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BMC Biology

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https://www.readbyqxmd.com/read/28222723/rapid-precise-quantification-of-bacterial-cellular-dimensions-across-a-genomic-scale-knockout-library
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/28196492/long-term-microfluidic-tracking-of-coccoid-cyanobacterial-cells-reveals-robust-control-of-division-timing
#4
Feiqiao Brian Yu, Lisa Willis, Rosanna Man Wah Chau, Alessandro Zambon, Mark Horowitz, Devaki Bhaya, Kerwyn Casey Huang, Stephen R Quake
BACKGROUND: Cyanobacteria are important agents in global carbon and nitrogen cycling and hold great promise for biotechnological applications. Model organisms such as Synechocystis sp. and Synechococcus sp. have advanced our understanding of photosynthetic capacity and circadian behavior, mostly using population-level measurements in which the behavior of individuals cannot be monitored. Synechocystis sp. cells are small and divide slowly, requiring long-term experiments to track single cells...
February 14, 2017: BMC Biology
https://www.readbyqxmd.com/read/28193269/how-flies-are-flirting-on-the-fly
#5
Courtney Eichorn, Michael Hrabar, Emma C Van Ryn, Bekka S Brodie, Adam J Blake, Gerhard Gries
BACKGROUND: Flies have some of the most elaborate visual systems in the Insecta, often featuring large, sexually dimorphic eyes with specialized "bright zones" that may have a functional role during mate-seeking behavior. The fast visual system of flies is considered to be an adaptation in support of their advanced flight abilities. Here, we show that the immense processing speed of the flies' photoreceptors plays a crucial role in mate recognition. RESULTS: Video-recording wing movements of abdomen-mounted common green bottle flies, Lucilia sericata, under direct light at 15,000 frames per second revealed that wing movements produce a single, reflected light flash per wing beat...
February 14, 2017: BMC Biology
https://www.readbyqxmd.com/read/28193262/nuclear-genetic-codes-with-a-different-meaning-of-the-uag-and-the-uaa-codon
#6
Tomáš Pánek, David Žihala, Martin Sokol, Romain Derelle, Vladimír Klimeš, Miluše Hradilová, Eliška Zadrobílková, Edward Susko, Andrew J Roger, Ivan Čepička, Marek Eliáš
BACKGROUND: Departures from the standard genetic code in eukaryotic nuclear genomes are known for only a handful of lineages and only a few genetic code variants seem to exist outside the ciliates, the most creative group in this regard. Most frequent code modifications entail reassignment of the UAG and UAA codons, with evidence for at least 13 independent cases of a coordinated change in the meaning of both codons. However, no change affecting each of the two codons separately has been documented, suggesting the existence of underlying evolutionary or mechanistic constraints...
February 13, 2017: BMC Biology
https://www.readbyqxmd.com/read/28193224/microrna-mir-29-controls-a-compensatory-response-to-limit-neuronal-iron-accumulation-during-adult-life-and-aging
#7
Roberto Ripa, Luca Dolfi, Marco Terrigno, Luca Pandolfini, Aurora Savino, Valeria Arcucci, Marco Groth, Eva Terzibasi Tozzini, Mario Baumgart, Alessandro Cellerino
BACKGROUND: A widespread modulation of gene expression occurs in the aging brain, but little is known as to the upstream drivers of these changes. MicroRNAs emerged as fine regulators of gene expression in many biological contexts and they are modulated by age. MicroRNAs may therefore be part of the upstream drivers of the global gene expression modulation correlated with aging and aging-related phenotypes. RESULTS: Here, we show that microRNA-29 (miR-29) is induced during aging in short-lived turquoise killifish brain and genetic antagonism of its function induces a gene-expression signature typical of aging...
February 13, 2017: BMC Biology
https://www.readbyqxmd.com/read/28193222/phosphorylation-dependent-regulation-of-aldh1a1-by-aurora-kinase-a-insights-on-their-synergistic-relationship-in-pancreatic-cancer
#8
Jing Wang, Kumar Nikhil, Keith Viccaro, Lei Chang, Jacoba White, Kavita Shah
BACKGROUND: Epithelial-to-mesenchymal transition (EMT) and cancer stem cell (CSC) formation are key underlying causes that promote extensive metastasis, drug resistance, and tumor recurrence in highly lethal pancreatic cancer. The mechanisms leading to EMT and CSC phenotypes are not fully understood, which has hindered the development of effective targeted therapies capable of improving treatment outcomes in patients with pancreatic cancer. RESULTS: We show a central role of Aurora kinase A (AURKA) in promoting EMT and CSC phenotypes via ALDH1A1, which was discovered as its direct substrate using an innovative chemical genetic screen...
