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https://www.readbyqxmd.com/read/28716924/insights-into-the-red-algae-and-eukaryotic-evolution-from-the-genome-of-porphyra-umbilicalis-bangiophyceae-rhodophyta
#1
Susan H Brawley, Nicolas A Blouin, Elizabeth Ficko-Blean, Glen L Wheeler, Martin Lohr, Holly V Goodson, Jerry W Jenkins, Crysten E Blaby-Haas, Katherine E Helliwell, Cheong Xin Chan, Tara N Marriage, Debashish Bhattacharya, Anita S Klein, Yacine Badis, Juliet Brodie, Yuanyu Cao, Jonas Collén, Simon M Dittami, Claire M M Gachon, Beverley R Green, Steven J Karpowicz, Jay W Kim, Ulrich Johan Kudahl, Senjie Lin, Gurvan Michel, Maria Mittag, Bradley J S C Olson, Jasmyn L Pangilinan, Yi Peng, Huan Qiu, Shengqiang Shu, John T Singer, Alison G Smith, Brittany N Sprecher, Volker Wagner, Wenfei Wang, Zhi-Yong Wang, Juying Yan, Charles Yarish, Simone Zäuner-Riek, Yunyun Zhuang, Yong Zou, Erika A Lindquist, Jane Grimwood, Kerrie W Barry, Daniel S Rokhsar, Jeremy Schmutz, John W Stiller, Arthur R Grossman, Simon E Prochnik
Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28710131/gene-regulatory-networks-for-the-haploid-to-diploid-transition-of-chlamydomonas-reinhardtii
#2
Sunjoo Joo, Yoshiki Nishimura, Evan Cronmiller, Ran Ha Hong, Thamali Kariyawasam, Ming Hsiu Wang, Nai Chun Shao, Saif-El-Din El Akkad, Takamasa Suzuki, Tetsuya Higashiyama, EonSeon Jin, Jae-Hyeok Lee
The sexual cycle of the unicellular Chlamydomonas reinhardtii culminates in the formation of diploid zygotes which differentiate into dormant spores that eventually undergo meiosis. Mating between gametes induces rapid cell wall shedding via the enzyme g-lysin; cell fusion is followed by heterodimerization of sex-specific homeobox transcription factors, GSM1 and GSP1, and initiation of zygote-specific gene expression. To investigate the genetic underpinnings of the zygote developmental pathway, we performed comparative transcriptome analysis of both pre- and post-fertilization samples...
July 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28710008/identifying-synthetic-lethal-targets-using-crispr-cas9-system
#3
Jaspreet Kaur Dhanjal, Navaneethan Radhakrishnan, Durai Sundar
Synthetic lethality occurs when co-occurrence of two genetic events is unfavorable for the survival of the cell or organism. The conventional approach of high throughput screening of synthetic lethal targets using chemical compounds has been replaced by RNAi technology. CRISPR/Cas9, an RNA guided endonuclease system is the most recent technology for this work. Here, we have discussed the major considerations involved in designing a CRISPR/Cas9 based screening experiment for identification of synthetic lethal targets...
July 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28706533/inhibition-of-histone-h3k9-methylation-by-bix-01294-promotes-stress-induced-microspore-totipotency-and-enhances-embryogenesis-initiation
#4
Eduardo Berenguer, Ivett Bárány, María-Teresa Solís, Yolanda Pérez-Pérez, María C Risueño, Pilar S Testillano
Microspore embryogenesis is a process of cell reprogramming, totipotency acquisition and embryogenesis initiation, induced in vitro by stress treatments and widely used in plant breeding for rapid production of doubled-haploids, but its regulating mechanisms are still largely unknown. Increasing evidence has revealed epigenetic reprogramming during microspore embryogenesis, through DNA methylation, but less is known about the involvement of histone modifications. In this study, we have analyzed the dynamics and possible role of histone H3K9 methylation, a major repressive modification, as well as the effects on microspore embryogenesis initiation of BIX-01294, an inhibitor of histone methylation, tested for the first time in plants, in Brassica napus and Hordeum vulgare...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28701726/genotype-by-random-environmental-interactions-gives-an-advantage-to-non-favored-minor-alleles
#5
A Mahdipour-Shirayeh, A H Darooneh, A D Long, N L Komarova, M Kohandel
Fixation probability, the probability that the frequency of a newly arising mutation in a population will eventually reach unity, is a fundamental quantity in evolutionary genetics. Here we use a number of models (several versions of the Moran model and the haploid Wright-Fisher model) to examine fixation probabilities for a constant size population where the fitness is a random function of both allelic state and spatial position, despite neither allele being favored on average. The concept of fitness varying with respect to both genotype and environment is important in models of cancer initiation and progression, bacterial dynamics, and drug resistance...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28701347/a-casein-kinase-1-prevents-expulsion-of-the-oocyte-meiotic-spindle-into-a-polar-body-by-regulating-cortical-contractility
#6
Jonathan R Flynn, Francis J McNally
During female meiosis, haploid eggs are generated from diploid oocytes. This reduction in chromosome number occurs through two highly asymmetric cell divisions resulting in one large egg and two small polar bodies. Unlike mitosis, where an actomyosin contractile ring forms between the sets of segregating chromosomes, the meiotic contractile ring forms on the cortex adjacent to one spindle pole, then ingresses down the length of the spindle to position itself at the exact midpoint between the two sets of segregating chromosomes...
