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BMC Biology

Asghar M Razavi, George Khelashvili, Harel Weinstein
BACKGROUND: Much of the structure-based mechanistic understandings of the function of SLC6A neurotransmitter transporters emerged from the study of their bacterial LeuT-fold homologs. It has become evident, however, that structural differences such as the long N- and C-termini of the eukaryotic neurotransmitter transporters are involved in an expanded set of functional properties to the eukaryotic transporters. These functional properties are not shared by the bacterial homologs, which lack the structural elements that appeared later in evolution...
March 14, 2018: BMC Biology
Raphaël Méheust, Debashish Bhattacharya, Jananan S Pathmanathan, James O McInerney, Philippe Lopez, Eric Bapteste
BACKGROUND: Eukaryotes evolved from the symbiotic association of at least two prokaryotic partners, and a good deal is known about the timings, mechanisms, and dynamics of these evolutionary steps. Recently, it was shown that a new class of nuclear genes, symbiogenetic genes (S-genes), was formed concomitant with endosymbiosis and the subsequent evolution of eukaryotic photosynthetic lineages. Understanding their origins and contributions to eukaryogenesis would provide insights into the ways in which cellular complexity has evolved...
March 13, 2018: BMC Biology
Lael D Barlow, Eva Nývltová, Maria Aguilar, Jan Tachezy, Joel B Dacks
BACKGROUND: The Golgi apparatus is a central meeting point for the endocytic and exocytic systems in eukaryotic cells, and the organelle's dysfunction results in human disease. Its characteristic morphology of multiple differentiated compartments organized into stacked flattened cisternae is one of the most recognizable features of modern eukaryotic cells, and yet how this is maintained is not well understood. The Golgi is also an ancient aspect of eukaryotes, but the extent and nature of its complexity in the ancestor of eukaryotes is unclear...
March 7, 2018: BMC Biology
Virginia Tajadura-Ortega, Ritu Garg, Richard Allen, Claudia Owczarek, Michael D Bright, Samuel Kean, Aisyah Mohd-Noor, Anita Grigoriadis, Timothy C Elston, Klaus M Hahn, Anne J Ridley
BACKGROUND: Cell migration is essential for development and tissue repair, but it also contributes to disease. Rho GTPases regulate cell migration, but a comprehensive analysis of how each Rho signalling component affects migration has not been carried out. RESULTS: Through an RNA interference screen, and using a prostate cancer cell line, we find that approximately 25% of Rho network components alter migration. Some genes enhance migration while others decrease basal and/or hepatocyte growth factor-stimulated migration...
March 6, 2018: BMC Biology
Paul Simion, Khalid Belkhir, Clémentine François, Julien Veyssier, Jochen C Rink, Michaël Manuel, Hervé Philippe, Maximilian J Telford
BACKGROUND: Multiple RNA samples are frequently processed together and often mixed before multiplex sequencing in the same sequencing run. While different samples can be separated post sequencing using sample barcodes, the possibility of cross contamination between biological samples from different species that have been processed or sequenced in parallel has the potential to be extremely deleterious for downstream analyses. RESULTS: We present CroCo, a software package for identifying and removing such cross contaminants from assembled transcriptomes...
March 5, 2018: BMC Biology
Dana A Opulente, Emily J Rollinson, Cleome Bernick-Roehr, Amanda Beth Hulfachor, Antonis Rokas, Cletus P Kurtzman, Chris Todd Hittinger
BACKGROUND: Associations between traits are prevalent in nature, occurring across a diverse range of taxa and traits. Individual traits may co-evolve with one other, and these correlations can be driven by factors intrinsic or extrinsic to an organism. However, few studies, especially in microbes, have simultaneously investigated both across a broad taxonomic range. Here we quantify pairwise associations among 48 traits across 784 diverse yeast species of the ancient budding yeast subphylum Saccharomycotina, assessing the effects of phylogenetic history, genetics, and ecology...
March 2, 2018: BMC Biology
Gemma Navarro, Arnau Cordomí, Marc Brugarolas, Estefanía Moreno, David Aguinaga, Laura Pérez-Benito, Sergi Ferre, Antoni Cortés, Vicent Casadó, Josefa Mallol, Enric I Canela, Carme Lluís, Leonardo Pardo, Peter J McCormick, Rafael Franco
BACKGROUND: G-protein-coupled receptor (GPCR) heteromeric complexes have distinct properties from homomeric GPCRs, giving rise to new receptor functionalities. Adenosine receptors (A1 R or A2A R) can form A1 R-A2A R heteromers (A1 -A2A Het), and their activation leads to canonical G-protein-dependent (adenylate cyclase mediated) and -independent (β-arrestin mediated) signaling. Adenosine has different affinities for A1 R and A2A R, allowing the heteromeric receptor to detect its concentration by integrating the downstream Gi - and Gs -dependent signals...