February 13, 2017: BMC Biology
https://www.readbyqxmd.com/read/28173793/the-landscape-of-sex-differential-transcriptome-and-its-consequent-selection-in-human-adults
#9
Moran Gershoni, Shmuel Pietrokovski
BACKGROUND: The prevalence of several human morbid phenotypes is sometimes much higher than intuitively expected. This can directly arise from the presence of two sexes, male and female, in one species. Men and women have almost identical genomes but are distinctly dimorphic, with dissimilar disease susceptibilities. Sexually dimorphic traits mainly result from differential expression of genes present in both sexes. Such genes can be subject to different, and even opposing, selection constraints in the two sexes...
February 7, 2017: BMC Biology
https://www.readbyqxmd.com/read/28137258/ancient-coexistence-of-norepinephrine-tyramine-and-octopamine-signaling-in-bilaterians
#10
Philipp Bauknecht, Gáspár Jékely
BACKGROUND: Norepinephrine/noradrenaline is a neurotransmitter implicated in arousal and other aspects of vertebrate behavior and physiology. In invertebrates, adrenergic signaling is considered absent and analogous functions are performed by the biogenic amines octopamine and its precursor tyramine. These chemically similar transmitters signal by related families of G-protein-coupled receptors in vertebrates and invertebrates, suggesting that octopamine/tyramine are the invertebrate equivalents of vertebrate norepinephrine...
January 30, 2017: BMC Biology
https://www.readbyqxmd.com/read/28122620/the-golgin-coiled-coil-proteins-capture-different-types-of-transport-carriers-via-distinct-n-terminal-motifs
#11
Mie Wong, Alison K Gillingham, Sean Munro
BACKGROUND: The internal organization of cells depends on mechanisms to ensure that transport carriers, such as vesicles, fuse only with the correct destination organelle. Several types of proteins have been proposed to confer specificity to this process, and we have recently shown that a set of coiled-coil proteins on the Golgi, called golgins, are able to capture specific classes of carriers when relocated to an ectopic location. RESULTS: Mapping of six different golgins reveals that, in each case, a short 20-50 residue region is necessary and sufficient to capture specific carriers...
January 26, 2017: BMC Biology
https://www.readbyqxmd.com/read/28122559/search-strategy-is-regulated-by-somatostatin-signaling-and-deep-brain-photoreceptors-in-zebrafish
#12
Eric J Horstick, Yared Bayleyen, Jennifer L Sinclair, Harold A Burgess
BACKGROUND: Animals use sensory cues to efficiently locate resources, but when sensory information is insufficient, they may rely on internally coded search strategies. Despite the importance of search behavior, there is limited understanding of the underlying neural mechanisms in vertebrates. RESULTS: Here, we report that loss of illumination initiates sophisticated light-search behavior in larval zebrafish. Using three-dimensional tracking, we show that at the onset of darkness larvae swim in a helical trajectory that is spatially restricted in the horizontal plane, before gradually transitioning to an outward movement profile...
January 26, 2017: BMC Biology
https://www.readbyqxmd.com/read/28122547/amyloid-like-aggregation-of-provasopressin-in-diabetes-insipidus-and-secretory-granule-sorting
#13
Nicole Beuret, Franziska Hasler, Cristina Prescianotto-Baschong, Julia Birk, Jonas Rutishauser, Martin Spiess
BACKGROUND: Aggregation of peptide hormone precursors in the trans-Golgi network is an essential process in the biogenesis of secretory granules in endocrine cells. It has recently been proposed that this aggregation corresponds to the formation of functional amyloids. Our previous finding that dominant mutations in provasopressin, which cause cell degeneration and diabetes insipidus, prevent native folding and produce fibrillar aggregates in the endoplasmic reticulum (ER) might thus reflect mislocalized amyloid formation by sequences that evolved to mediate granule sorting...
