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https://www.readbyqxmd.com/read/28918301/mathematical-fundamentals-for-the-noise-immunity-of-the-genetic-code
#1
Elena Fimmel, Lutz Strüngmann
Symmetry is one of the essential and most visible patterns that can be seen in nature. Starting from the left-right symmetry of the human body, all types of symmetry can be found in crystals, plants, animals and nature as a whole. Similarly, principals of symmetry are also some of the fundamental and most useful tools in modern mathematical natural science that play a major role in theory and applications. As a consequence, it is not surprising that the desire to understand the origin of life, based on the genetic code, forces us to involve symmetry as a mathematical concept...
September 13, 2017: Bio Systems
https://www.readbyqxmd.com/read/28918073/a-directed-evolution-approach-to-select-for-novel-adeno-associated-virus-capsids-on-an-hiv-1-producer-t-cell-line
#2
Dawn P Wooley, Priyanka Sharma, John R Weinstein, Poornima Kotha Lakshmi Narayan, David V Schaffer, Katherine J D A Excoffon
A directed evolution approach was used to select for Adeno-associated virus (AAV) capsids that would exhibit more tropism toward an HIV-1 producer T cell line with the long-term goal of developing improved gene transfer vectors. A library of AAV variants was used to infect H9T cells previously infected or uninfected by HIV-1 followed by AAV amplification with wild-type adenovirus. Six rounds of biological selection were performed, including negative selection and diversification after round three. The H9T cells were successfully infected with all three wild-type viruses (AAV, adenovirus, and HIV-1)...
September 13, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28917658/multiple-events-of-gene-manipulation-via-in-pouch-electroporation-in-a-marsupial-model-of-mammalian-forebrain-development
#3
Annalisa Paolino, Laura R Fenlon, Peter Kozulin, Linda J Richards, Rodrigo Suárez
BACKGROUND: The technique of in utero electroporation has been widely used in eutherians, such as mice and rats, to investigate brain development by selectively manipulating gene expression in specific neuronal populations. A major challenge, however, is that surgery is required to access the embryos, affecting animal survival and limiting the number of times it can be performed within the same litter. New method: Marsupials are born at an early stage of brain development as compared to eutherians...
September 13, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28917590/karyotype-stability-and-unbiased-fractionation-in-the-paleo-allotetraploid-cucurbita-genomes
#4
Honghe Sun, Shan Wu, Guoyu Zhang, Chen Jiao, Shaogui Guo, Yi Ren, Jie Zhang, Haiying Zhang, Guoyi Gong, Zhangcai Jia, Fan Zhang, Jiaxing Tian, William J Lucas, Jeff J Doyle, Haizhen Li, Zhangjun Fei, Yong Xu
The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C...
September 13, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28916791/genomic-structure-and-evolution-of-the-mating-type-locus-in-the-green-seaweed-ulva-partita
#5
Tomokazu Yamazaki, Kensuke Ichihara, Ryogo Suzuki, Kenshiro Oshima, Shinichi Miyamura, Kazuyoshi Kuwano, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Masahira Hattori, Shigeyuki Kawano
The evolution of sex chromosomes and mating loci in organisms with UV systems of sex/mating type determination in haploid phases via genes on UV chromosomes is not well understood. We report the structure of the mating type (MT) locus and its evolutionary history in the green seaweed Ulva partita, which is a multicellular organism with an isomorphic haploid-diploid life cycle and mating type determination in the haploid phase. Comprehensive comparison of a total of 12.0 and 16.6 Gb of genomic next-generation sequencing data for mt(-) and mt(+) strains identified highly rearranged MT loci of 1...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916743/comparative-analysis-reveals-regulatory-motifs-at-the-ains-ainr-pheromone-signaling-locus-of-vibrio-fischeri
#6
John H Kimbrough, Eric V Stabb
Vibrio fischeri uses the AinS/AinR pheromone-signaling system to control bioluminescence and other symbiotic colonization factors. The Ain system is thought to initiate cell-cell signaling at moderate cell densities and to prime the LuxI/LuxR signaling system. Here we compared and analyzed the ain locus from two V. fischeri strains and a Vibrio salmonicida strain to explore ain regulation. The ainS and ainR genes were predicted to constitute an operon, which we corroborated using RT-PCR. Comparisons between strains revealed a stark area of conservation across the ainS-ainR junction, including a large inverted repeat in ainR...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916329/ecological-extension-of-the-theory-of-evolution-by-natural-selection-from-a-perspective-of-western-and-eastern-holistic-philosophy
#7
REVIEW
Toshiyuki Nakajima
Evolution by natural selection requires the following conditions: (1) a particular selective environment, (2) variation of traits in the population; (3) differential survival/reproduction among types of organisms; and (4) heritable traits. However, the traditional (standard) model does not unclearly explain how and why these conditions are generated or determined. What generates a selective environment? What generates new types? How does a certain type replace, or coexist, with others? In this paper, based on the holistic philosophy in Western and Eastern traditions, I focus on the ecosystem as a higher-level system and generator of conditions that induce the evolution of local populations; I also aim to identify the ecosystem processes that generate those conditions...