February 28, 2018: BMC Biology
Longhua Guo, Alice Accorsi, Shuonan He, Carlos Guerrero-Hernández, Shamilene Sivagnanam, Sean McKinney, Matthew Gibson, Alejandro Sánchez Alvarado
BACKGROUND: The ability to efficiently visualize and manipulate chromosomes is fundamental to understanding the genome architecture of organisms. Conventional chromosome preparation protocols developed for mammalian cells and those relying on species-specific conditions are not suitable for many invertebrates. Hence, a simple and inexpensive chromosome preparation protocol, adaptable to multiple invertebrate species, is needed. RESULTS: We optimized a chromosome preparation protocol and applied it to several planarian species (phylum Platyhelminthes), the freshwater apple snail Pomacea canaliculata (phylum Mollusca), and the starlet sea anemone Nematostella vectensis (phylum Cnidaria)...
February 26, 2018: BMC Biology
Gordon J Berman
The need for high-throughput, precise, and meaningful methods for measuring behavior has been amplified by our recent successes in measuring and manipulating neural circuitry. The largest challenges associated with moving in this direction, however, are not technical but are instead conceptual: what numbers should one put on the movements an animal is performing (or not performing)? In this review, I will describe how theoretical and data analytical ideas are interfacing with recently-developed computational and experimental methodologies to answer these questions across a variety of contexts, length scales, and time scales...
February 23, 2018: BMC Biology
Mel Greaves
Paraphrasing Dobzhansky's famous dictum, I discuss how interrogating cancer through the lens of evolution has transformed our understanding of its development, causality and treatment resistance. The emerging picture of cancer captures its extensive diversity and therapeutic resilience, highlighting the need for more innovative approaches to control.
February 21, 2018: BMC Biology
Xingyun Qi, Keiko U Torii
Stomata are pores on plant epidermis that facilitate gas exchange and water evaporation between plants and the environment. Given the central role of stomata in photosynthesis and water-use efficiency, two vital events for plant growth, stomatal development is tightly controlled by a diverse range of signals. A family of peptide hormones regulates stomatal patterning and differentiation. In addition, plant hormones as well as numerous environmental cues influence the decision of whether to make stomata or not in distinct and complex manners...
February 20, 2018: BMC Biology
Thomas Stanislas, Matthieu Pierre Platre, Mengying Liu, Léa E S Rambaud-Lavigne, Yvon Jaillais, Olivier Hamant
BACKGROUND: In plants, the shoot apical meristem (SAM) has two main functions, involving the production of all aerial organs on the one hand and self-maintenance on the other, allowing the production of organs during the entire post-embryonic life of the plant. Transcription factors, microRNA, hormones, peptides and forces have been involved in meristem function. Whereas phosphatidylinositol phosphates (PIPs) have been involved in almost all biological functions, including stem cell maintenance and organogenesis in animals, the processes in meristem biology to which PIPs contribute still need to be delineated...
February 7, 2018: BMC Biology
Sarah C Pearce, Arwa Al-Jawadi, Kunihiro Kishida, Shiyan Yu, Madeleine Hu, Luke F Fritzky, Karen L Edelblum, Nan Gao, Ronaldo P Ferraris
BACKGROUND: Mammalian small intestinal tight junctions (TJ) link epithelial cells to one another and function as a permselective barrier, strictly modulating the passage of ions and macromolecules through the pore and leak pathways, respectively, thereby preventing the absorption of harmful compounds and microbes while allowing regulated transport of nutrients and electrolytes. Small intestinal epithelial permeability is ascribed primarily to the properties of TJs between adjoining enterocytes (ENTs), because there is almost no information on TJ composition and the paracellular permeability of nonenterocyte cell types that constitute a small but significant fraction of the intestinal epithelia...
