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Biological evolution

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https://www.readbyqxmd.com/read/27936220/effects-of-ion-irradiation-on-seedlings-growth-monitored-by-ultraweak-delayed-luminescence
#1
Rosaria Grasso, Tomoko Abe, Giuseppe A P Cirrone, Giacomo Cuttone, Marisa Gulino, Francesco Musumeci, Francesco Romano, Hiromichi Ryuto, Agata Scordino
The optical technique based on the measurement of delayed luminescence emitted from the biological samples has demonstrated its ability to provide valid and predictive information on the functional status of various biological systems. We want to extend this technique to study the effect of ionizing radiation on biological systems. In particular we are interested in the action of ion beams, used for therapeutic purposes or to increase the biological diversity. In general, the assessment of the damage that radiation produces both in the target objects and in the surrounding tissues, requires considerable time because is based on biochemical analysis or on the examination of the evolution of the irradiated systems...
2016: PloS One
https://www.readbyqxmd.com/read/27935934/beyond-the-hypercube-evolutionary-accessibility-of-fitness-landscapes-with-realistic-mutational-networks
#2
Marcin Zagorski, Zdzislaw Burda, Bartlomiej Waclaw
Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27934853/clinical-and-biological-progress-over-50-years-in-rett-syndrome
#3
REVIEW
Helen Leonard, Stuart Cobb, Jenny Downs
In the 50 years since Andreas Rett first described the syndrome that came to bear his name, and is now known to be caused by a mutation in the methyl-CpG-binding protein 2 (MECP2) gene, a compelling blend of astute clinical observations and clinical and laboratory research has substantially enhanced our understanding of this rare disorder. Here, we document the contributions of the early pioneers in Rett syndrome (RTT) research, and describe the evolution of knowledge in terms of diagnostic criteria, clinical variation, and the interplay with other Rett-related disorders...
December 9, 2016: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/27933430/structural-dynamics-of-nucleosome-mediated-by-acetylations-at-h3k56-and-h3k115-122
#4
Muthukumaran Rajagopalan, Sangeetha Balasubramanian, Ilya Ioshikhes, Amutha Ramaswamy
Post translational modifications have a profound role in the regulation of several biological processes such as transcription, replication, and DNA repair. Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its structure. The effect of post translational modifications on nucleosome structure could be better explored when the molecular trajectories explaining the time dependent structural evolution over a period of time is examined at the atomic level...
December 8, 2016: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27932852/evolutionary-connectionism-algorithmic-principles-underlying-the-evolution-of-biological-organisation-in-evo-devo-evo-eco-and-evolutionary-transitions
#5
Richard A Watson, Rob Mills, C L Buckley, Kostas Kouvaris, Adam Jackson, Simon T Powers, Chris Cox, Simon Tudge, Adam Davies, Loizos Kounios, Daniel Power
The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation...
2016: Evolutionary Biology
https://www.readbyqxmd.com/read/27932023/molecular-cloning-and-expression-analysis-of-a-fish-specific-interferon-regulatory-factor-irf11-in-orange-spotted-grouper-epinephelus-coioides
#6
Wen Shu Huang, Mei Hua Zhu, Shan Chen, Zhi Xuan Wang, Ying Liang, Bei Huang, P Nie
Interferon regulatory factors (IRFs) are transcription mediators which play vital roles in multiple biological processes, such as antiviral defense, immune response, cell growth regulation and apoptosis. A fish specific IRF, termed IRF11, has been identified in previous study through searching fish genome databases. Herein, a transcript of IRF11, EcIRF11 was cloned from orange-spotted grouper, Epinephelus coioides. The EcIRF11 cDNA sequence has 1573 bp in length, encoding a putative protein of 261 amino acids, with a high degree of similarity found between EcIRF11 and its teleost counterparts...
December 5, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27931224/cyprinid-herpesvirus-3-and-its-evolutionary-future-as-a-biological-control-agent-for-carp-in-australia
#7
EDITORIAL
Kenneth A McColl, Agus Sunarto, Edward C Holmes
Biological invasions are a major threat to global biodiversity. Australia has experienced many invasive species, with the common carp (Cyprinus carpio L.) a prominent example. Cyprinid herpesvirus 3 (CyHV-3) has been proposed as a biological control (biocontrol) agent for invasive carp in Australia. Safety and efficacy are critical factors in assessing the suitability of biocontrol agents, and extensive host-specificity testing suggests that CyHV-3 is safe. Efficacy depends on the relationship between virus transmissibility and virulence...
