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BMC Biology

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https://www.readbyqxmd.com/read/28629474/q-a-expansion-microscopy
#1
Ruixuan Gao, Shoh M Asano, Edward S Boyden
Expansion microscopy (ExM) is a recently invented technology that uses swellable charged polymers, synthesized densely and with appropriate topology throughout a preserved biological specimen, to physically magnify the specimen 100-fold in volume, or more, in an isotropic fashion. ExM enables nanoscale resolution imaging of preserved samples on inexpensive, fast, conventional microscopes. How does ExM work? How good is its performance? How do you get going on using it? In this Q&A, we provide the answers to these and other questions about this new and rapidly spreading toolbox...
June 19, 2017: BMC Biology
https://www.readbyqxmd.com/read/28619053/who-needs-registered-reports
#2
EDITORIAL
Miranda Robertson
Registered Reports, an article format initiated to help promote transparency and reproducibility in the preclinical and social sciences, are spreading into the biological literature. The format is now offered by BMC Biology, in a spirit of experiment.
June 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28599653/dynamics-of-transcriptional-re-programming-of-syncytial-nuclei-in-developing-muscles
#3
Laetitia Bataillé, Hadi Boukhatmi, Jean-Louis Frendo, Alain Vincent
BACKGROUND: A stereotyped array of body wall muscles enables precision and stereotypy of animal movements. In Drosophila, each syncytial muscle forms via fusion of one founder cell (FC) with multiple fusion competent myoblasts (FCMs). The specific morphology of each muscle, i.e. distinctive shape, orientation, size and skeletal attachment sites, reflects the specific combination of identity transcription factors (iTFs) expressed by its FC. Here, we addressed three questions: Are FCM nuclei naive? What is the selectivity and temporal sequence of transcriptional reprogramming of FCMs recruited into growing syncytium? Is transcription of generic myogenic and identity realisation genes coordinated during muscle differentiation? RESULTS: The tracking of nuclei in developing muscles shows that FCM nuclei are competent to be transcriptionally reprogrammed to a given muscle identity, post fusion...
June 9, 2017: BMC Biology
https://www.readbyqxmd.com/read/28595578/open-questions-completing-the-parts-list-and-finding-the-integrating-signals
#4
Aurelio A Teleman, Norbert Perrimon
One of the great revelations of post-genomic biology has been the extent to which essential functions and mechanisms are conserved across vast phylogenetic distances. Because of this, we can look to the fruit fly for answers to pressing open questions on the unknown functions of genes and the mechanisms of their physiological integration.
June 8, 2017: BMC Biology
https://www.readbyqxmd.com/read/28571576/matriptase-zymogen-supports-epithelial-development-homeostasis-and-regeneration
#5
Stine Friis, Daniel Tadeo, Sylvain M Le-Gall, Henrik Jessen Jürgensen, Katiuchia Uzzun Sales, Eric Camerer, Thomas H Bugge
BACKGROUND: Matriptase is a membrane serine protease essential for epithelial development, homeostasis, and regeneration, as well as a central orchestrator of pathogenic pericellular signaling in the context of inflammatory and proliferative diseases. Matriptase is an unusual protease in that its zymogen displays measurable enzymatic activity. RESULTS: Here, we used gain and loss of function genetics to investigate the possible biological functions of zymogen matriptase...
June 1, 2017: BMC Biology
https://www.readbyqxmd.com/read/28526034/differential-darc-ackr1-expression-distinguishes-venular-from-non-venular-endothelial-cells-in-murine-tissues
#6
Aude Thiriot, Carolina Perdomo, Guiying Cheng, Igor Novitzky-Basso, Sara McArdle, Jamie K Kishimoto, Olga Barreiro, Irina Mazo, Robinson Triboulet, Klaus Ley, Antal Rot, Ulrich H von Andrian
BACKGROUND: Intravascular leukocyte recruitment in most vertebrate tissues is restricted to postcapillary and collecting venules, whereas capillaries and arterioles usually support little or no leukocyte adhesion. This segmental restriction is thought to be mediated by endothelial, rather than hemodynamic, differences. The underlying mechanisms are largely unknown, in part because effective tools to distinguish, isolate, and analyze venular endothelial cells (V-ECs) and non-venular endothelial cells (NV-ECs) have been unavailable...