February 1, 2018: BMC Biology
Matthew R Meiselman, Timothy G Kingan, Michael E Adams
BACKGROUND: Environmental stressors induce changes in endocrine state, leading to energy re-allocation from reproduction to survival. Female Drosophila melanogaster respond to thermal and nutrient stressors by arresting egg production through elevation of the steroid hormone ecdysone. However, the mechanisms through which this reproductive arrest occurs are not well understood. RESULTS: Here we report that stress-induced elevation of ecdysone is accompanied by decreased levels of ecdysis triggering hormone (ETH)...
January 30, 2018: BMC Biology
Meghan Lee Arnold, Ilija Melentijevic, Anna Joelle Smart, Monica Driscoll
Caenorhabditis elegans neurons have recently been found to throw out cellular debris for remote degradation and/or storage, adding an "extracellular garbage elimination" option to known intracellular protein and organelle degradation pathways. This Q&A describes initial insights into the biology of seemingly selective protein and organelle elimination by challenged neurons, highlighting mysteries of how garbage is distinguished and sorted in the sending neuron, how the garbage-filled "exophers" appear to elicit degradative responses as they transit neighboring tissue, and how non-digestible materials get thrown out of cells again via processes that may be highly relevant to human neurodegenerative disease mechanisms...
January 30, 2018: BMC Biology
Manfred Schartl, Susanne Schories, Yuko Wakamatsu, Yusuke Nagao, Hisashi Hashimoto, Chloé Bertin, Brigitte Mourot, Cornelia Schmidt, Dagmar Wilhelm, Lazaro Centanin, Yann Guiguen, Amaury Herpin
BACKGROUND: Sex determination relies on a hierarchically structured network of genes, and is one of the most plastic processes in evolution. The evolution of sex-determining genes within a network, by neo- or sub-functionalization, also requires the regulatory landscape to be rewired to accommodate these novel gene functions. We previously showed that in medaka fish, the regulatory landscape of the master male-determining gene dmrt1bY underwent a profound rearrangement, concomitantly with acquiring a dominant position within the sex-determining network...
January 29, 2018: BMC Biology
Irene Julca, Marina Marcet-Houben, Pablo Vargas, Toni Gabaldón
BACKGROUND: Polyploidization is one of the major evolutionary processes that shape eukaryotic genomes, being particularly common in plants. Polyploids can arise through direct genome doubling within a species (autopolyploidization) or through the merging of genomes from distinct species after hybridization (allopolyploidization). The relative contribution of both mechanisms in plant evolution is debated. Here we used phylogenomics to dissect the tempo and mode of duplications in the genome of the olive tree (Olea europaea), one of the first domesticated Mediterranean fruit trees...
January 25, 2018: BMC Biology
Nunu Mchedlishvili, Helen K Matthews, Adam Corrigan, Buzz Baum
BACKGROUND: Entry into mitosis triggers profound changes in cell shape and cytoskeletal organisation. Here, by studying microtubule remodelling in human flat mitotic cells, we identify a two-step process of interphase microtubule disassembly. RESULTS: First, a microtubule-stabilising protein, Ensconsin/MAP7, is inactivated in prophase as a consequence of its phosphorylation downstream of Cdk1/cyclin B. This leads to a reduction in interphase microtubule stability that may help to fuel the growth of centrosomally nucleated microtubules...
January 23, 2018: BMC Biology
Avi Leibovich, Hadas Kot-Leibovich, Danny Ben-Zvi, Abraham Fainsod
BACKGROUND: The bone morphogenetic protein (BMP) signaling gradient is central for dorsoventral patterning in amphibian embryos. This gradient is established through the interaction of several BMPs and BMP antagonists and modulators, some secreted by Spemann's organizer, a cluster of cells coordinating embryonic development. Anti-dorsalizing morphogenetic protein (ADMP), a BMP-like transforming growth factor beta ligand, negatively affects the formation of the organizer, although it is robustly expressed within the organizer itself...
January 22, 2018: BMC Biology
Fabian Moine, Julien Brechbühl, Monique Nenniger Tosato, Manon Beaumann, Marie-Christine Broillet
BACKGROUND: The mouse Grueneberg ganglion (GG) is an olfactory subsystem specialized in the detection of volatile heterocyclic compounds signalling danger. The signalling pathways transducing the danger signals are only beginning to be characterized. RESULTS: Screening chemical libraries for compounds structurally resembling the already-identified GG ligands, we found a new category of chemicals previously identified as bitter tastants that initiated fear-related behaviours in mice depending on their volatility and evoked neuronal responses in mouse GG neurons...
January 18, 2018: BMC Biology
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