September 12, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28916155/ancestral-resurrection-of-anthropoid-estrogen-receptor-%C3%AE-demonstrates-functional-consequences-of-positive-selection
#8
Amy Weckle, Michael R McGowen, Jun Xing, Caoyi Chen, Kirstin N Sterner, Zhuo-Cheng Hou, Roberto Romero, Derek E Wildman
Anthropoid primates arose during the Eocene approximately 55 million years ago (mya), and extant anthropoids share a most recent common ancestor ∼40 mya. Paleontology has been very successful at describing the morphological phenotypes of extinct anthropoids. Less well understood is the molecular biology of these extinct species as well as the phenotypic consequences of evolutionary variation in their genomes. Here we resurrect the most recent common ancestral anthropoid estrogen receptor β gene (ESR2) and demonstrate that the function of this ancestral estrogen receptor has been maintained during human descent but was altered during early New World monkey (NWM) evolution by becoming a more potent transcriptional activator...
September 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28916147/microbial-associates-of-the-southern-mole-cricket-scapteriscus-borellii-are-highly-pathogenic
#9
Sudarshan K Aryal, Derreck Carter-House, Jason E Stajich, Adler R Dillman
We report the isolation and identification of seven bacterial strains and one fungal strain from dead and diseased Scapteriscus borellii mole crickets collected from a golf course in southern California. Using 16S and 18S rRNA gene sequence analysis we identified the microbes as Serratia marcescens (red), S. marcescens (white), S. marcescens (purple), Achromobacter xylosoxidans, Chryseobacterium sp., Ochrobactrum anthropi, Tsukamurella tryosinosolvens, and Beauveria bassiana. We performed a dose response curve for each of these cricket-associated microbial strains (except T...
September 12, 2017: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/28915922/recent-urbanization-in-china-is-correlated-with-a-westernized-microbiome-encoding-increased-virulence-and-antibiotic-resistance-genes
#10
Kathryn Winglee, Annie Green Howard, Wei Sha, Raad Z Gharaibeh, Jiawu Liu, Donghui Jin, Anthony A Fodor, Penny Gordon-Larsen
BACKGROUND: Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28915920/current-situation-of-h9n2-subtype-avian-influenza-in-china
#11
REVIEW
Min Gu, Lijun Xu, Xiaoquan Wang, Xiufan Liu
In China, H9N2 subtype avian influenza outbreak is firstly reported in Guangdong province in 1992. Subsequently, the disease spreads into vast majority regions nationwide and has currently become endemic there. Over vicennial genetic evolution, the viral pathogenicity and transmissibility have showed an increasing trend as year goes by, posing serious threat to poultry industry. In addition, H9N2 has demonstrated significance to public health as it could not only directly infect mankind, but also donate partial or even whole cassette of internal genes to generate novel human-lethal reassortants like H5N1, H7N9, H10N8 and H5N6 viruses...
September 15, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28915794/genome-sequence-of-the-ectophytic-fungus-ramichloridium-luteum-reveals-unique-evolutionary-adaptations-to-plant-surface-niche
#12
Bo Wang, Xiaofei Liang, Mark L Gleason, Rong Zhang, Guangyu Sun
BACKGROUND: Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate adaptation to this environment remains unclear. In this study, we sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis. RESULTS: The R...
September 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28913932/hox-d-genes-and-the-fin-to-limb-transition-insights-from-fish-studies
#13
REVIEW
Ana Paço, Renata Freitas
Genes in the 5' extremity of the HoxD cluster encode DNA-binding transcription factors essential for development of the autopod and digits, regulating primarily gene expression and, consequently, morphogenesis and skeletal differentiation. Comparative studies focused on their expression and regulation have led to the idea that evolution of a bimodal regulation of the HoxD cluster, mainly due to the activation of cis-regulatory units in the centromeric side of the cluster, was a fundamental mechanism that potentiated the fin-to-limb transition in vertebrates...
September 14, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28913870/mimicry-in-butterflies-co-option-and-a-bag-of-magnificent-developmental-genetic-tricks
#14
REVIEW
Riddhi Deshmukh, Saurav Baral, A Gandhimathi, Muktai Kuwalekar, Krushnamegh Kunte
Butterfly wing patterns are key adaptations that are controlled by remarkable developmental and genetic mechanisms that facilitate rapid evolutionary change. With swift advancements in the fields of genomics and genetic manipulations, identifying the regulators of wing development and mimetic wing patterns has become feasible even in nonmodel organisms such as butterflies. Recent mapping and gene expression studies have identified single switch loci of major effects such as transcription factors and supergenes as the main drivers of adaptive evolution of mimetic and polymorphic butterfly wing patterns...