May 19, 2017: BMC Biology
https://www.readbyqxmd.com/read/28526029/cell-fixation-and-preservation-for-droplet-based-single-cell-transcriptomics
#7
Jonathan Alles, Nikos Karaiskos, Samantha D Praktiknjo, Stefanie Grosswendt, Philipp Wahle, Pierre-Louis Ruffault, Salah Ayoub, Luisa Schreyer, Anastasiya Boltengagen, Carmen Birchmeier, Robert Zinzen, Christine Kocks, Nikolaus Rajewsky
BACKGROUND: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not altered by stress or ageing. Other challenges are rare cells that need to be collected over several days or samples prepared at different times or locations. METHODS: Here, we used chemical fixation to address these problems...
May 19, 2017: BMC Biology
https://www.readbyqxmd.com/read/28514946/open-questions-we-don-t-really-know-anything-do-we-open-questions-in-sensory-biology
#8
Sönke Johnsen
Senses connect organisms to both the world and to each other, yet there is much we don't know about them. Using examples drawn primarily from the author's subfield of vision research, this article discusses five major open questions.
May 17, 2017: BMC Biology
https://www.readbyqxmd.com/read/28506280/optimouse-a-comprehensive-open-source-program-for-reliable-detection-and-analysis-of-mouse-body-and-nose-positions
#9
Yoram Ben-Shaul
BACKGROUND: Accurate determination of mouse positions from video data is crucial for various types of behavioral analyses. While detection of body positions is straightforward, the correct identification of nose positions, usually more informative, is far more challenging. The difficulty is largely due to variability in mouse postures across frames. RESULTS: Here, we present OptiMouse, an extensively documented open-source MATLAB program providing comprehensive semiautomatic analysis of mouse position data...
May 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28506236/knowing-where-the-nose-is
#10
LETTER
Winthrop F Gillis, Sandeep R Datta
Improvements in imaging technology and the development of powerful machine learning algorithms are revolutionizing the study of animal behavior in the laboratory. These innovations promise to reveal both global and local features of action relevant to understanding how the brain functions. A study in BMC Biology describes one such tool called OptiMouse, which is an open source platform that uses video to capture key features of mouse behavior, including information relevant to olfactory investigation.See research article: 10...
May 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28506231/optogenetic-interrogation-reveals-separable-g-protein-dependent-and-independent-signalling-linking-g-protein-coupled-receptors-to-the-circadian-oscillator
#11
Helena J Bailes, Nina Milosavljevic, Ling-Yu Zhuang, Elliot J Gerrard, Tomoki Nishiguchi, Takeaki Ozawa, Robert J Lucas
BACKGROUND: Endogenous circadian oscillators distributed across the mammalian body are synchronised among themselves and with external time via a variety of signalling molecules, some of which interact with G-protein-coupled receptors (GPCRs). GPCRs can regulate cell physiology via pathways originating with heterotrimeric G-proteins or β-arrestins. We applied an optogenetic approach to determine the contribution of these two signalling modes on circadian phase. RESULTS: We employed a photopigment (JellyOp) that activates Gαs signalling with better selectivity and higher sensitivity than available alternatives, and a point mutant of this pigment (F112A) biased towards β-arrestin signalling...
May 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28494792/heterosis-as-a-consequence-of-regulatory-incompatibility
#12
Rebecca H Herbst, Dana Bar-Zvi, Sharon Reikhav, Ilya Soifer, Michal Breker, Ghil Jona, Eyal Shimoni, Maya Schuldiner, Avraham A Levy, Naama Barkai
BACKGROUND: The merging of genomes in inter-specific hybrids can result in novel phenotypes, including increased growth rate and biomass yield, a phenomenon known as heterosis. Heterosis is typically viewed as the opposite of hybrid incompatibility. In this view, the superior performance of the hybrid is attributed to heterozygote combinations that compensate for deleterious mutations accumulating in each individual genome, or lead to new, over-dominating interactions with improved performance...
May 11, 2017: BMC Biology
https://www.readbyqxmd.com/read/28494759/time-resolved-dual-transcriptomics-reveal-early-induced-nicotiana-benthamiana-root-genes-and-conserved-infection-promoting-phytophthora-palmivora-effectors
#13
Edouard Evangelisti, Anna Gogleva, Thomas Hainaux, Mehdi Doumane, Frej Tulin, Clément Quan, Temur Yunusov, Kévin Floch, Sebastian Schornack
BACKGROUND: Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection...
