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https://www.readbyqxmd.com/read/29330052/esco2-knockdown-inhibits-cell-proliferation-and-induces-apoptosis-in-human-gastric-cancer-cells
#1
Hongmei Chen, Lei Zhang, Wenting He, Liu Tao, Yang Zhao, Hao Chen, Yumin Li
Establishment of cohesion 1 homolog 2 (ESCO2), an essential gene for cohesion regulation and genomic stability, has not been studied in human gastric cancer (GC). We found that ESCO2 knockdown in human GC cell lines dramatically inhibited cell proliferation and induced cell apoptosis in vitro and suppressed tumor xenograft development in vivo. Furthermore, adenosine monophosphate-activated protein kinase (AMPK) was activated following the suppression of its downstream targets, including mammalian target of rapamycin (mTOR) and p70 ribosomal S6 kinase 1 (p70S6K1), and this result was consistent with p53 activation...
January 9, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29325119/mir-96-is-required-for-normal-development-of-the-auditory-hindbrain
#2
Tina Schlüter, Christina Berger, Elena Rosengauer, Pascal Fieth, Constanze Krohs, Kathy Ushakov, Karen P Steel, Karen B Avraham, Alexander Hartmann, Felix Felmy, Hans Gerd Nothwang
The peripheral deafness gene Mir96 is expressed in both the cochlea and central auditory circuits. To investigate whether it plays a role in the auditory system beyond the cochlea, we characterized homozygous Dmdo/Dmdo mice with a point mutation in miR-96. Anatomical analysis demonstrated a significant decrease in volume of auditory nuclei in Dmdo/Dmdo mice. This decrease resulted from decreased cell size. Non-auditory structures in the brainstem of Dmdo/Dmdo mice or auditory nuclei of the congenital deaf Cldn14-/- mice revealed no such differences...
January 9, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29325037/mediator-complex-component-med13-regulates-zygotic-genome-activation-and-is-required-for-postimplantation-development-in-the-mouse
#3
Yi-Liang Miao, Andrés Gambini, Yingpei Zhang, Elizabeth Padilla-Banks, Wendy N Jefferson, Miranda L Bernhardt, Weichun Huang, Leping Li, Carmen J Williams
Understanding factors that regulate zygotic genome activation (ZGA) is critical for determining how cells are reprogrammed to become totipotent or pluripotent. There is limited information regarding how this process occurs physiologically in early mammalian embryos. Here we identify a mediator complex subunit, MED13, as translated during mouse oocyte maturation and transcribed early from the zygotic genome. Knockdown and conditional knockout approaches demonstrate that MED13 is essential for ZGA in the mouse, in part by regulating expression of the embryo-specific chromatin remodeling complex, esBAF...
January 9, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29321601/crispr-cas9-mediated-gene-modification-and-gene-knock-out-in-the-human-infective-parasite-trichomonas-vaginalis
#4
Brian D Janssen, Yi-Pei Chen, Brenda M Molgora, Shuqi E Wang, Augusto Simoes-Barbosa, Patricia J Johnson
The sexually-transmitted parasite Trichomonas vaginalis infects ~1/4 billion people worldwide. Despite its prevalence and myriad adverse outcomes of infection, the mechanisms underlying T. vaginalis pathogenesis are poorly understood. Genetic manipulation of this single-celled eukaryote has been hindered by challenges presented by its complex, repetitive genome and inefficient methods for introducing DNA (i.e. transfection) into the parasite. Here, we have developed methods to increase transfection efficiency using nucleofection, with the goal of efficiently introducing multiple DNA elements into a single T...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29311279/a-robust-crispri-gene-repression-system-in-pseudomonas
#5
Sue Zanne Tan, Christopher R Reisch, Kristala L J Prather
Pseudomonas spp. are widely used model organisms in different areas of research. Despite its relevance in many applications, protein depletion tools in this host remain limited. Here, we developed the CRISPR interference system for gene repression in Pseudomonas spp. using the Streptococcus pasteurianus dCas9. We demonstrate a robust and titratable gene depletion system with up to 100-fold repression in β-galactosidase activity in P. aeruginosa and 300-fold repression in pyoverdine production in P. putida This inducible system enables the study of essential genes, as shown by ftsZ depletions in P...
January 8, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29301959/multiplexed-gene-synthesis-in-emulsions-for-exploring-protein-functional-landscapes
#6
Calin Plesa, Angus M Sidore, Nathan B Lubock, Di Zhang, Sriram Kosuri
Improving our ability to construct and functionally characterize DNA sequences would broadly accelerate progress in biology. Here, we introduce DropSynth, a scalable, low-cost method to build thousands of defined gene-length constructs in a pooled (multiplexed) manner. DropSynth uses a library of barcoded beads that pull down the oligonucleotides necessary for a gene's assembly, which are then processed and assembled in water-in-oil emulsions. We use DropSynth to successfully build >7000 synthetic genes that encode phylogenetically-diverse homologs of two essential genes in E...
