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molecular evolution

Nicholas J Strausfeld, Xiaoya Ma, Gregory D Edgecombe
The discovery of fossilized brains and ventral nerve cords in lower and mid-Cambrian arthropods has led to crucial insights about the evolution of their central nervous system, the segmental identity of head appendages and the early evolution of eyes and their underlying visual systems. Fundamental ground patterns of lower Cambrian arthropod brains and nervous systems correspond to the ground patterns of brains and nervous systems belonging to three of four major extant panarthropod lineages. These findings demonstrate the evolutionary stability of early neural arrangements over an immense time span...
October 24, 2016: Current Biology: CB
William B Kristan
How did a structure as complex as our own brain ever evolve? Although biologists have pondered this question since Charles Darwin, the explosion of molecular information in recent years has provided new insights into this question, particularly its first step: the evolution of neurons. Meshing information about genomes with insights from more classical anatomical, physiological, and developmental approaches has led to some remarkable insights and surprises. Because 'phylogenomics' is still a young field, however, there are arguments about which genes to include in comparisons, how much to weigh genetic versus 'classical' features, and which algorithms to use in making such comparisons...
October 24, 2016: Current Biology: CB
Wolfgang Enard
Humans are a remarkable species, especially because of the remarkable properties of their brain. Since the split from the chimpanzee lineage, the human brain has increased three-fold in size and has acquired abilities for vocal learning, language and intense cooperation. To better understand the molecular basis of these changes is of great biological and biomedical interest. However, all the about 16 million fixed genetic changes that occurred during human evolution are fully correlated with all molecular, cellular, anatomical and behavioral changes that occurred during this time...
October 24, 2016: Current Biology: CB
Irving E Wang, Thomas R Clandinin
The activity and maintenance of neurons requires substantial metabolic energy, resulting in selective pressure to decrease resource consumption by the nervous system. The wiring economy principle proposes that animals have evolved mechanisms that wire circuits efficiently by minimizing neurite length. Computational modeling of neuronal morphology, microcircuit organization, and neural networks reveals that wiring economy is a significant determinant of nervous system layout. The strategies for reducing wiring costs are shared across phyla and point to the possibility of generalizable rules that specify the development of efficient nervous systems...
October 24, 2016: Current Biology: CB
Daniel Ricardo Nascimento, A Eugene DePrince
We report an explicitly time-dependent approach to the generation of linear absorption spectra for molecular systems within the framework of equation-of-motion (EOM) coupled-cluster (CC) theory. While most time-dependent CC approaches consider the perturbation and time-evolution of a CC wave function, the present work considers the time-evolution of a CC dipole function. The dipole function formalism introduces no approximations and requires the evolution of only one time-dependent quantity, either the left or the right dipole function...
October 25, 2016: Journal of Chemical Theory and Computation
Z W Wu, F X Li, C W Huo, M Z Li, W H Wang, K X Liu
The temperature evolution of icosahedral medium-range order formed by interpenetrating icosahedra in CuZr metallic glassforming liquids was investigated via molecular dynamics simulations. Scaling analysis based on percolation theory was employed, and it is found that the size distribution of clusters formed by the central atoms of icosahedra at various temperatures follows a very good scaling law with the cluster number density scaled by S(-τ) and the cluster size S scaled by |1 - Tc/T|(-1/σ), respectively...
October 25, 2016: Scientific Reports
David S Domozych, Zoë A Popper, Iben Sørensen
Charophytes are the group of green algae whose ancestral lineage gave rise to land plants in what resulted in a profoundly transformative event in the natural history of the planet. Extant charophytes exhibit many features that are similar to those found in land plants and their relatively simple phenotypes make them efficacious organisms for the study of many fundamental biological phenomena. Several taxa including Micrasterias, Penium, Chara, and Coleochaete are valuable model organisms for the study of cell biology, development, physiology and ecology of plants...
