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Biological evolution

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https://www.readbyqxmd.com/read/28087932/the-complexity-of-fungal-vision
#1
Reinhard Fischer, Jesus Aguirre, Alfredo Herrera-Estrella, Luis M Corrochano
Life, as we know it, would not be possible without light. Light is not only a primary source of energy, but also an important source of information for many organisms. To sense light, only a few photoreceptor systems have developed during evolution. They are all based on an organic molecule with conjugated double bonds that allows energy transfer from visible (or UV) light to its cognate protein to translate the primary physical photoresponse to cell-biological actions. The three main classes of receptors are flavin-based blue-light, retinal-based green-light (such as rhodopsin), and linear tetrapyrrole-based red-light sensors...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087771/genome-wide-convergence-during-evolution-of-mangroves-from-woody-plants
#2
Shaohua Xu, Ziwen He, Zixiao Guo, Zhang Zhang, Gerald J Wyckoff, Anthony Greenberg, Chung-I Wu, Suhua Shi
When living organisms independently invade a new environment, the evolution of similar phenotypic traits is often observed. An interesting but contentious issue is whether the underlying molecular biology also converges in the new habitat. Independent invasions of tropical intertidal zones by woody plants, collectively referred to as mangrove trees, represent some dramatic examples. The high salinity, hypoxia and other stressors in the new habitat might have affected both genomic features and protein structures...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087495/comparative-analysis-of-variation-and-selection-in-the-hcv-genome
#3
Juan Ángel Patiño-Galindo, Fernando González-Candelas
Genotype 1 of the hepatitis C virus (HCV) is the most prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and CD8), and secondary protein structure...
January 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28087256/manganese-superoxide-dismutase-and-glutathione-peroxidase-1-contribute-to-the-rise-and-fall-of-mitochondrial-reactive-oxygen-species-which-drive-oncogenesis
#4
REVIEW
Dede N Ekoue, Chenxia He, Alan M Diamond, Marcelo G Bonini
Reactive oxygen species (ROS) largely originating in the mitochondria play essential roles in the metabolic and (epi)genetic reprogramming of cancer cell evolution towards more aggressive phenotypes. Recent studies have indicated that the activity of superoxide dismutase (SOD2) may promote tumor progression by serving as a source of hydrogen peroxide (H2O2). H2O2 is a form of ROS that is particularly active as a redox agent affecting cell signaling due to its ability to freely diffuse out of the mitochondria and alter redox active amino acid residues on regulatory proteins...
January 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28079112/microbes-can-help-explain-the-evolution-of-host-altruism
#5
Ohad Lewin-Epstein, Ranit Aharonov, Lilach Hadany
The evolution of altruistic behaviour, which is costly to the donor but beneficial for the recipient, is among the most intriguing questions in evolutionary biology. Several theories have been proposed to explain it, including kin selection, group selection and reciprocity. Here we propose that microbes that manipulate their hosts to act altruistically could be favoured by selection, and may play a role in the widespread occurrence of altruism. Using computational models, we find that microbe-induced altruism can explain the evolution of host altruistic behaviour under wider conditions than host-centred theories, including in a fully mixed host population, without repeating interactions or individual recognition...
January 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28078538/the-sleep-in-caenorhabditis-elegans-what-we-know-until-now
#6
REVIEW
Maryam Moosavi, Gholam Reza Hatam
Sleep, as one of the most important requirements of our brain, has a mystical nature. Despite long-standing studies, the molecular mechanisms and physiological properties of sleep have not been defined well as the complexity of the mammals' brain make it difficult to investigate the mechanisms and properties of sleep. Although some features of sleep have changed during evolution, its existence in such a simple animal, Caenorhabditis elegans, not only signifies the importance of sleep in even simple animals, but also allows the scientist to assess the core mechanism and biological events in an uncomplicated organism...
January 11, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28077462/bromodomains-in-protozoan-parasites-evolution-function-and-opportunities-for-drug-development
#7
REVIEW
Victoria Jeffers, Chunlin Yang, Sherri Huang, William J Sullivan
Parasitic infections remain one of the most pressing global health concerns of our day, affecting billions of people and producing unsustainable economic burdens. The rise of drug-resistant parasites has created an urgent need to study their biology in hopes of uncovering new potential drug targets. It has been established that disrupting gene expression by interfering with lysine acetylation is detrimental to survival of apicomplexan (Toxoplasma gondii and Plasmodium spp.) and kinetoplastid (Leishmania spp...