January 4, 2018: Science
https://www.readbyqxmd.com/read/29300974/the-elongation-factor-spn1-is-a-multi-functional-chromatin-binding-protein
#7
Sha Li, Adam R Almeida, Catherine A Radebaugh, Ling Zhang, Xu Chen, Liangqun Huang, Alison K Thurston, Anna A Kalashnikova, Jeffrey C Hansen, Karolin Luger, Laurie A Stargell
The process of transcriptional elongation by RNA polymerase II (RNAPII) in a chromatin context involves a large number of crucial factors. Spn1 is a highly conserved protein encoded by an essential gene and is known to interact with RNAPII and the histone chaperone Spt6. Spn1 negatively regulates the ability of Spt6 to interact with nucleosomes, but the chromatin binding properties of Spn1 are largely unknown. Here, we demonstrate that full length Spn1 (amino acids 1-410) binds DNA, histones H3-H4, mononucleosomes and nucleosomal arrays, and has weak nucleosome assembly activity...
December 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29298424/an-aneuploidy-free-and-structurally-defined-balancer-chromosome-toolkit-for-caenorhabditis-elegans
#8
Katsufumi Dejima, Sayaka Hori, Satoru Iwata, Yuji Suehiro, Sawako Yoshina, Tomoko Motohashi, Shohei Mitani
Balancer chromosomes are critical tools for genetic research. In C. elegans, reciprocal translocations that lead to aneuploidy have been widely used to maintain lethal and sterile mutations in stable stocks. Here, we generated a set of aneuploidy-free and structurally defined crossover suppressors that contain two overlapping inversions using the CRISPR/Cas9 system. The toolkit includes 13 crossover suppressors and covers approximately 63% of all C. elegans coding genes. Together with the classical intrachromosomal crossover suppressors, the system now covers 89% of the coding genes...
January 2, 2018: Cell Reports
https://www.readbyqxmd.com/read/29281966/global-transcriptional-landscape-and-promoter-mapping-of-the-gut-commensal-bifidobacterium-breve-ucc2003
#9
Francesca Bottacini, Aldert Zomer, Christian Milani, Chiara Ferrario, Gabriele Andrea Lugli, Muireann Egan, Marco Ventura, Douwe van Sinderen
BACKGROUND: Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to investigate and understand the molecular mechanisms underlying the establishment, persistence and activities of this gut commensal in the host environment. RESULTS: The assessment of vegetative promoters in the bifidobacterial prototype Bifidobacterium breve UCC2003 was performed employing a combination of RNA tiling array analysis and cDNA sequencing...
December 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29277086/the-challenges-of-integrating-two-genomes-in-one-cell
#10
REVIEW
Erik Hagström, Siv Ge Andersson
Mutualistic bacteria and mitochondria have small genomes that harbor host-essential genes. A major question is why a distinct bacterial or mitochondrial genome is needed to encode these functions. The dual location of genes demand two sets of information processing systems, coordination of gene expression and elaborate transport systems. A simpler solution would be to harbor all genes in a single genome. Functional gene transfers to the host nuclear genome is uncommon in mutualistic bacteria and lost gene functions are rather rescued by co-symbiotic bacteria...
December 22, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29259000/genes-important-for-schizosaccharomyces-pombe-meiosis-identified-through-a-functional-genomics-screen
#11
Julie Blyth, Vasso Makrantoni, Rachael E Barton, Christos Spanos, Juri Rappsilber, Adele L Marston
Meiosis is a specialized cell division that generates gametes, such as eggs and sperm. Errors in meiosis result in miscarriages and are the leading cause of birth defects, however the molecular origins of these defects remain unknown. Studies in model organisms are beginning to identify the genes and pathways important for meiosis, but the parts list is still poorly defined. Here we present a comprehensive catalog of genes important for meiosis in the fission yeast, Schizosaccharomyces pombe Our genome-wide functional screen surveyed all non-essential genes for roles in chromosome segregation and spore formation...
December 19, 2017: Genetics
https://www.readbyqxmd.com/read/29233099/pronounced-strain-specific-chemosensory-receptor-gene-expression-in-the-mouse-vomeronasal-organ
#12
Kyle Duyck, Vasha DuTell, Limei Ma, Ariel Paulson, C Ron Yu
BACKGROUND: The chemosensory system plays an important role in orchestrating sexual behaviors in mammals. Pheromones trigger sexually dimorphic behaviors and different mouse strains exhibit differential responses to pheromone stimuli. It has been speculated that differential gene expression in the sensory organs that detect pheromones may underlie sexually-dimorphic and strain-specific responses to pheromone cues. RESULTS: We have performed transcriptome analyses of the mouse vomeronasal organ, a sensory organ recognizing pheromones and interspecies cues...