May 11, 2017: BMC Biology
https://www.readbyqxmd.com/read/28482894/can-a-biologist-fix-a-smartphone-just-hack-it
#14
Sophien Kamoun
Biological systems integrate multiscale processes and networks and are, therefore, viewed as difficult to dissect. However, because of the clear-cut separation between the software code (the information encoded in the genome sequence) and hardware (organism), genome editors can operate as software engineers to hack biological systems without any particularly deep understanding of the complexity of the systems.
May 8, 2017: BMC Biology
https://www.readbyqxmd.com/read/28482888/noxious-gases-and-the-unpredictability-of-emerging-plant-pathogens-under-climate-change
#15
REVIEW
Helen N Fones, Sarah J Gurr
Emerging pathogens of crops threaten food security and are increasingly problematic due to intensive agriculture and high volumes of trade and transport in plants and plant products. The ability to predict pathogen risk to agricultural regions would therefore be valuable. However, predictions are complicated by multi-faceted relationships between crops, their pathogens, and climate change. Climate change is related to industrialization, which has brought not only a rise in greenhouse gas emissions but also an increase in other atmospheric pollutants...
May 8, 2017: BMC Biology
https://www.readbyqxmd.com/read/28476120/central-peptidergic-modulation-of-peripheral-olfactory-responses
#16
Sion Lee, Young-Joon Kim, Walton D Jones
BACKGROUND: Animal olfactory systems detect volatile environmental chemicals and integrate this information to direct the discovery of food and mates as well as danger avoidance. Rather than remaining constant, olfactory response thresholds are modulated by internal and external cues to adapt odor-guided behaviors to changing conditions. RESULTS: Here, we show in Drosophila melanogaster that neuropeptide F (NPF) modulates the responses of a specific population of antennal olfactory sensory neurons (OSNs) to food-derived odors...
May 5, 2017: BMC Biology
https://www.readbyqxmd.com/read/28464931/the-biological-function-of-the-cellular-prion-protein-an-update
#17
REVIEW
Marie-Angela Wulf, Assunta Senatore, Adriano Aguzzi
The misfolding of the cellular prion protein (PrP(C)) causes fatal neurodegenerative diseases. Yet PrP(C) is highly conserved in mammals, suggesting that it exerts beneficial functions preventing its evolutionary elimination. Ablation of PrP(C) in mice results in well-defined structural and functional alterations in the peripheral nervous system. Many additional phenotypes were ascribed to the lack of PrP(C), but some of these were found to arise from genetic artifacts of the underlying mouse models. Here, we revisit the proposed physiological roles of PrP(C) in the central and peripheral nervous systems and highlight the need for their critical reassessment using new, rigorously controlled animal models...
May 2, 2017: BMC Biology
https://www.readbyqxmd.com/read/28454545/cleavage-modification-did-not-alter-blastomere-fates-during-bryozoan-evolution
#18
Bruno C Vellutini, José M Martín-Durán, Andreas Hejnol
BACKGROUND: Stereotypic cleavage patterns play a crucial role in cell fate determination by precisely positioning early embryonic blastomeres. Although misplaced cell divisions can alter blastomere fates and cause embryonic defects, cleavage patterns have been modified several times during animal evolution. However, it remains unclear how evolutionary changes in cleavage impact the specification of blastomere fates. Here, we analyze the transition from spiral cleavage - a stereotypic pattern remarkably conserved in many protostomes - to a biradial cleavage pattern, which occurred during the evolution of bryozoans...
April 28, 2017: BMC Biology
https://www.readbyqxmd.com/read/28449681/fin-modules-an-evolutionary-perspective-on-appendage-disparity-in-basal-vertebrates
#19
Olivier Larouche, Miriam L Zelditch, Richard Cloutier
BACKGROUND: Fishes are extremely speciose and also highly disparate in their fin configurations, more specifically in the number of fins present as well as their structure, shape, and size. How they achieved this remarkable disparity is difficult to explain in the absence of any comprehensive overview of the evolutionary history of fish appendages. Fin modularity could provide an explanation for both the observed disparity in fin configurations and the sequential appearance of new fins...
April 27, 2017: BMC Biology
https://www.readbyqxmd.com/read/28431535/ion-and-water-binding-sites-inside-an-occluded-hourglass-pore-of-a-trimeric-intracellular-cation-tric-channel
#20
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
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