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Communicative & Integrative Biology

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https://www.readbyqxmd.com/read/29149223/two-genetic-codes-repetitive-syntax-for-active-non-coding-rnas-non-repetitive-syntax-for-the-dna-archives
#1
Guenther Witzany
Current knowledge of the RNA world indicates 2 different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share-as main characteristics-a non-repetitive syntax. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their syntax structure are coherent with the differences of the functions they represent...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28919941/a-test-of-the-submentalizing-hypothesis-apes-performance-in-a-false-belief-task-inanimate-control
#2
Christopher Krupenye, Fumihiro Kano, Satoshi Hirata, Josep Call, Michael Tomasello
Much debate concerns whether any nonhuman animals share with humans the ability to infer others' mental states, such as desires and beliefs. In a recent eye-tracking false-belief task, we showed that great apes correctly anticipated that a human actor would search for a goal object where he had last seen it, even though the apes themselves knew that it was no longer there. In response, Heyes proposed that apes' looking behavior was guided not by social cognitive mechanisms but rather domain-general cueing effects, and suggested the use of inanimate controls to test this alternative submentalizing hypothesis...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28919940/calcitox-aging-counterbalanced-by-endogenous-farnesol-like-sesquiterpenoids-an-undervalued-evolutionarily-ancient-key-signaling-pathway
#3
Arnold De Loof
Cells are powerful miniature electrophoresis chambers, at least during part of their life cycle. They die at the moment the voltage gradient over their plasma membrane, and their ability to drive a self-generated electric current carried by inorganic ions through themselves irreversibly collapses. Senescence is likely due to the progressive, multifactorial damage to the cell's electrical system. This is the essence of the "Fading electricity theory of aging" (De Loof et al., Aging Res. Rev. 2013;12:58-66)...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28919939/sequence-and-biochemical-analysis-of-arabidopsis-sp1-protein-a-regulator-of-organelle-biogenesis
#4
Ronghui Pan, Jianping Hu
Peroxisomes, chloroplasts, and mitochondria are essential eukaryotic organelles that host a suite of metabolic processes crucial to energy metabolism and development. Regulatory mechanisms of the dynamics and biogenesis of these important organelles have begun to be discovered in plants. We recently showed that, aside from its previously reported role in targeting chloroplast protein import proteins, the Arabidopsis ubiquitin E3 ligase SP1 (suppressor of ppi1 locus1) negatively regulates peroxisome matrix protein import by promoting the ubiquitination and destabilization of PEX13 and possibly PEX14 and other components of the peroxisome protein import apparatus...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28919938/keep-it-on-the-edge-the-post-mitotic-midbody-as-a-polarity-signal-unit
#5
Pablo Lujan, Teresa Rubio, Giulia Varsano, Maja Köhn
The maintenance of the epithelial architecture during tissue proliferation is achieved by apical positioning of the midbody after cell division. Consequently, midbody mislocalization contributes to epithelial architecture disruption, a fundamental event during epithelial tumorigenesis. Studies in 3D polarized epithelial MDCK or Caco2 cell models, where midbody misplacement leads to multiple ectopic but fully polarized lumen-containing cysts, revealed that this phenotype can be caused by 2 different scenarios: the loss of mitotic spindle orientation or the loss of asymmetric abscission...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28919937/gene-meter-accurate-abundance-calculations-of-gene-expression
#6
Alexander E Pozhitkov, Peter A Noble
We previously reported that thousands of transcripts in the mouse and zebrafish significantly increased in abundance in a time series spanning from life to several days after death. Transcript abundances were determined by: calibrating each microarray probe using a dilution series of pooled RNAs, fitting the probe-responses to adsorption models, and back-calculating abundances using the probe signal intensity of a sample and the best fitting model. The accuracy of the abundance measurements was not assessed in our previous study because individual transcript concentrations in the calibration pool were not known...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28702129/immunogold-em-analysis-reveal-brefeldin-a-sensitive-clusters-of-auxin-in-arabidopsis-root-apex-cells
#7
U Mettbach, M Strnad, S Mancuso, F Baluška
Immunogold electron microscopy (EM) study of Arabidopsis root apices analyzed using specific IAA antibody and high-pressure freeze fixation technique allowed, for the first time, vizualization of subcellular localization of IAA in cells assembled intactly within plant tissues. Our quantitative analysis reveals that there is considerable portion of IAA gold particles that clusters within vesicles and membraneous compartments in all root apex cells. There are clear tissue-specific and developmental differences of clustered IAA in root apices...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28702128/a-novel-host-factor-for-human-respiratory-syncytial-virus
#8
COMMENT