December 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29230204/a-comprehensive-overview-of-online-resources-to-identify-and-predict-bacterial-essential-genes
#13
REVIEW
Chong Peng, Yan Lin, Hao Luo, Feng Gao
Genes critical for the survival or reproduction of an organism in certain circumstances are classified as essential genes. Essential genes play a significant role in deciphering the survival mechanism of life. They may be greatly applied to pharmaceutics and synthetic biology. The continuous progress of experimental method for essential gene identification has accelerated the accumulation of gene essentiality data which facilitates the study of essential genes in silico. In this article, we present some available online resources related to gene essentiality, including bioinformatic software tools for transposon sequencing (Tn-seq) analysis, essential gene databases and online services to predict bacterial essential genes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29229007/de-novo-synthesis-of-thiamine-vitamin-b1-is-the-ancestral-state-in-plasmodium-parasites-evidence-from-avian-haemosporidians
#14
Olof Hellgren, Staffan Bensch, Elin Videvall
Parasites often have reduced genomes as their own genes become redundant when utilizing their host as a source of metabolites, thus losing their own de novo production of metabolites. Primate malaria parasites can synthesize vitamin B1 (thiamine) de novo but rodent malaria and other genome-sequenced apicomplexans cannot, as the three essential genes responsible for this pathway are absent in their genomes. The unique presence of functional thiamine synthesis genes in primate malaria parasites and their sequence similarities to bacterial orthologues, have led to speculations that this pathway was horizontally acquired from bacteria...
December 12, 2017: Parasitology
https://www.readbyqxmd.com/read/29222103/a-novel-non-antibiotic-lgt-based-selection-system-for-stable-maintenance-of-expression-vectors-in-escherichia-coli-and-vibrio-cholerae
#15
Manuela Terrinoni, Stefan L Nordqvist, Susanne Källgård, Jan Holmgren, Michael Lebens
Antibiotic selection for maintenance of expression plasmids is discouraged in production of recombinant proteins for pharmaceutical or other human uses due to the risks of antibiotic residue contamination of the final products and release of DNA encoding antibiotic resistance into the environment. We describe the construction of expression plasmids that are instead maintained by complementation of the lgt gene encoding a (pro)lipoprotein glyceryl transferase essential for biosynthesis of bacterial lipoprotein...
December 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29216381/de-novo-gene-evolution-of-antifreeze-glycoproteins-in-codfishes-revealed-by-whole-genome-sequence-data
#16
Helle Tessand Baalsrud, Ole Kristian Tørresen, Monica Hongrø Solbakken, Walter Salzburger, Reinhold Hanel, Kjetill S Jakobsen, Sissel Jentoft
New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown...
December 5, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29208119/comparative-analysis-of-the-burkholderia-cenocepacia-k56-2-essential-genome-reveals-cell-envelope-functions-that-are-uniquely-required-for-survival-in-species-of-the-genus-burkholderia
#17
April S Gislason, Keith Turner, Mike Domaratzki, Silvia T Cardona
Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations...
November 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29206858/extreme-metal-adapted-knockout-and-knockdown-strains-reveal-a-coordinated-gene-expression-among-different-tetrahymena-thermophila-metallothionein-isoforms
#18
Patricia de Francisco, Ana Martín-González, Aaron P Turkewitz, Juan Carlos Gutiérrez
Metallothioneins (MT) constitute a superfamily of small cytosolic proteins that are able to bind metal cations through numerous cysteine (Cys) residues. Like other organisms the ciliate Tetrahymena thermophila presents several MT isoforms, which have been classified into two subfamilies (Cd- and Cu-metallothioneins). The main aim of this study was to examine the specific functions and transcriptional regulation of the five MT isoforms present in T. thermophila, by using several strains of this ciliate. After a laboratory evolution experiment over more than two years, three different T...
2017: PloS One
https://www.readbyqxmd.com/read/29205229/crispr-cas-mediated-gene-silencing-reveals-racr-to-be-a-negative-regulator-of-ydas-and-ydat-toxins-in-escherichia-coli-k-12
#19
Gargi Bindal, Revathy Krishnamurthi, Aswin Sai Narain Seshasayee, Devashish Rath
Bacterial genomes are rich in horizontally acquired prophages. racR is an essential gene located in the rac prophage that is resident in many Escherichia coli genomes. Employing a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas-based gene silencing approach, we show that RacR is a negative regulator of the divergently transcribed and adjacent ydaS-ydaT operon in Escherichia coli K-12. Overexpression of YdaS and YdaT due to RacR depletion leads to cell division defects and decrease in survival...
November 2017: MSphere
https://www.readbyqxmd.com/read/29196747/a-small-cassette-enables-conditional-gene-inactivation-by-crispr-cas9
#20
Paloma M Guzzardo, Christina Rashkova, Rodrigo L Dos Santos, Raha Tehrani, Philippe Collin, Tilmann Bürckstümmer
The availability of CRISPR/Cas9 technology has enabled the rapid establishment of gene knockouts in many cell types and even whole organisms. However, conditional inactivation of essential genes remains a challenge. We devised an approach named DECAI (DEgradation based on Cre-regulated- Artificial Intron). It utilizes a small cassette of just 201 nucleotides that is inserted into the coding exon of a target gene using CRISPR/Cas9 technology and homology-directed repair. As its sequence is derived from an artificial intron, the cassette is removed by the splicing machinery and thus leaves no trace in the "off-state"...
December 1, 2017: Scientific Reports
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