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"Essential gene"

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https://www.readbyqxmd.com/read/28095407/a-novel-imprinted-gene-nuwa-controls-mitochondrial-function-in-early-seed-development-in-arabidopsis
#1
Shan He, Yan Sun, Qian Yang, Xiangyu Zhang, Qingpei Huang, Peng Zhao, Mengxiang Sun, Jingjing Liu, Weiqiang Qian, Genji Qin, Hongya Gu, Li-Jia Qu
Imprinted genes display biased expression of paternal and maternal alleles- and are only found in mammals and flowering plants. Compared to several hundred imprinted genes that are functionally characterized in mammals, very few imprinted genes were confirmed in plants and even fewer of them have been functionally investigated. Here, we report a new imprinted gene, NUWA, in plants. NUWA is an essential gene, because loss of its function resulted in reduced transmission through the female gametophyte and defective cell/nuclear proliferation in early Arabidopsis embryo and endosperm...
January 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28088723/discovery-and-metagenomic-analysis-of-an-anammox-bacterial-enrichment-related-to-candidatus-brocadia-caroliniensis-in-a-full-scale-glycerol-fed-nitritation-denitritation-separate-centrate-treatment-process
#2
Hongkeun Park, Ariane C Brotto, Mark C M van Loosdrecht, Kartik Chandran
A distinctive red biofilm was observed in a glycerol-fed digester liquid effluent treatment process coupling partial nitrification (nitritation) and partial denitrification (denitritation) processes. Based on initial phylogenetic screening using 16S rRNA clone libraries and quantitative polymerase chain reaction, the biofilm was enriched in novel anaerobic ammonium oxidizing bacteria (AMX/anammox) closely related to Candidatus "Brocadia caroliniensis". The metabolic functionality of the C. "Brocadia caroliniensis" enrichment was further explored using high-throughput sequencing and de novo metagenome assembly...
January 6, 2017: Water Research
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#3
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28065598/cas13b-is-a-type-vi-b-crispr-associated-rna-guided-rnase-differentially-regulated-by-accessory-proteins-csx27-and-csx28
#4
Aaron A Smargon, David B T Cox, Neena K Pyzocha, Kaijie Zheng, Ian M Slaymaker, Jonathan S Gootenberg, Omar A Abudayyeh, Patrick Essletzbichler, Sergey Shmakov, Kira S Makarova, Eugene V Koonin, Feng Zhang
CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity...
January 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28060315/high-throughput-robotically-assisted-isolation-of-temperature-sensitive-lethal-mutants-in-chlamydomonas-reinhardtii
#5
Michal Breker, Kristi Lieberman, Frej Tulin, Frederick R Cross
Systematic identification and characterization of genetic perturbations have proven useful to decipher gene function and cellular pathways. However, the conventional approaches of permanent gene deletion cannot be applied to essential genes. We have pioneered a unique collection of ~70 temperature-sensitive (ts) lethal mutants for studying cell cycle regulation in the unicellular green algae Chlamydomonas reinhardtii(1). These mutations identify essential genes, and the ts alleles can be conditionally inactivated by temperature shift, providing valuable tools to identify and analyze essential functions...
December 5, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28055179/a-non-natural-protein-rescues-cells-deleted-for-a-key-enzyme-in-central-metabolism
#6
Katherine M Digianantonio, Maria Korolev, Michael H Hecht
An important goal of synthetic biology is to create novel proteins that provide life-sustaining functions in living organisms. Recent attempts to produce novel proteins have focused largely on rational design involving significant computational efforts. In contrast, nature does not design sequences a priori. Instead, nature relies on Darwinian evolution to select biologically functional sequences from non-designed sequence space. To mimic natural selection in the laboratory, we combed through libraries of novel sequences and selected proteins that rescue E...
January 5, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28053351/functional-analysis-of-the-abcs-of-eye-color-in-helicoverpa-armigera-with-crispr-cas9-induced-mutations
#7
Sher Afzal Khan, Michael Reichelt, David G Heckel
Many insect pigments are localized in subcellular pigment granules, and transport of pigment precursors from the cytoplasm is accomplished by ABC proteins. Drosophila melanogaster has three half-transporter genes (white, scarlet, and brown, all affecting eye pigments) and Bombyx mori has a fourth (ok). The White, Brown, Scarlet and Ok proteins each have one transmembrane and one cytoplasmic domain and they heterodimerize to form functional transporters with different substrate specificities. We used CRISPR/Cas9 to create somatic and germ-line knockout mutations of these four genes in the noctuid moth Helicoverpa armigera...
January 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28044234/development-of-a-regulatable-expression-system-for-the-functional-study-of-vibrio-vulnificus-essential-genes
#8
Yan-Jiao Zhang, Guozhong Chen, Huiyuan Lin, Pan Wang, Baozhi Kuang, Jing Liu, Shiyong Chen
We developed a regulatable gene expression system for Vibrio vulnificus, which contains a lacIq-pTrc cassette. Monomeric red fluorescence protein (mRFP) was used as a reporter to test this system. The results showed that this system tightly controlled the expression of mRFP without leaky expression and was suitable for the controlled expression of genes encoding recombinant proteins in V. vulnificus. To demonstrate the utility of this system, a dominant negative form of V. vulnificus VVMO6_RS04990, a homolog of Escherichia coli LolD that is essential in lipoprotein transport and membrane biogenesis, was inducibly expressed...