December 8, 2016: Virology Journal
https://www.readbyqxmd.com/read/27930879/melanoma-exosomes-deliver-a-complex-biological-payload-that-upregulates-ptpn11-to-suppress-t-lymphocyte-function
#8
Yueting Wu, Wentao Deng, Emily Chambers McGinley, David J Klinke
As exosomes are emerging as a new mode of intercellular communication, we hypothesized that the payload contained within exosomes is shaped by somatic evolution. To test this, we assayed the impact on primary CD8+ T cell function, a key mechanism for anti-tumor immunity, of exosomes derived from three melanoma-related cell lines. While morphologically similar, exosomes from each cell line were functionally different, as B16F0 exosomes dose-dependently suppressed T cell proliferation. In contrast, Cloudman S91 exosomes promoted T cell proliferation and Melan-A exosomes had a negligible effect on primary CD8+ T cells...
December 8, 2016: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/27929068/evolution-of-the-net-noca-nlz-elbow-tlp-1-protein-family-in-metazoans-insights-from-expression-data-and-phylogenetic-analysis
#9
Filipe Pereira, Sara Duarte-Pereira, Raquel M Silva, Luís Teixeira da Costa, Isabel Pereira-Castro
The NET (for NocA, Nlz, Elbow, TLP-1) protein family is a group of conserved zinc finger proteins linked to embryonic development and recently associated with breast cancer. The members of this family act as transcriptional repressors interacting with both class I histone deacetylases and Groucho/TLE co-repressors. In Drosophila, the NET family members Elbow and NocA are vital for the development of tracheae, eyes, wings and legs, whereas in vertebrates ZNF703 and ZNF503 are important for the development of the nervous system, eyes and limbs...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27928450/lipoprotein-associated-phospholipase-a2-myeloperoxidase-and-vascular-endothelial-growth-factor-predictors-of-high-vascular-risk-in-respiratory-bacterial-infections
#10
Seri A, Marta Ds, Madalan A, Popescu M, Tiglea Ai, Moldoveanu E
Objective. Respiratory bacterial infections are associated with important coagulation disturbances that amplify the pulmonary lesions and determine a more severe course of the disease. The aim of our study was to investigate the correlation between the evolution of the general clinical parameters and the occurrence of thrombotic events on one side, and plasma levels of selected proteins involved in inflammation and coagulation on the other side, with the intent to establish and to validate a laboratory test panel for the assessment of the vascular risk in patients with bacterial respiratory infections...
October 2016: Journal of Medicine and Life
https://www.readbyqxmd.com/read/27927898/the-full-breadth-of-mendel-s-genetics
#11
Peter J van Dijk, T H Noel Ellis
Gregor Mendel's "Experiments on Plant Hybrids" (1865/1866), published 150 years ago, is without doubt one of the most brilliant works in biology. Curiously, Mendel's later studies on Hieracium (hawkweed) are usually seen as a frustrating failure, because it is assumed that they were intended to confirm the segregation ratios he found in Pisum Had this been his intention, such a confirmation would have failed, since, unknown to Mendel, Hieracium species mostly reproduce by means of clonal seeds (apomixis). Here we show that this assumption arises from a misunderstanding that could be explained by a missing page in Mendel's first letter to Carl Nägeli...
December 2016: Genetics
https://www.readbyqxmd.com/read/27923877/poison-and-alarm-the-asian-hornet-vespa-velutina-uses-sting-venom-volatiles-as-alarm-pheromone
#12
Ya-Nan Cheng, Ping Wen, Shi-Hao Dong, Ken Tan, James C Nieh
In colonial organisms, alarm pheromones can provide a key fitness advantage by enhancing colony defense and warning of danger. Learning which species use alarm pheromone and the key compounds involved therefore enhances our understanding of how this important signal has evolved. However, our knowledge of alarm pheromones is more limited in the social wasps and hornets as compared to the social bees and ants. Vespa velutina is an economically important and widespread hornet predator that attacks humans and honey bees...
December 6, 2016: Journal of Experimental Biology
https://www.readbyqxmd.com/read/27923679/evolutionary-scalpels-for-dissecting-tumor-ecosystems
#13
Daniel I S Rosenbloom, Pablo G Camara, Tim Chu, Raul Rabadan
Amidst the growing literature on cancer genomics and intratumor heterogeneity, essential principles in evolutionary biology recur time and time again. Here we use these principles to guide the reader through major advances in cancer research, highlighting issues of "hit hard, hit early" treatment strategies, drug resistance, and metastasis. We distinguish between two frameworks for understanding heterogeneous tumors, both of which can inform treatment strategies: (1) The tumor as diverse ecosystem, a Darwinian population of sometimes-competing, sometimes-cooperating cells; (2) The tumor as tightly integrated, self-regulating organ, which may hijack developmental signals to restore functional heterogeneity after treatment...