2016: Frontiers in Plant Science
José A L Fernandes, Tâmara H R Prandini, Maria da Conceiçao A Castro, Thales D Arantes, Juliana Giacobino, Eduardo Bagagli, Raquel C Theodoro
Inteins are invasive intervening sequences that perform an autocatalytic splicing from their host proteins. Among eukaryotes, these elements are present in many fungal species, including those considered opportunistic or primary pathogens, such as Candida spp. Here we reviewed and updated the list of Candida species containing inteins in the genes VMA, THRRS and GLT1 and pointed out the importance of these elements as molecular markers for molecular epidemiological researches and species-specific diagnosis, since the presence, as well as the size of these inteins, is polymorphic among the different species...
2016: Frontiers in Microbiology
Jullien M Flynn, Frédéric J J Chain, Daniel J Schoen, Melania E Cristescu
Understanding the rates, spectra, and fitness effects of spontaneous mutations is fundamental to answering key questions in evolution, molecular biology, disease genetics and conservation biology. To estimate mutation rates and evaluate the effect of selection on new mutations, we propagated mutation accumulation (MA) lines of Daphnia pulex for more than 82 generations and maintained a non-MA population under conditions where selection could act. Both experiments were started with the same obligate asexual progenitor clone...
October 24, 2016: Molecular Biology and Evolution
Zhong-Hua Chen, Guang Chen, Fei Dai, Yizhou Wang, Adrian Hills, Yong-Ling Ruan, Guoping Zhang, Peter J Franks, Eviatar Nevo, Michael R Blatt
Grasses began to diversify in the late Cretaceous Period and now dominate more than one third of global land area, including three-quarters of agricultural land. We hypothesize that their success is likely attributed to the evolution of highly responsive stomata capable of maximizing productivity in rapidly changing environments. Grass stomata harness the active turgor control mechanisms present in stomata of more ancient plant lineages, maximizing several morphological and developmental features to ensure rapid responses to environmental inputs...
October 21, 2016: Trends in Plant Science
Arif Uddin, Monisha Nath Choudhury, Supriyo Chakraborty
The mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) gene is a subunit of the respiratory chain complex I and involved in the first step of the electron transport chain of oxidative phosphorylation (OXPHOS). To understand the pattern of compositional properties, codon usage and expression level of mitochondrial ND1 genes in pisces, aves, and mammals, we used bioinformatic approaches as no work was reported earlier. In this study, a perl script was used for calculating nucleotide contents and different codon usage bias parameters...
October 24, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Julio Vargas, Vincenzo Landi, Amparo Martínez, Mayra Gómez, María Esperanza Camacho, Luz Ángela Álvarez, Lenin Aguirre, Juan Vicente Delgado
Macabea cattle are the only Bos taurus breed that have adapted to the wet tropical conditions of the Amazon. This breed has integrated into the culture of the indigenous Shuar-Asuar nations probably since its origins, being one of the few European zoogenetic resources assimilated by the deep-jungle Amazon communities. Despite its potential for local endogenous sustainable development, this breed is currently endangered. The present study used molecular genetics tools to investigate the within- and between-breeds diversity, in order to characterize the breed population, define its associations with other breeds, and infer its origin and evolution...
2016: PloS One
Meng Zhou, Chenjie Zeng, Yuxiang Chen, Shuo Zhao, Matthew Y Sfeir, Manzhou Zhu, Rongchao Jin
The evolution from the metallic (or plasmonic) to molecular state in metal nanoparticles constitutes a central question in nanoscience research because of its importance in revealing the origin of metallic bonding and offering fundamental insights into the birth of surface plasmon resonance. Previous research has not been able to probe the transition due to the unavailability of atomically precise nanoparticles in the 1-3 nm size regime. Herein, we investigate the transition by performing ultrafast spectroscopic studies on atomically precise thiolate-protected Au25, Au38, Au144, Au333, Au∼520 and Au∼940 nanoparticles...