January 2, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28035597/identification-of-essential-genes-of-pseudomonas-aeruginosa-for-its-growth-in-airway-mucus
#9
Mohammed Abd Alrahman, Sang Sun Yoon
Pseudomonas aeruginosa has been identified as an important causative agent of airway infection, mainly in cystic fibrosis. This disease is characterized by defective mucociliary clearance induced in part by mucus hyper-production. Mucin is a major component of airway mucus and is heavily O-glycosylated, with a protein backbone. Airway infection is known to be established with bacterial adhesion to mucin. However, the genes involved in mucin degradation or utilization remain elusive. In this study, we sought to provide a genetic basis of P...
January 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28029379/characterization-of-nuclear-foci-targeting-of-luman-creb3-recruitment-factor-lrf-crebrf-and-its-potential-role-in-inhibition-of-herpes-simplex-virus-1-replication
#10
Timothy E Audas, Philip W Hardy-Smith, Jenna Penney, Tiegh Taylor, Ray Lu
The recently identified Luman/CREB3-binding partner LRF (Luman/CREB3 recruitment factor) was shown to localize to discrete sub-nuclear foci. Luman is implicated in herpes simplex virus-1 (HSV-1) latency/reactivation and the unfolded protein response (UPR) pathway; therefore, we sought to characterize the formation of the LRF nuclear foci in the context of cellular signaling and HSV-1 replication. Here, we mapped the nuclear foci-targeting sequence to the central region containing the first leucine zipper (a...
October 26, 2016: European Journal of Cell Biology
https://www.readbyqxmd.com/read/28027311/somatic-mutation-patterns-in-hemizygous-genomic-regions-unveil-purifying-selection-during-tumor-evolution
#11
Jimmy Van den Eynden, Swaraj Basu, Erik Larsson
Identification of cancer driver genes using somatic mutation patterns indicative of positive selection has become a major goal in cancer genomics. However, cancer cells additionally depend on a large number of genes involved in basic cellular processes. While such genes should in theory be subject to strong purifying (negative) selection against damaging somatic mutations, these patterns have been elusive and purifying selection remains inadequately explored in cancer. Here, we hypothesized that purifying selection should be evident in hemizygous genomic regions, where damaging mutations cannot be compensated for by healthy alleles...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/28018942/murine-leukemia-virus-mlv-based-coronavirus-spike-pseudotyped-particle-production-and-infection
#12
Jean Kaoru Millet, Gary R Whittaker
Viral pseudotyped particles (pp) are enveloped virus particles, typically derived from retroviruses or rhabdoviruses, that harbor heterologous envelope glycoproteins on their surface and a genome lacking essential genes. These synthetic viral particles are safer surrogates of native viruses and acquire the tropism and host entry pathway characteristics governed by the heterologous envelope glycoprotein used. They have proven to be very useful tools used in research with many applications, such as enabling the study of entry pathways of enveloped viruses and to generate effective gene-delivery vectors...
December 5, 2016: Bio-protocol
https://www.readbyqxmd.com/read/28018434/a-nonsense-pax6-mutation-in-a-family-with-congenital-aniridia
#13
Kyoung Hee Han, Hye Jin Lee, Il-Soo Ha, Hee Gyung Kang, Hae Il Cheong
Congenital aniridia is a rare ocular malformation that presents with severe hypoplasia of the iris and various ocular manifestations. Most cases of congenital aniridia are known to be related to mutations in the paired box gene-6 (PAX6), which is an essential gene in eye development. Herein, we report a familial case of autosomal dominant congenital aniridia with four affected members in 3 consecutive generations and describe the detailed ophthalmologic findings for one of these members. As expected, mutational analysis revealed a nonsense mutation (p...
November 2016: Korean Journal of Pediatrics
https://www.readbyqxmd.com/read/28013241/oup-lethal-gene-drive-selects-inbreeding
#14
James J Bull
The use of 'selfish' gene drive systems to suppress or even extinguish populations has been proposed on theoretical grounds for almost half a century. Creating these genes has recently become possible with CRISPR technology. One seemingly feasible approach, originally proposed by Burt, is to create a homing endonuclease gene (HEG) that inserts into an essential gene, enabling heterozygote viability but causing homozygote lethality. With 100% segregation distortion in gametes, such genes can cause profound population suppression if resistance does not evolve...