January 26, 2017: BMC Biology
https://www.readbyqxmd.com/read/28100223/surface-attachment-promoted-by-the-actomyosin-system-of-toxoplasma-gondii-is-important-for-efficient-gliding-motility-and-invasion
#14
Jamie A Whitelaw, Fernanda Latorre-Barragan, Simon Gras, Gurman S Pall, Jacqueline M Leung, Aoife Heaslip, Saskia Egarter, Nicole Andenmatten, Shane R Nelson, David M Warshaw, Gary E Ward, Markus Meissner
BACKGROUND: Apicomplexan parasites employ a unique form of movement, termed gliding motility, in order to invade the host cell. This movement depends on the parasite's actomyosin system, which is thought to generate the force during gliding. However, recent evidence questions the exact molecular role of this system, since mutants for core components of the gliding machinery, such as parasite actin or subunits of the MyoA-motor complex (the glideosome), remain motile and invasive, albeit at significantly reduced efficiencies...
January 18, 2017: BMC Biology
https://www.readbyqxmd.com/read/28034300/frequency-of-influenza-h3n2-intra-subtype-reassortment-attributes-and-implications-of-reassortant-spread
#15
Irina Maljkovic Berry, Melanie C Melendrez, Tao Li, Anthony W Hawksworth, Gary T Brice, Patrick J Blair, Eric S Halsey, Maya Williams, Stefan Fernandez, In-Kyu Yoon, Leslie D Edwards, Robert Kuschner, Xiaoxu Lin, Stephen J Thomas, Richard G Jarman
BACKGROUND: Increasing evidence suggests that influenza reassortment not only contributes to the emergence of new human pandemics but also plays an important role in seasonal influenza epidemics, disease severity, evolution, and vaccine efficacy. We studied this process within 2091 H3N2 full genomes utilizing a combination of the latest reassortment detection tools and more conventional phylogenetic analyses. RESULTS: We found that the amount of H3N2 intra-subtype reassortment depended on the number of sampled genomes, occurred with a steady frequency of 3...
December 29, 2016: BMC Biology
https://www.readbyqxmd.com/read/28031029/quantifying-western-blots-none-more-black
#16
Graham Bell
Western blotting is among the most common techniques used in molecular biology and a simple way of assessing the presence or absence of a protein. It is also commonly used to compare protein levels in different conditions or in different tissues. This article illustrates some of the easy ways to arrive at a false conclusion when trying to quantify protein levels from western blots.
December 28, 2016: BMC Biology
https://www.readbyqxmd.com/read/28010727/quantitative-imaging-of-mammalian-transcriptional-dynamics-from-single-cells-to-whole-embryos
#17
REVIEW
Ziqing W Zhao, Melanie D White, Stephanie Bissiere, Valeria Levi, Nicolas Plachta
Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space...
December 23, 2016: BMC Biology
https://www.readbyqxmd.com/read/28010725/splendor-and-misery-of-adaptation-or-the-importance-of-neutral-null-for-understanding-evolution
#18
Eugene V Koonin
The study of any biological features, including genomic sequences, typically revolves around the question: what is this for? However, population genetic theory, combined with the data of comparative genomics, clearly indicates that such a "pan-adaptationist" approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection...
December 23, 2016: BMC Biology
https://www.readbyqxmd.com/read/28007032/q-a-what-are-brassinosteroids-and-how-do-they-act-in-plants
#19
Jiao Tang, Zhifu Han, Jijie Chai
Brassinosteroids (BRs) are a class of polyhydroxylated steroidal phytohormones in plants with similar structures to animals' steroid hormones. Brassinosteroids regulate a wide range of physiological processes including plant growth, development and immunity. Brassinosteroid signalling and its integration with other signalling pathways have been investigated thoroughly at the molecular level.
December 22, 2016: BMC Biology
https://www.readbyqxmd.com/read/28007029/arabidopsis-prc1-core-component-atring1-regulates-stem-cell-determining-carpel-development-mainly-through-repression-of-class-i-knox-genes
#20
Donghong Chen, Anne M Molitor, Lin Xu, Wen-Hui Shen
BACKGROUND: Polycomb repressive complex 2 (PRC2)-catalyzed H3K27me3 marks are tightly associated with the WUS-AG negative feedback loop to terminate floral stem cell fate to promote carpel development, but the roles of Polycomb repressive complex 1 (PRC1) in this event remain largely uncharacterized. RESULTS: Here we show conspicuous variability in the morphology and number of carpels among individual flowers in the absence of the PRC1 core components AtRING1a and AtRING1b, which contrasts with the wild-type floral meristem consumed by uniform carpel production in Arabidopsis thaliana...
December 22, 2016: BMC Biology
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