March 2017: Microbiology and Molecular Biology Reviews: MMBR
https://www.readbyqxmd.com/read/28077259/the-growth-of-language-universal-grammar-experience-and-principles-of-computation
#8
REVIEW
Charles Yang, Stephen Crain, Robert C Berwick, Noam Chomsky, Johan J Bolhuis
YANG, C., S. Crain, R.C. Berwick, N. Chomsky and J.J. Bolhuis. The growth of language. NEUROSCI BIOBEHAV REV VOL (ISSUE) XXX-XXX, 2016. Human infants develop language remarkably rapidly and without overt instruction. We argue that the distinctive ontogenesis of child language arises from the interplay of three factors: domain-specific principles of language (Universal Grammar), external experience, and properties of non-linguistic domains of cognition including general learning mechanisms and principles of efficient computation...
January 7, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28077082/the-arabidopsis-paralogs-pub46-and-pub48-encoding-u-box-e3-ubiquitin-ligases-are-essential-for-plant-response-to-drought-stress
#9
Guy Adler, Zvia Konrad, Lyad Zamir, Amit Kumar Mishra, Dina Raveh, Dudy Bar-Zvi
BACKGROUND: Plants respond to abiotic stress on physiological, biochemical and molecular levels. This includes a global change in their cellular proteome achieved by changes in the pattern of their protein synthesis and degradation. The ubiquitin-proteasome system (UPS) is a key player in protein degradation in eukaryotes. Proteins are marked for degradation by the proteasome by coupling short chains of ubiquitin polypeptides in a three-step pathway. The last and regulatory stage is catalyzed by a member of a large family of substrate-specific ubiquitin ligases...
January 11, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28076811/modeling-the-effect-of-curvature-on-the-collective-behavior-of-cells-growing-new-tissue
#10
Mohd Almie Alias, Pascal R Buenzli
The growth of several biological tissues is known to be controlled in part by local geometrical features, such as the curvature of the tissue interface. This control leads to changes in tissue shape that in turn can affect the tissue's evolution. Understanding the cellular basis of this control is highly significant for bioscaffold tissue engineering, the evolution of bone microarchitecture, wound healing, and tumor growth. Although previous models have proposed geometrical relationships between tissue growth and curvature, the role of cell density and cell vigor remains poorly understood...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28074220/biology-dynamics-and-applications-of-transposable-elements-in-basidiomycete-fungi
#11
REVIEW
Raúl Castanera, Alessandra Borgognone, Antonio G Pisabarro, Lucía Ramírez
The phylum Basidiomycota includes filamentous fungi and yeast species with different ecological and genomic characteristics. Transposable elements (TEs) are abundant components of most eukaryotic genomes, and their transition from being genomic parasites to key drivers of genomic architecture, functionality, and evolution is a subject receiving much attention. In light of the abundant genomic information released during the last decade, the aims of this mini-review are to discuss the dynamics and impact of TEs in basidiomycete fungi...
January 10, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28073890/pancreatic-cancer-cell-lines-as-patient-derived-avatars-genetic-characterisation-and-functional-utility
#12
Erik S Knudsen, Uthra Balaji, Brian Mannakee, Paris Vail, Cody Eslinger, Christopher Moxom, John Mansour, Agnieszka K Witkiewicz
OBJECTIVE: Pancreatic ductal adenocarcinoma (PDAC) is a therapy recalcitrant disease with the worst survival rate of common solid tumours. Preclinical models that accurately reflect the genetic and biological diversity of PDAC will be important for delineating features of tumour biology and therapeutic vulnerabilities. DESIGN: 27 primary PDAC tumours were employed for genetic analysis and development of tumour models. Tumour tissue was used for derivation of xenografts and cell lines...
January 10, 2017: Gut
https://www.readbyqxmd.com/read/28073551/the-common-bloom-forming-cyanobacterium-microcystis-is-prone-to-a-wide-array-of-microbial-antagonists
#13
REVIEW
Jeroen Van Wichelen, Pieter Vanormelingen, Geoffrey A Codd, Wim Vyverman
Many degraded waterbodies around the world are subject to strong proliferations of cyanobacteria - notorious for their toxicity, high biomass build-up and negative impacts on aquatic food webs - the presence of which puts serious limits on the human use of affected water bodies. Cyanobacterial blooms are largely regarded as trophic dead ends since they are a relatively poor food source for zooplankton. As a consequence, their population dynamics are generally attributed to changes in abiotic conditions (bottom-up control)...
May 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073449/harmful-algal-bloom-forecast-system-for-sw-ireland-part-ii-are-operational-oceanographic-models-useful-in-a-hab-warning-system
#14
Caroline Cusack, Tomasz Dabrowski, Kieran Lyons, Alan Berry, Guy Westbrook, Rafael Salas, Conor Duffy, Glenn Nolan, Joe Silke
This study investigated the application of a three-dimensional physical hydrodynamic model in a harmful algal bloom forecast system for Bantry Bay, southwest Ireland. Modelled oceanographic conditions were studied and used to help understand observed changes in the chemical and biological patterns from the national biotoxins and phytoplankton monitoring program. The study focused on two toxic events in 2013. An upwelling event was predicted by the model prior to the appearance and population increase of potentially toxic diatoms, Pseudo-nitzschia, and associated domoic acid in shellfish...