July 12, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28700723/position-effects-influencing-intrachromosomal-repair-of-a-double-strand-break-in-budding-yeast
#7
Ruoxi W Wang, Cheng-Sheng Lee, James E Haber
Repair of a double-strand break (DSB) by an ectopic homologous donor sequence is subject to the three-dimensional arrangement of chromosomes in the nucleus of haploid budding yeast. The data for interchromosomal recombination suggest that searching for homology is accomplished by a random collision process, strongly influenced by the contact probability of the donor and recipient sequences. Here we explore how recombination occurs on the same chromosome and whether there are additional constraints imposed on repair...
2017: PloS One
https://www.readbyqxmd.com/read/28700625/pooling-strategy-and-chromosome-painting-characterize-a-living-zebroid-for-the-first-time
#8
Alessandra Iannuzzi, Jorge Pereira, Clara Iannuzzi, Beiyuan Fu, Malcolm Ferguson-Smith
We have investigated the complex karyotype of a living zebra-donkey hybrid for the first time using chromosome-specific painting probes produced from flow-sorted chromosomes from a zebra (Equus burchelli) and horse (Equus caballus). As the chromosomes proved difficult to distinguish from one another, a successful new strategy was devised to resolve the difficulty and characterize each chromosome. This was based on selecting five panels of whole chromosome painting probes that could differentiate zebra and donkey chromosomes by labelling the probes with either FITC or Cy3 fluorochromes...
2017: PloS One
https://www.readbyqxmd.com/read/28698378/haploid-selection-within-a-single-ejaculate-increases-offspring-fitness
#9
Ghazal Alavioon, Cosima Hotzy, Khriezhanuo Nakhro, Sandra Rudolf, Douglas G Scofield, Susanne Zajitschek, Alexei A Maklakov, Simone Immler
An inescapable consequence of sex in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid phases. The occurrence of selection during the haploid phase can have far-reaching consequences for fundamental evolutionary processes including the rate of adaptation, the extent of inbreeding depression, and the load of deleterious mutations, as well as for applied research into fertilization technology. Although haploid selection is well established in plants, current dogma assumes that in animals, intact fertile sperm within a single ejaculate are equivalent at siring viable offspring...
July 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28696245/the-histone-codes-for-meiosis
#10
REVIEW
Lina Wang, Zhiliang Xu, Muhammad Babar Khawar, Chao Liu, Wei Li
Meiosis is a specialized process that produces haploid gametes from diploid cells by a single round of DNA replication followed by two successive cell divisions. It contains many special events, such as programmed DNA double-strand break (DSB) formation, homologous recombination, crossover formation and resolution. These events are associated with dynamically regulated chromosomal structures, the dynamic transcriptional regulation and chromatin remodeling are mainly modulated by histone modifications, termed 'histone codes'...
September 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28696210/role-of-chromosomal-instability-in-cancer-progression
#11
Sarah E McClelland
Cancer cells often display chromosomal instability (CIN), a defect that involves loss or rearrangement of the cell's genetic material - chromosomes - during cell division (Lengauer, et al. 1998; McGranahan, et al. 2012). This process results in the generation of aneuploidy, a deviation from the haploid number of chromosomes, and structural alterations of chromosomes in over 90% of solid tumours and many haematological cancers (Mitelman). This trait is unique to cancer cells as normal cells in the body generally strictly maintain the correct number and structure of chromosomes...
July 10, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28696027/atz-1-influences-meiosis-to-maintain-germline-chromosomal-stability-in-caenorhabditis-elegans
#12
Joseph A Dawson, Caitlin Methven-Kelley, Gregory M Davis
Exchange of genetic information during meiosis occurs in all sexually reproducing species to produce haploid gametes from diploid cells. This process involves tight coordination of a meiotic specific cohesin complex, the synaptonemal complex, and DNA damage repair mechanisms. In this study, we describe a putative myosin heavy chain protein orthologous to human myosin 1, F28D1.2, which we named atz-1 (Abnormal Transition Zone). Deletion of atz-1 results in embryonic lethality and a depleted transition zone, accompanied by reduced expression of the meiotic cohesin protein, REC-8...
July 11, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28693746/so-similar-yet-so-different-the-two-ends-of-a-double-strand-break
#13
REVIEW
Keun P Kim, Ekaterina V Mirkin
Homologous recombination (HR) is essential for ensuring proper segregation of chromosomes in the first round of meiotic division. HR is also crucial for preserving genomic integrity of somatic cells due to its ability to rescue collapsed replication forks and eliminate deleterious DNA lesions, such as double-strand breaks (DSBs), interstrand crosslinks, and single-strand DNA gaps. Here, we review the early steps of HR (homology search and strand exchange), focusing on the roles of the two ends of a DSB. A detailed overview of the basic HR machinery and its mechanism for template selection and capture of duplex DNA via strand exchange is provided...