December 3, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27923053/different-evolutionary-paths-to-complexity-for-small-and-large-populations-of-digital-organisms
#14
Thomas LaBar, Christoph Adami
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for the emergence of novel traits, that is, the origination of complexity. Population size is one parameter that alters the relative importance of adaptive and non-adaptive processes: as population size decreases, selection weakens and genetic drift grows in importance...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27923045/tumor-evolution-in-two-patients-with-basal-like-breast-cancer-a-retrospective-genomics-study-of-multiple-metastases
#15
Katherine A Hoadley, Marni B Siegel, Krishna L Kanchi, Christopher A Miller, Li Ding, Wei Zhao, Xiaping He, Joel S Parker, Michael C Wendl, Robert S Fulton, Ryan T Demeter, Richard K Wilson, Lisa A Carey, Charles M Perou, Elaine R Mardis
BACKGROUND: Metastasis is the main cause of cancer patient deaths and remains a poorly characterized process. It is still unclear when in tumor progression the ability to metastasize arises and whether this ability is inherent to the primary tumor or is acquired well after primary tumor formation. Next-generation sequencing and analytical methods to define clonal heterogeneity provide a means for identifying genetic events and the temporal relationships between these events in the primary and metastatic tumors within an individual...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27922024/improvements-in-the-long-term-outcome-of-crohn-s-disease-over-the-past-two-decades-and-the-relation-to-changes-in-medical-management-results-from-the-population-based-ibdsl-cohort
#16
Steven F G Jeuring, Tim R A van den Heuvel, Limmie Y L Liu, Maurice P Zeegers, Wim H Hameeteman, Mariëlle J L Romberg-Camps, Liekele E Oostenbrug, Ad A M Masclee, Daisy M A E Jonkers, Marieke J Pierik
OBJECTIVES: Medical treatment options and strategies for Crohn's disease (CD) have changed over the past decades. To assess its impact, we studied the evolution of the long-term disease outcome in the Dutch Inflammatory Bowel Disease South Limburg (IBDSL) cohort. METHODS: In total, 1,162 CD patients were included. Three eras were distinguished: 1991-1998 (n=316), 1999-2005 (n=387), and 2006-2011 (n=459), and patients were followed until 2014. Medication exposure and the rates of hospitalization, surgery, and phenotype progression were estimated using Kaplan-Meier survival analyses and compared between eras by multivariable Cox regression models...
December 6, 2016: American Journal of Gastroenterology
https://www.readbyqxmd.com/read/27921363/morphomechanics-and-developmental-constraints-in-the-evolution-of-ammonites-shell-form
#17
Alexander Erlich, Derek E Moulton, Alain Goriely, Regis Chirat
The idea that physical processes involved in biological development underlie morphogenetic rules and channel morphological evolution has been central to the rise of evolutionary developmental biology. Here, we explore this idea in the context of seashell morphogenesis. We show that a morphomechanical model predicts the effects of variations in shell shape on the ornamental pattern in ammonites, a now extinct group of cephalopods with external chambered shell. Our model shows that several seemingly unrelated characteristics of synchronous, ontogenetic, intraspecific, and evolutionary variations in ornamental patterns among various ammonite species may all be understood from the fact that the mechanical forces underlying the oscillatory behavior of the shell secreting system scale with the cross-sectional curvature of the shell aperture...
December 6, 2016: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/27921292/cranial-joint-histology-in-the-mallard-duck-anas-platyrhynchos-new-insights-on-avian-cranial-kinesis
#18
Alida M Bailleul, Lawrence M Witmer, Casey M Holliday
The evolution of avian cranial kinesis is a phenomenon in part responsible for the remarkable diversity of avian feeding adaptations observable today. Although osteological, developmental and behavioral features of the feeding system are frequently studied, comparatively little is known about cranial joint skeletal tissue composition and morphology from a microscopic perspective. These data are key to understanding the developmental, biomechanical and evolutionary underpinnings of kinesis. Therefore, here we investigated joint microstructure in juvenile and adult mallard ducks (Anas platyrhynchos; Anseriformes)...
December 6, 2016: Journal of Anatomy
https://www.readbyqxmd.com/read/27920384/antibiotic-resistance-in-the-wild-an-eco-evolutionary-perspective
#19
REVIEW
Teppo Hiltunen, Marko Virta, Anna-Liisa Laine
The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920381/harvest-induced-evolution-insights-from-aquatic-and-terrestrial-systems
#20
REVIEW
Anna Kuparinen, Marco Festa-Bianchet
Commercial and recreational harvests create selection pressures for fitness-related phenotypic traits that are partly under genetic control. Consequently, harvesting can drive evolution in targeted traits. However, the quantification of harvest-induced evolutionary life history and phenotypic changes is challenging, because both density-dependent feedback and environmental changes may also affect these changes through phenotypic plasticity. Here, we synthesize current knowledge and uncertainties on six key points: (i) whether or not harvest-induced evolution is happening, (ii) whether or not it is beneficial, (iii) how it shapes biological systems, (iv) how it could be avoided, (v) its importance relative to other drivers of phenotypic changes, and (vi) whether or not it should be explicitly accounted for in management...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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