea of how these have evolved.
April 3, 2017: BMC Biology
https://www.readbyqxmd.com/read/28372543/giardia-intestinalis-mitosomes-undergo-synchronized-fission-but-not-fusion-and-are-constitutively-associated-with-the-endoplasmic-reticulum
#6
Luboš Voleman, Vladimíra Najdrová, Ásgeir Ástvaldsson, Pavla Tůmová, Elin Einarsson, Zdeněk Švindrych, Guy M Hagen, Jan Tachezy, Staffan G Svärd, Pavel Doležal
BACKGROUND: Mitochondria of opisthokonts undergo permanent fission and fusion throughout the cell cycle. Here, we investigated the dynamics of the mitosomes, the simplest forms of mitochondria, in the anaerobic protist parasite Giardia intestinalis, a member of the Excavata supergroup of eukaryotes. The mitosomes have abandoned typical mitochondrial traits such as the mitochondrial genome and aerobic respiration and their single role known to date is the formation of iron-sulfur clusters...
April 3, 2017: BMC Biology
https://www.readbyqxmd.com/read/28356154/patterns-of-cross-contamination-in-a-multispecies-population-genomic-project-detection-quantification-impact-and-solutions
#7
Marion Ballenghien, Nicolas Faivre, Nicolas Galtier
BACKGROUND: Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing. RESULTS: Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected...
March 29, 2017: BMC Biology
https://www.readbyqxmd.com/read/28347335/triper-an-optical-probe-tuned-to-the-endoplasmic-reticulum-tracks-changes-in-luminal-h2o2
#8
Eduardo Pinho Melo, Carlos Lopes, Peter Gollwitzer, Stephan Lortz, Sigurd Lenzen, Ilir Mehmeti, Clemens F Kaminski, David Ron, Edward Avezov
BACKGROUND: The fate of hydrogen peroxide (H2O2) in the endoplasmic reticulum (ER) has been inferred indirectly from the activity of ER-localized thiol oxidases and peroxiredoxins, in vitro, and the consequences of their genetic manipulation, in vivo. Over the years hints have suggested that glutathione, puzzlingly abundant in the ER lumen, might have a role in reducing the heavy burden of H2O2 produced by the luminal enzymatic machinery for disulfide bond formation. However, limitations in existing organelle-targeted H2O2 probes have rendered them inert in the thiol-oxidizing ER, precluding experimental follow-up of glutathione's role in ER H2O2 metabolism...
March 27, 2017: BMC Biology
https://www.readbyqxmd.com/read/28335774/how-does-the-multifaceted-plant-hormone-salicylic-acid-combat-disease-in-plants-and-are-similar-mechanisms-utilized-in-humans
#9
D'Maris Amick Dempsey, Daniel F Klessig
Salicylic acid (SA) is an important plant hormone that regulates many aspects of plant growth and development, as well as resistance to (a)biotic stress. Efforts to identify SA effector proteins have revealed that SA binds to and alters the activity of multiple plant proteins-this represents a shift from the paradigm that hormones mediate their functions via one or a few receptors. SA and its derivatives also have multiple targets in animals; some of these proteins, like their plant counterparts, are associated with pathological processes...
March 23, 2017: BMC Biology
https://www.readbyqxmd.com/read/28327131/transcriptome-analysis-of-pancreatic-cells-across-distant-species-highlights-novel-important-regulator-genes
#10
Estefania Tarifeño-Saldivia, Arnaud Lavergne, Alice Bernard, Keerthana Padamata, David Bergemann, Marianne L Voz, Isabelle Manfroid, Bernard Peers
BACKGROUND: Defining the transcriptome and the genetic pathways of pancreatic cells is of great interest for elucidating the molecular attributes of pancreas disorders such as diabetes and cancer. As the function of the different pancreatic cell types has been maintained during vertebrate evolution, the comparison of their transcriptomes across distant vertebrate species is a means to pinpoint genes under strong evolutionary constraints due to their crucial function, which have therefore preserved their selective expression in these pancreatic cell types...