June 27, 2017: Mutation Research
https://www.readbyqxmd.com/read/28692865/live-cell-confocal-laser-imaging-studies-on-the-nuclear-behavior-during-meiosis-and-ascosporogenesis-in-morchella-importuna-under-artificial-cultivation
#14
Peixin He, Ke Wang, Yingli Cai, Wei Liu
The commercial production of Morchella mushrooms, especially M. importuna, has been realized since 2012 in China, which facilitates the fundamental studies of Morchella spp. In this paper, the cytological characteristics at three stages of ascocarpic development and the nuclear behavior during meiosis and ascosporogenesis in cultivated strain M. importuna 1(#) was visualized by confocal laser scanning microscopy. The results suggested that the strain sporulated at sporulation stage of ascocarpic development...
June 29, 2017: Micron: the International Research and Review Journal for Microscopy
https://www.readbyqxmd.com/read/28691663/quantitative-trait-loci-in-pepper-control-the-effective-population-size-of-two-rna-viruses-at-inoculation
#15
Lucie Tamisier, Elsa Rousseau, Sebastien Barraillé, Ghislaine Nemouchi, Marion Szadkowski, Ludovic Mailleret, Frederic Grognard, Frederic Fabre, Benoit Moury, Alain Palloix
Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne...
July 8, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28686341/three-regulators-of-g-protein-signaling-differentially-affect-mating-morphology-and-virulence-in-the-smut-fungus-ustilago-maydis
#16
Marino Moretti, Lei Wang, Pierre Grognet, Daniel Lanver, Hannes Link, Regine Kahmann
Regulators of G protein signaling (RGS) proteins modulate heterotrimeric G protein signaling negatively. To broaden an understanding of the roles of RGS proteins in fungal pathogens, we functionally characterized the three RGS protein-encoding genes (rgs1, rgs2 and rgs3) in the phytopathogenic fungus Ustilago maydis. We found that RGS proteins play distinct roles in the regulation of development and virulence. rgs1 had a minor role in virulence when deleted in a solopathogenic strain. In crosses, rgs1 was dispensable for mating and filamentation, but was required for teliospore production...
July 7, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28680740/haploinsufficient-tumor-suppressor-genes
#17
Kazushi Inoue, Elizabeth A Fry
Haploinsufficiency of tumor suppressor genes (TSGs) indicates that the reduced levels of proteins in cells that lack one allele of the genomic locus results in the inability of the cell to execute normal cellular functions contributing to tumor development. Representative cases of haploinsufficient TSGs are p27(Kip1), p53, DMP1, NF1, and PTEN. Tumor development is significantly accelerated in both mice with homozygous and heterozygous gene deletion, with expression of the wild type allele in the latter. Newly characterized TSGs such as AML1, EGR1, TGFβR1/2, and SMAD4 have also shown haploid insufficiency for tumor suppression...
2017: Advances in Medicine and Biology
https://www.readbyqxmd.com/read/28679703/spore-analysis-and-tetrad-dissection-of-schizosaccharomyces-pombe
#18
Karl Ekwall, Geneviève Thon
Here we describe the processing of Schizosaccharomyces pombe spores in batches (random spore analysis) or through tetrad dissections. Spores are usually prepared from matings between haploid strains (producing zygotic asci) or from sporulating diploids (producing azygotic asci). In random spore analysis, a snail enzyme preparation is used to digest the walls of asci to release free spores that are diluted and plated to form colonies. In tetrad dissection, a needle attached to a micromanipulator is used to pick asci and separate spores...
July 5, 2017: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/28679701/setting-up-schizosaccharomyces-pombe-crosses-matings
#19
Karl Ekwall, Geneviève Thon
Here we provide methods for setting up standard crosses with Schizosaccharomyces pombe strains. All strain genotypes and pedigrees should be recorded in a laboratory strain book. Matings between two haploid strains of interest are induced on solid medium poor in nitrogen. Usually, sporulation agar (SPA) plates are preferred, but for difficult matings it is advisable to try several mating media in parallel because one medium might allow for more efficient mating. Protoplast fusion can be used to produce zygotes from sterile mutants that fail to mate...
July 5, 2017: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/28679543/tracing-genetic-exchange-and-biogeography-of-cryptococcus-neoformans-var-grubii-at-the-global-population-level
#20
Johanna Rhodes, Christopher A Desjardins, Sean M Sykes, Mathew A Beale, Mathieu Vanhove, Sharadha Sakthikumar, Yuan Chen, Sharvari Gujja, Sakina Saif, Anuradha Chowdhary, Daniel John Lawson, Vinicius Ponzio, Arnaldo Lopes Colombo, Wieland Meyer, David M Engelthaler, Ferry Hagen, Maria Teresa Illnait-Zaragozi, Alexandre Alanio, Jo-Marie Vreulink, Joseph Heitman, John R Perfect, Anastasia Litvintseva, Tihana Bicanic, Thomas S Harrison, Matthew C Fisher, Christina A Cuomo
Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major subdivisions, their relative diversity and the level of genetic exchange between them...
July 5, 2017: Genetics
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