Masfique Mehedi, Peter L Collins, Ursula J Buchholz
Human respiratory syncytial virus (RSV) is the leading viral cause of severe lower respiratory disease in young children worldwide. As part of a genome-wide siRNA screen, we recently discovered that actin-related protein 2 (ARP2) is a host factor in the RSV replication cycle. ARP2 is a major constituent of the ARP2/3 complex, which catalyzes actin polymerization involved in cell morphology and motility. In the course of investigating this finding, we also found that RSV infection of human lung epithelial A459 cells induced filopodia formation and stimulated cell motility...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28702127/coordinating-heart-morphogenesis-a-novel-role-for-hyperpolarization-activated-cyclic-nucleotide-gated-hcn-channels-during-cardiogenesis-in-xenopus-laevis
#9
Emily Pitcairn, Hannah Harris, Justine Epiney, Vaibhav P Pai, Joan M Lemire, Bin Ye, Nian-Qing Shi, Michael Levin, Kelly A McLaughlin
Hyperpolarization-activated cyclic-nucleotide gated channel (HCN) proteins are important regulators of both neuronal and cardiac excitability. Among the 4 HCN isoforms, HCN4 is known as a pacemaker channel, because it helps control the periodicity of contractions in vertebrate hearts. Although the physiological role of HCN4 channel has been studied in adult mammalian hearts, an earlier role during embryogenesis has not been clearly established. Here, we probe the embryonic roles of HCN4 channels, providing the first characterization of the expression profile of any of the HCN isoforms during Xenopus laevis development and investigate the consequences of altering HCN4 function on embryonic pattern formation...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28702126/impairing-dna-methylation-obstructs-memory-enhancement-for-at-least-24%C3%A2-hours-in-lymnaea
#10
Cailin M Rothwell, Ken D Lukowiak
Stressor-induced memory enhancement has previously been shown to involve DNA methylation in the mollusc Lymnaea stagnalis. Specifically, injection of the DNA methylation inhibitor 5-AZA one hour before exposure to a memory-enhancing stressor obstructs memory augmentation. However, the duration of the influence of 5-AZA on this memory enhancement has not yet been examined. In this study, 2 memory-enhancing stressors (a thermal stress and exposure to the scent of a predator) were used to examine whether injection of the DNA methylation inhibitor 5-AZA 24 hours before stress exposure would still impair memory enhancement...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28702125/self-organizing-actin-patterns-shape-cytoskeletal-cortex-organization
#11
Marco Fritzsche
Living systems rely, for biological function, on the spatiotemporal organization of their structures. Cellular order naturally emerges by dissipation of energy. Consequently, energy-consuming processes operating far from thermodynamic equilibrium are a necessary condition to enable biological systems to respond to environmental cues that allow their transitions between different steady-states. Such self-organization was predicted for the actin cytoskeleton in theoretical considerations and has repeatedly been observed in cell-free systems...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28702124/6-hydroxy-5-nitrobenzo-d-oxazol-2-3h-one-a-degradable-derivative-of-natural-6-hydroxybenzoxazolin-2-3h-one-produced-by-pantoea-ananatis
#12
Margot Schulz, Dieter Sicker, Oliver Schackow, Lothar Hennig, Diana Hofmann, Ulrich Disko, Marina Ventura, Kateryna Basyuk
Pantoea ananatis is a bacterium associated with other microorganisms on Abutilon theophrasti Medik. roots. It converts 6-hydroxybenzoxazolin-2(3H)-one (BOA-6-OH), a hydroxylated derivative of the allelochemical benzoxazolin-2(3H)-one, into 6-hydroxy-5-nitrobenzo[d]oxazol-2(3H)-one. The compound was identified by NMR and mass spectrometric methods. In vitro synthesis succeeded with Pantoea protein, with isolated proteins from the Abutilon root surface or with horseradish peroxidase in the presence of nitrite and H2O2...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28702123/the-evolution-of-life-a-metadarwinian-integrative-approach
#13
Arnold De Loof
It is undeniably very logical to first formulate an unambiguous definition of "Life" before engaging in defining the parameters instrumental to Life's evolution. Because nearly everybody assumes, erroneously in my opinion, that catching Life's essence in a single sentence is impossible, this way of thinking remained largely unexplored in evolutionary theory. Upon analyzing what exactly happens at the transition from "still alive" to "just dead," the following definition emerged. What we call "Life" (L) is an activity...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28702122/gaba-signaling-stimulates-%C3%AE-cell-mediated-%C3%AE-like-cell-neogenesis
#14
Tiziana Napolitano, Fabio Avolio, Andhira Vieira, Nouha Ben-Othman, Monica Courtney, Elisabet Gjernes, Biljana Hadzic, Noémie Druelle, Sergi Navarro Sanz, Serena Silvano, Ahmed Mansouri, Patrick Collombat
Diabetes is a chronic and progressing disease, the number of patients increasing exponentially, especially in industrialized countries. Regenerating lost insulin-producing cells would represent a promising therapeutic alternative for most diabetic patients. To this end, using the mouse as a model, we reported that GABA, a food supplement, could induce insulin-producing beta-like cell neogenesis offering an attractive and innovative approach for diabetes therapeutics.