December 2016: Evolution, Medicine, and Public Health
https://www.readbyqxmd.com/read/28009265/rna-structural-determinants-of-optimal-codons-revealed-by-mage-seq
#15
Eric D Kelsic, Hattie Chung, Niv Cohen, Jimin Park, Harris H Wang, Roy Kishony
Synonymous codon choices at the beginning of genes optimize 5' RNA structures for enhanced translation initiation, but less is known about mechanisms that drive codon optimization downstream within the gene. To understand what determines codon choices across a gene, we generated 12,726 in situ codon mutants in the Escherichia coli essential gene infA and measured their fitness by combining multiplex automated genome engineering mutagenesis with amplicon deep sequencing (MAGE-seq). Correlating predicted 5' RNA structure with fitness revealed that codons even far from the start of the gene are deleterious if they disrupt the native 5' RNA conformation...
December 21, 2016: Cell Systems
https://www.readbyqxmd.com/read/28003196/an-expanded-transposon-mutant-library-reveals-that-vibrio-fischeri-%C3%AE-aminolevulinate-auxotrophs-can-colonize-euprymna-scolopes
#16
Noreen L Lyell, Alecia N Septer, Anne K Dunn, Drew Duckett, Julie L Stoudenmire, Eric V Stabb
: Libraries of defined mutants are valuable research tools but necessarily lack gene knockouts that are lethal under the conditions used in library construction. Here we augmented a Vibrio fischeri mutant library generated on a rich medium (LBS) by selecting transposon-insertion mutants on supplemented LBS and screening for those unable to grow on LBS. We isolated strains with insertions in alr, glr (murI), glmS, several heme-biosynthesis genes, and ftsA, as well as a mutant disrupted fourteen base pairs upstream of ftsQ Mutants with insertions in ftsA or upstream of ftsQ were recovered by addition of Mg(2+) to LBS, but their cell morphology and motility were affected...
December 21, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28000736/unraveling-the-genetic-basis-of-xylose-consumption-in-engineered-saccharomyces-cerevisiae-strains
#17
Leandro Vieira Dos Santos, Marcelo Falsarella Carazzolle, Sheila Tiemi Nagamatsu, Nádia Maria Vieira Sampaio, Ludimila Dias Almeida, Renan Augusto Siqueira Pirolla, Guilherme Borelli, Thamy Lívia Ribeiro Corrêa, Juan Lucas Argueso, Gonçalo Amarante Guimarães Pereira
The development of biocatalysts capable of fermenting xylose, a five-carbon sugar abundant in lignocellulosic biomass, is a key step to achieve a viable production of second-generation ethanol. In this work, a robust industrial strain of Saccharomyces cerevisiae was modified by the addition of essential genes for pentose metabolism. Subsequently, taken through cycles of adaptive evolution with selection for optimal xylose utilization, strains could efficiently convert xylose to ethanol with a yield of about 0...
December 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27999988/arabidopsis-phosphatidylinositol-phospholipase-c2-plc2-is-required-for-female-gametogenesis-and-embryo-development
#18
Luciano M Di Fino, Juan Martín D'Ambrosio, Ricardo Tejos, Ringo van Wijk, Lorenzo Lamattina, Teun Munnik, Gabriela C Pagnussat, Ana M Laxalt
AtPLC2 is an essential gene in Arabidopsis, since it is required for female gametogenesis and embryo development. AtPLC2 might play a role in cell division during embryo-sac development and early embryogenesis. Phosphoinositide-specific phospholipase C (PI-PLC) plays an important role in signal transduction during plant development and in the response to various biotic- and abiotic stresses. The Arabidopsis PI-PLC gene family is composed of nine members, named PLC1 to PLC9. Here, we report that PLC2 is involved in female gametophyte development and early embryogenesis...
December 20, 2016: Planta
https://www.readbyqxmd.com/read/27999939/heat-survival-and-phenotype-microarray-profiling-of-salmonella-typhimurium-mutants
#19
Turki M Dawoud, Anita Khatiwara, Si Hong Park, Morgan L Davis, Christopher A Baker, Steven C Ricke, Young Min Kwon
Contamination of food products by pathogenic microorganisms continues to be a major public health and food industry concern. Non-typhoidal Salmonella species have led to numerous outbreaks associated with various foods. A wide variety of methods have been applied and introduced for treatment of fresh foods to eliminate pathogenic as well as spoilage microorganisms. Salmonella can become exposed to elevated temperatures while associated with hosts such as poultry. In addition, heat treatment is also applied at various stages of processing to retain the shelf life of food products...
December 21, 2016: Current Microbiology
https://www.readbyqxmd.com/read/27997585/essential-genes-embody-increased-mutational-robustness-to-compensate-for-the-lack-of-backup-genetic-redundancy
#20
Osher Cohen, Matthew Oberhardt, Keren Yizhak, Eytan Ruppin
Genetic robustness is a hallmark of cells, occurring through many mechanisms and at many levels. Essential genes lack the common robustness mechanism of genetic redundancy (i.e., existing alongside other genes with the same function), and thus appear at first glance to leave cells highly vulnerable to genetic or environmental perturbations. Here we explore a hypothesis that cells might protect against essential gene loss through mechanisms that occur at various cellular levels aside from the level of the gene...
2016: PloS One
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