March 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28327113/low-cell-number-single-tube-amplification-sta-of-total-rna-revealed-transcriptome-changes-from-pluripotency-to-endothelium
#11
Yi-Hsuan Lee, Ya-Wen Hsueh, Yao-Hung Peng, Kung-Chao Chang, Kuen-Jer Tsai, H Sunny Sun, Ih-Jen Su, Po-Min Chiang
BACKGROUND: In addition to messenger RNA (mRNA), noncoding RNAs (ncRNAs) are essential components in cellular machineries for translation and splicing. Besides their housekeeping functions, ncRNAs are involved in cell type-specific regulation of translation, mRNA stability, genome structure, and accessibility. To have a comprehensive understanding of the identities and functions of different cell types, a method to comprehensively quantify both mRNA and ncRNA in a sensitive manner is highly desirable...
March 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28320402/albugo-imposed-changes-to-tryptophan-derived-antimicrobial-metabolite-biosynthesis-may-contribute-to-suppression-of-non-host-resistance-to-phytophthora-infestans-in-arabidopsis-thaliana
#12
David C Prince, Ghanasyam Rallapalli, Deyang Xu, Henk-Jan Schoonbeek, Volkan Çevik, Shuta Asai, Eric Kemen, Neftaly Cruz-Mireles, Ariane Kemen, Khaoula Belhaj, Sebastian Schornack, Sophien Kamoun, Eric B Holub, Barbara A Halkier, Jonathan D G Jones
BACKGROUND: Plants are exposed to diverse pathogens and pests, yet most plants are resistant to most plant pathogens. Non-host resistance describes the ability of all members of a plant species to successfully prevent colonization by any given member of a pathogen species. White blister rust caused by Albugo species can overcome non-host resistance and enable secondary infection and reproduction of usually non-virulent pathogens, including the potato late blight pathogen Phytophthora infestans on Arabidopsis thaliana...
March 20, 2017: BMC Biology
https://www.readbyqxmd.com/read/28264718/exploring-the-floristic-diversity-of-tropical-africa
#13
Marc S M Sosef, Gilles Dauby, Anne Blach-Overgaard, Xander van der Burgt, Luís Catarino, Theo Damen, Vincent Deblauwe, Steven Dessein, John Dransfield, Vincent Droissart, Maria Cristina Duarte, Henry Engledow, Geoffrey Fadeur, Rui Figueira, Roy E Gereau, Olivier J Hardy, David J Harris, Janneke de Heij, Steven Janssens, Yannick Klomberg, Alexandra C Ley, Barbara A Mackinder, Pierre Meerts, Jeike L van de Poel, Bonaventure Sonké, Tariq Stévart, Piet Stoffelen, Jens-Christian Svenning, Pierre Sepulchre, Rainer Zaiss, Jan J Wieringa, Thomas L P Couvreur
BACKGROUND: Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa...
March 7, 2017: BMC Biology
https://www.readbyqxmd.com/read/28264673/the-important-challenge-of-quantifying-tropical-diversity
#14
EDITORIAL
Anne E Magurran
The tropics are the repository of much of the world's biodiversity, yet are undersampled relative to temperate regions. To help fill this knowledge gap, a paper in BMC Biology explores diversity patterns in tropical African plants, as revealed by the RAINBIO database. The paper documents spatial variation in diversity and data coverage, but also highlights the challenges faced in quantifying diversity patterns using data collated from a range of sources including herbaria.See research article: http://bmcbiol...
March 7, 2017: BMC Biology
https://www.readbyqxmd.com/read/28257642/meta-evaluation-of-meta-analysis-ten-appraisal-questions-for-biologists
#15
REVIEW
Shinichi Nakagawa, Daniel W A Noble, Alistair M Senior, Malgorzata Lagisz
Meta-analysis is a statistical procedure for analyzing the combined data from different studies, and can be a major source of concise up-to-date information. The overall conclusions of a meta-analysis, however, depend heavily on the quality of the meta-analytic process, and an appropriate evaluation of the quality of meta-analysis (meta-evaluation) can be challenging. We outline ten questions biologists can ask to critically appraise a meta-analysis. These questions could also act as simple and accessible guidelines for the authors of meta-analyses...