September 14, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28913585/on-the-number-of-non-equivalent-ancestral-configurations-for-matching-gene-trees-and-species-trees
#15
Filippo Disanto, Noah A Rosenberg
An ancestral configuration is one of the combinatorially distinct sets of gene lineages that, for a given gene tree, can reach a given node of a specified species tree. Ancestral configurations have appeared in recursive algebraic computations of the conditional probability that a gene tree topology is produced under the multispecies coalescent model for a given species tree. For matching gene trees and species trees, we study the number of ancestral configurations, considered up to an equivalence relation introduced by Wu (Evolution 66:763-775, 2012) to reduce the complexity of the recursive probability computation...
September 14, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28913558/only-setbp1-hotspot-mutations-are-associated-with-refractory-disease-in-myeloid-malignancies
#16
Nils Winkelmann, Vivien Schäfer, Jenny Rinke, Alexander Kaiser, Philipp Ernst, Sebastian Scholl, Andreas Hochhaus, Thomas Ernst
INTRODUCTION: SETBP1 mutations have been established as a diagnostic marker in myeloid malignancies and are associated with inferior survival. Since there is limited data on their clinical impact and stability during disease progression, we sought to investigate the relationship between SETBP1 mutations and disease evolution. METHODS: Bidirectional Sanger sequencing of the SETBP1 gene was performed for 442 unselected patients with World Health Organization (WHO) defined myeloid disorders...
September 14, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28913165/molecular-characterization-of-babesia-peircei-and-babesia-ugwidiensis-provides-insight-into-the-evolution-and-host-specificity-of-avian-piroplasmids
#17
Michael J Yabsley, Ralph E T Vanstreels, Barbara C Shock, Michaelle Purdee, Elizabeth C Horne, Michael A Peirce, Nola J Parsons
There are 16 recognized species of avian-infecting Babesia spp. (Piroplasmida: Babesiidae). While the classification of piroplasmids has been historically based on morphological differences, geographic isolation and presumed host and/or vector specificities, recent studies employing gene sequence analysis have provided insight into their phylogenetic relationships and host distribution and specificity. In this study, we analyzed the sequences of the 18S rRNA gene and ITS-1 and ITS-2 regions of two Babesia species from South African seabirds: Babesia peircei from African penguins (Spheniscus demersus) and Babesia ugwidiensis from Bank and Cape cormorants (Phalacrocorax neglectus and P...
December 2017: International Journal for Parasitology. Parasites and Wildlife
https://www.readbyqxmd.com/read/28913164/haemoprotozoa-making-biological-sense-of-molecular-phylogenies
#18
REVIEW
Peter O'Donoghue
A range of protistan parasites occur in the blood of vertebrates and are transmitted by haematophagous invertebrate vectors. Some 48 genera are recognized in bood primarily on the basis of parasite morphology and host specificity; including extracellular kinetoplastids (trypanosomatids) and intracellular apicomplexa (haemogregarines, haemococcidia, haemosporidia and piroplasms). Gene sequences are available for a growing number of species and molecular phylogenies often link parasite and host or vector evolution...
December 2017: International Journal for Parasitology. Parasites and Wildlife
https://www.readbyqxmd.com/read/28912838/phylogenomics-of-colombian-helicobacter-pylori-isolates
#19
Andrés Julián Gutiérrez-Escobar, Esperanza Trujillo, Orlando Acevedo, María Mercedes Bravo
BACKGROUND: During the Spanish colonisation of South America, African slaves and Europeans arrived in the continent with their corresponding load of pathogens, including Helicobacter pylori. Colombian strains have been clustered with the hpEurope population and with the hspWestAfrica subpopulation in multilocus sequence typing (MLST) studies. However, ancestry studies have revealed the presence of population components specific to H. pylori in Colombia. The aim of this study was to perform a thorough phylogenomic analysis to describe the evolution of the Colombian urban H...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28912835/a-unique-set-of-complex-chromosomal-abnormalities-in-an-infant-with-myeloid-leukemia-associated-with-down-syndrome
#20
Daiane Correa de Souza, Amanda Faria de Figueiredo, Daniela R Ney Garcia, Elaine Sobral da Costa, Moneeb A K Othman, Thomas Liehr, Eliana Abdelhay, Maria Luiza Macedo Silva, Teresa de Souza Fernandez
BACKGROUND: Children with Down syndrome (DS) have an enhanced risk of developing acute leukemia, with the most common subtype being acute megakaryoblastic leukemia (AMKL). Myeloid leukemia in Down syndrome (ML-DS) is considered a disease with distinct clinical and biological features. There are few studies focusing on the clonal cytogenetic changes during evolution of ML-DS. CASE PRESENTATION: Here, we describe a complex karyotype involving a previously unreported set of chromosomal abnormalities acquired during progression of ML-DS in an infant boy: derivative der(1)t(1;15)(q24;q23), translocation t(4;5)(q26;q33) and derivative der(15)t(7;15)(p21;q23)...
2017: Molecular Cytogenetics
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