March 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073398/-candidatus-moeniiplasma-glomeromycotorum-an-endobacterium-of-arbuscular-mycorrhizal-fungi
#15
Mizue Naito, Alessandro Desirò, Jonathan B Gonzalez, Gang Tao, Joseph B Morton, Paola Bonfante, Teresa E Pawlowska
Arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are symbionts of most terrestrial plants. They commonly harbour endobacteria of a largely unknown biology, referred to as MRE (Mollicutes/mycoplasma-related endobacteria). Here, we propose to accommodate MRE in the novel genus 'Candidatus Moeniiplasma.' Phylogeny reconstructions based on the 16S rRNA gene sequences cluster 'Ca. Moeniiplasma' with representatives of the class Mollicutes, whereas phylogenies derived from amino acid sequences of 19 genes indicate that it is a discrete lineage sharing ancestry with the members of the family Mycoplasmataceae...
January 10, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28073050/genome-wide-identification-of-atp-binding-cassette-abc-transporters-and-their-roles-in-response-to-polycyclic-aromatic-hydrocarbons-pahs-in-the-copepod-paracyclopina-nana
#16
Chang-Bum Jeong, Duck-Hyun Kim, Hye-Min Kang, Young Hwan Lee, Hui-Su Kim, Il-Chan Kim, Jae-Seong Lee
The ATP-binding cassette (ABC) protein superfamily is one of the largest gene families and is highly conserved in all domains. The ABC proteins play roles in several biological processes, including multi-xenobiotic resistance (MXR), by functioning as transporters in the cellular membrane. They also mediate the cellular efflux of a wide range of substrates against concentration gradients. In this study, 37 ABC genes belonging to eight distinct subfamilies were identified in the marine copepod Paracyclopina nana and annotated based on a phylogenetic analysis...
December 30, 2016: Aquatic Toxicology
https://www.readbyqxmd.com/read/28072865/reading-the-evolution-of-compartmentalization-in-the-ribosome-assembly-toolbox-the-yrg-protein-family
#17
Pablo Mier, Antonio J Pérez-Pulido, Emmanuel G Reynaud, Miguel A Andrade-Navarro
Reconstructing the transition from a single compartment bacterium to a highly compartmentalized eukaryotic cell is one of the most studied problems of evolutionary cell biology. However, timing and details of the establishment of compartmentalization are unclear and difficult to assess. Here, we propose the use of molecular markers specific to cellular compartments to set up a framework to advance the understanding of this complex intracellular process. Specifically, we use a protein family related to ribosome biogenesis, YRG (YlqF related GTPases), whose evolution is linked to the establishment of cellular compartments, leveraging the current genomic data...
2017: PloS One
https://www.readbyqxmd.com/read/28071908/mechanically-induced-homochirality-in-nucleated-enantioselective-polymerization
#18
Celia Blanco, Michael Stich, David Hochberg
Understanding how biological homochirality may have emerged during chemical evolution remains a challenge for origin of life research. In keeping with this goal, we introduce and solve numerically a kinetic rate equation model of nucleated cooperative enantioselective polymerization in closed systems. The microreversible scheme includes (i) solution phase racemization of the monomers, (ii) linear chain growth by stepwise monomer attachment, in both the nucleation and elongation phases, and (iii) annealing or fusion of homochiral chains...
January 10, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28071669/use-of-fibonacci-numbers-in-lipidomics-enumerating-various-classes-of-fatty-acids
#19
Stefan Schuster, Maximilian Fichtner, Severin Sasso
In lipid biochemistry, a fundamental question is how the potential number of fatty acids increases with their chain length. Here, we show that it grows according to the famous Fibonacci numbers when cis/trans isomerism is neglected. Since the ratio of two consecutive Fibonacci numbers tends to the Golden section, 1.618, organisms can increase fatty acid variability approximately by that factor per carbon atom invested. Moreover, we show that, under consideration of cis/trans isomerism and/or of modification by hydroxy and/or oxo groups, diversity can be described by generalized Fibonacci numbers (e...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070900/chemoselective-henry-condensations-catalyzed-by-artificial-carboligases
#20
Xavier Garrabou Pi, Duncan Stewart Macdonald, Donald Hilvert
The promiscuity of de novo designed enzymes provides a privileged platform for diverse abiological reactions. In this work we report the first example of a nitroolefin synthase that catalyzes the Henry condensation between aromatic aldehydes and nitromethane. Significant catalytic activity was discovered in a computationally designed and evolved carboligase, RA95.5-8, and mutations around the active site were shown to improve the reaction rate, demonstrating the potential to optimize the enzyme with directed evolution...
January 10, 2017: Chemistry: a European Journal
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