March 3, 2017: BMC Biology
https://www.readbyqxmd.com/read/28257634/structural-basis-for-potency-differences-between-gdf8-and-gdf11
#16
Ryan G Walker, Magdalena Czepnik, Erich J Goebel, Jason C McCoy, Ana Vujic, Miook Cho, Juhyun Oh, Senem Aykul, Kelly L Walton, Gauthier Schang, Daniel J Bernard, Andrew P Hinck, Craig A Harrison, Erik Martinez-Hackert, Amy J Wagers, Richard T Lee, Thomas B Thompson
BACKGROUND: Growth/differentiation factor 8 (GDF8) and GDF11 are two highly similar members of the transforming growth factor β (TGFβ) family. While GDF8 has been recognized as a negative regulator of muscle growth and differentiation, there are conflicting studies on the function of GDF11 and whether GDF11 has beneficial effects on age-related dysfunction. To address whether GDF8 and GDF11 are functionally identical, we compared their signaling and structural properties. RESULTS: Here we show that, despite their high similarity, GDF11 is a more potent activator of SMAD2/3 and signals more effectively through the type I activin-like receptor kinase receptors ALK4/5/7 than GDF8...
March 3, 2017: BMC Biology
https://www.readbyqxmd.com/read/28241828/population-genomics-reveals-that-an-anthropophilic-population-of-aedes-aegypti-mosquitoes-in-west-africa-recently-gave-rise-to-american-and-asian-populations-of-this-major-disease-vector
#17
Jacob E Crawford, Joel M Alves, William J Palmer, Jonathan P Day, Massamba Sylla, Ranjan Ramasamy, Sinnathamby N Surendran, William C Black, Arnab Pain, Francis M Jiggins
BACKGROUND: The mosquito Aedes aegypti is the main vector of dengue, Zika, chikungunya and yellow fever viruses. This major disease vector is thought to have arisen when the African subspecies Ae. aegypti formosus evolved from being zoophilic and living in forest habitats into a form that specialises on humans and resides near human population centres. The resulting domestic subspecies, Ae. aegypti aegypti, is found throughout the tropics and largely blood-feeds on humans. RESULTS: To understand this transition, we have sequenced the exomes of mosquitoes collected from five populations from around the world...
February 28, 2017: BMC Biology
https://www.readbyqxmd.com/read/28222723/rapid-precise-quantification-of-bacterial-cellular-dimensions-across-a-genomic-scale-knockout-library
#18
Tristan Ursell, Timothy K Lee, Daisuke Shiomi, Handuo Shi, Carolina Tropini, Russell D Monds, Alexandre Colavin, Gabriel Billings, Ilina Bhaya-Grossman, Michael Broxton, Bevan Emma Huang, Hironori Niki, Kerwyn Casey Huang
BACKGROUND: The determination and regulation of cell morphology are critical components of cell-cycle control, fitness, and development in both single-cell and multicellular organisms. Understanding how environmental factors, chemical perturbations, and genetic differences affect cell morphology requires precise, unbiased, and validated measurements of cell-shape features. RESULTS: Here we introduce two software packages, Morphometrics and BlurLab, that together enable automated, computationally efficient, unbiased identification of cells and morphological features...
February 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28196538/functional-studies-of-drosophila-zinc-transporters-reveal-the-mechanism-for-zinc-excretion-in-malpighian-tubules
#19
Sai Yin, Qiuhong Qin, Bing Zhou
BACKGROUND: Zinc is an essential metal involved in many physiological processes. Previous work has identified a set of zinc transporters involved in Drosophila dietary zinc absorption. However, zinc excretion and reabsorption, the other two important processes to maintain zinc homeostasis, are not as well understood. In this work, we screened all the potential zinc transporter Zip (SLC39) and ZnT (SLC30) members for their likely roles in zinc excretion in Malpighian tubules, an insect organ functionally analogous to mammalian kidneys...
February 14, 2017: BMC Biology
https://www.readbyqxmd.com/read/28196531/enhancing-circadian-clock-function-in-cancer-cells-inhibits-tumor-growth
#20
Silke Kiessling, Lou Beaulieu-Laroche, Ian D Blum, Dominic Landgraf, David K Welsh, Kai-Florian Storch, Nathalie Labrecque, Nicolas Cermakian
BACKGROUND: Circadian clocks control cell cycle factors, and circadian disruption promotes cancer. To address whether enhancing circadian rhythmicity in tumor cells affects cell cycle progression and reduces proliferation, we compared growth and cell cycle events of B16 melanoma cells and tumors with either a functional or dysfunctional clock. RESULTS: We found that clock genes were suppressed in B16 cells and tumors, but treatments inducing circadian rhythmicity, such as dexamethasone, forskolin and heat shock, triggered rhythmic clock and cell cycle gene expression, which resulted in fewer cells in S phase and more in G1 phase...
February 14, 2017: BMC Biology
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