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28451059/eye-tracking-uncovered-great-apes-ability-to-anticipate-that-other-individuals-will-act-according-to-false-beliefs
#15
REVIEW
Fumihiro Kano, Christopher Krupenye, Satoshi Hirata, Josep Call
Using a novel eye-tracking test, we recently showed that great apes anticipate that other individuals will act according to false beliefs. This finding suggests that, like humans, great apes understand others' false beliefs, at least in an implicit way. One key question raised by our study is why apes have passed our tests but not previous ones. In this article, we consider this question by detailing the development of our task. We considered 3 major differences in our task compared with the previous ones. First, we monitored apes' eye movements, and specifically their anticipatory looks, to measure their predictions about how agents will behave...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28451058/specific-phospholipid-scramblases-are-involved-in-exposure-of-phosphatidylserine-an-eat-me-signal-for-phagocytes-on-degenerating-axons
#16
Shuji Wakatsuki, Toshiyuki Araki
Axonal degeneration is a key pathological feature of several neurological disorders. Emerging evidence has suggested a pathological connection between axonal degeneration and autophagy, a lysosomal degradation pathway. We recently reported that GSK3B-mediated phosphorylation of MCL1 regulates axonal autophagy to promote axonal degeneration. GSK3B-MCL1 pathway affects ATP production locally in degenerating axons and the exposure of phosphatidylserine (PS), an "eat-me" signal for phagocytes, on degenerating axons, resulting in the failed engulfment of axonal debris in vivo...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28451057/a-network-perspective-on-the-virus-world
#17
COMMENT
Jaime Iranzo, Mart Krupovic, Eugene V Koonin
Viral evolution is characterized by high rates of horizontal gene transfer and fast sequence divergence. Furthermore, there are no universal genes shared by all viruses. As a result, distant relationships among viruses are better represented by a network than by a tree. Here we discuss 3 network representations of the virus world with decreasing levels of complexity, from a multilayer network that integrates sequence conservation and patterns of gene sharing to a classic genome similarity network. As new tools for network analysis are developed, we expect that novel insights into virus evolution will result from the study of more complex representations of the virus world...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28451056/neutrophil-extracellular-trap-release-driven-by-bacterial-motility-relevance-to-cystic-fibrosis-lung-disease
#18
Balázs Rada
Neutrophil extracellular trap (NET) formation represents a unique effector function of neutrophils (PMN). The mechanism of NET release in response to bacteria is largely unknown. We studied the process by which Pseudomonas aeruginosa, an opportunistic pathogen, interacts with primary PMNs, and found that flagellar swimming motility of the bacterium is essential for inducing NET extrusion. Cystic fibrosis (CF) lung disease is associated with P. aeruginosa infection and PMN-dominated inflammation. Although NETs are abundant in CF airways, the main factors triggering NET release in CF remain unclear...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28451055/hierarchal-order-in-the-formation-of-chloroplast-division-machinery-in-the-red-alga-cyanidioschyzon-merolae
#19
COMMENT
Nobuko Sumiya, Shin-Ya Miyagishima
Chloroplasts have evolved from a cyanobacterial endosymbiont and multiply by dividing. Chloroplast division is performed by constriction of the ring-like protein complex (the PD machinery), which forms at the division site. The PD machinery is composed of cyanobacteria-descended components such as FtsZ and eukaryote-derived proteins such as the dynamin-related protein, DRP5B. In the red alga Cyanidioschyzon merolae, FtsZ ring formation on the stromal side precedes PDR1 and DRP5B ring formation on the cytosolic side...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28428832/a-meta-analysis-testing-eusocial-co-option-theories-in-termite-gut-physiology-and-symbiosis
#20
Michael E Scharf, Yunpeng Cai, Yijun Sun, Ruchira Sen, Rhitoban Raychoudhury, Drion G Boucias
The termite gut accomplishes key physiologic functions that underlie termite symbiosis and sociality. However, potential candidate functions of the host-symbiont holobiome have not yet been explored across seemingly divergent processes such as digestion, immunity, caste differentiation, and xenobiotic tolerance. This study took a meta-analysis approach for concurrently studying host and symbiont gut metatranscriptome responses of the lower termite Reticulitermes flavipes, which has ancestral characteristics and hosts a diverse mix of eukaryotic and bacterial symbionts...
2017: Communicative & Integrative Biology
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