October 24, 2016: Nature Communications
Joanna Melonek, James D Stone, Ian Small
Hybrid seed production in rice relies on cytoplasmic male sterility (CMS) induced by specific mitochondrial proteins, whose deleterious effects are suppressed by nuclear Restorer of Fertility (RF) genes. The majority of RF proteins belong to a specific clade of the RNA-binding pentatricopeptide repeat protein family. We have characterised 'restorer-of-fertility-like' (RFL) sequences from 13 Oryza genomes and the Brachypodium distachyon genome. The majority of the RFL sequences are found in genomic clusters located at two or three chromosomal loci with only a minor proportion being present as isolated genes...
October 24, 2016: Scientific Reports
Vishvanath Tiwari
Enzymes catalyze various biochemical functions with high efficiency and specificity. In vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. Enzyme engineering technology involves directed evolution, rational designing, semi-rational designing, and structure-based designing using chemical modifications. Similarly, combined computational and in vitro evolution approaches together help in artificial designing of novel bioactivity in the natural enzyme...
2016: Frontiers in Chemistry
Marta Canuti, Kimberly E O'Leary, Bruce D Hunter, Grant Spearman, Davor Ojkic, Hugh G Whitney, Andrew S Lang
Aleutian mink disease virus (AMDV) causes plasmacytosis, an immune complex-associated syndrome that affects wild and farmed mink. The virus can also infect other small mammals (e.g., ferrets, skunks, ermines, and raccoons), but the disease in these hosts has been studied less. In 2007, a mink plasmacytosis outbreak began on the Island of Newfoundland, and the virus has been endemic in farms since then. In this study, we evaluated the molecular epidemiology of AMDV in farmed and wild animals of Newfoundland since before the beginning of the outbreak and investigated the epidemic in a global context by studying AMDV worldwide, thereby examining its diffusion and phylogeography...
January 2016: Virus Evolution
Shin-Ichi Yokobori, Yoshiki Nakajima, Satoshi Akanuma, Akihiko Yamagishi
Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis...
2016: Archaea: An International Microbiological Journal
Jing Wei, Linyan Liu, Zhenhua Fan, Yunhan Hong, Yang Zhao, Linyan Zhou, Deshou Wang
The origin and evolution of molecular mechanisms underlying the self-renewal and differentiation of spermatogonial stem cells (SSC) are fundamental questions in stem cell biology as well as reproduction medicine. In mammals, glial cell line-derived neurotrophic factor (GDNF) is crucial for SSC self-renewal and maintenance. However, in non-mammals, the role of Gdnf in SSC still remains unknown. Here we report that the two GDNF homologs from medaka fish (Oryzias latipes), namely OlGdnfa and OlGdnfb, can promote the proliferation activity and retain the spermatogonial property of SG3, a spermatogonial cell line derived from adult medaka showing the intrinsic property of SSC by self-renewal and differentiation potential during 2 years of culture...
October 22, 2016: Stem Cells and Development
Jianhe Peng, Jing Cao, Fui Mee Ng, Jeffrey Hill
: Pseudomonas aeruginosa infection is difficult to treat because of its drug resistance, but how it develops drug resistance remains largely unknown. In this study we investigated Ciprofloxacin resistance development in P. aeruginosa. Different Ciprofloxacin concentrations selected different low level resistant mutants, and high level resistant mutants emerged from low level resistant mutants if stressed further by Ciprofloxacin. A deep quantitative proteomic study of the Ciprofloxacin resistant mutants uncovered the cellular pathways that supported such resistances...
October 19, 2016: Journal of Proteomics
Samah Nassereddine, Taiga Nishihori, Eric Padron, Rami Mahfouz, Ali Bazarbachi, Rami S Komrokji, Mohamed A Kharfan-Dabaja
Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic neoplastic disorders most commonly occurring in the elderly population; MDS has a tendency to progress to acute leukemia. Although epigenetic therapies have improved the outcomes of MDS patients, allogeneic hematopoietic cell transplantation remains the only curative option. Molecular characterization of MDS using next-generation sequencing has expanded not only the knowledge on MDS but also the depth of understanding of evolution and contribution of recurrent somatic mutations in precursor conditions...
September 16, 2016: Clinical Lymphoma, Myeloma & Leukemia
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