Genomes and Genes
Summary: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
- Takada S, Sato T, Ito Y, Yamashita S, Kato T, Kawasumi M, et al. Targeted gene deletion of miRNAs in mice by TALEN system. PLoS ONE. 2013;8:e76004 pubmed publisher..This method will lead us to expand and accelerate our genetic research using mice in a high throughput way. ..
- Akinyi S, Hayden T, Gamboa D, Torres K, Bendezu J, Abdallah J, et al. Multiple genetic origins of histidine-rich protein 2 gene deletion in Plasmodium falciparum parasites from Peru. Sci Rep. 2013;3:2797 pubmed publisher..These findings indicate that the genetic origin of pfhrp2 deletion in Peru was not a single event, but likely occurred multiple times. ..
- Kostner D, Peters B, Mientus M, Liebl W, Ehrenreich A. Importance of codB for new codA-based markerless gene deletion in Gluconobacter strains. Appl Microbiol Biotechnol. 2013;97:8341-9 pubmed publisher..We found that the presence of E. coli codB, encoding a cytosine permease, was needed for a high efficiency of gene deletion. The system is applicable in wild-type strains because no preceding deletions are required...
- Kulkarni S, Vasantha K, Gogri H, Parchure D, Madkaikar M, Ferec C, et al. First report of Rhnull individuals in the Indian population and characterization of the underlying molecular mechanisms. Transfusion. 2017;57:1944-1948 pubmed publisher..In the other family, a novel splice site variant in RHCE in cis with whole RHD gene deletion was identified at the homozygous state...
- Potts K, Irwin C, Favis N, Pink D, Vincent K, Lewis J, et al. Deletion of F4L (ribonucleotide reductase) in vaccinia virus produces a selective oncolytic virus and promotes anti-tumor immunity with superior safety in bladder cancer models. EMBO Mol Med. 2017;9:638-654 pubmed publisher..Our findings demonstrate the enhanced safety and selectivity of F4L-deleted VACVs, with application as a promising therapy for patients with BCG-refractory cancers and immune dysregulation. ..
- Kino Y, Nakayama Imaohji H, Fujita M, Tada A, Yoneda S, Murakami K, et al. Counterselection employing mutated pheS for markerless genetic deletion in Bacteroides species. Anaerobe. 2016;42:81-88 pubmed publisherMarkerless gene deletion is necessary for multiple gene disruptions due to the limited number of antibiotic resistant markers for some bacteria...
- Kim E, Kim S, Lee J, Kwon Y, Lee M. Ablation of Arg-tRNA-protein transferases results in defective neural tube development. BMB Rep. 2016;49:443-8 pubmed..BMB Reports 2016; 49(8): 443-448]. ..
- Amano N, Narumi S, Hayashi M, Takagi M, Imai K, Nakamura T, et al. Genetic defects in pediatric-onset adrenal insufficiency in Japan. Eur J Endocrinol. 2017;177:187-194 pubmed publisher..Molecular testing is a rational approach to diagnosis in biochemically uncharacterized PAI patients. ..
- Chitty J, Blake K, Blundell R, Koh Y, Thompson M, Robertson A, et al. Cryptococcus neoformans ADS lyase is an enzyme essential for virulence whose crystal structure reveals features exploitable in antifungal drug design. J Biol Chem. 2017;292:11829-11839 pubmed publisher..neoformans ADS lyase inhibitors may also serve as potential therapeutics for metabolic disease; rather than disrupt ADS lyase, compounds that improve the stability the enzyme may be used to treat ADS lyase deficiency disease. ..
- Teschler J, Cheng A, Yildiz F. The Two-Component Signal Transduction System VxrAB Positively Regulates Vibrio cholerae Biofilm Formation. J Bacteriol. 2017;199: pubmed publisher..This research furthers our understanding of the role that TCSs play in the regulation of V. cholerae biofilm formation. ..
- Prince L, Prosseda S, Higgins K, Carlring J, Prestwich E, Ogryzko N, et al. NR4A orphan nuclear receptor family members, NR4A2 and NR4A3, regulate neutrophil number and survival. Blood. 2017;130:1014-1025 pubmed publisher..In summary, we show that NR4A2 and NR4A3 are components of a downstream transcriptional response to PKA activation in the neutrophil, and that they positively regulate neutrophil survival and homeostasis. ..
- Cao K, Collings C, Marshall S, Morgan M, Rendleman E, Wang L, et al. SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression. Genes Dev. 2017;31:787-801 pubmed publisher..Our results reveal multiple regulatory layers for Hox genes to fine-tune transcriptional programs essential for development. ..
- Rajakumar S, Ravi C, Nachiappan V. Defect of zinc transporter ZRT1 ameliorates cadmium induced lipid accumulation in Saccharomyces cerevisiae. Metallomics. 2016;8:453-60 pubmed publisher..Hence, these studies suggest that the zrt1? cells provide resistance towards Cd and aid in the maintenance of lipid homeostasis in yeast cells. ..
- Mridha A, Haczeyni F, Yeh M, Haigh W, Ioannou G, Barn V, et al. TLR9 is up-regulated in human and murine NASH: pivotal role in inflammatory recruitment and cell survival. Clin Sci (Lond). 2017;131:2145-2159 pubmed publisher..This response is mediated via M1-macrophages and neutrophil chemotaxis. ..
- Bhatia P, Singh A, Hedge A. A Novel g.55040074delT in ALAS2 Gene Resulting in a Monomeric Protein and Severe Sideroblastic Anemia Phenotype. J Pediatr Hematol Oncol. 2017;39:463-465 pubmed publisher..9 ?g/L. The protein structure as predicted by SWISS model was a monomeric form rather than wild-type homodimer, resulting in marked loss of function and protein instability. ..
- Ma H, Yang F, Butler M, Belcher J, Redmond T, Placzek A, et al. Inhibition of thyroid hormone receptor locally in the retina is a therapeutic strategy for retinal degeneration. FASEB J. 2017;31:3425-3438 pubmed publisher..Ma, H., Yang, F., Butler, M. R., Belcher, J., Redmond, T. M., Placzek, A. T., Scanlan, T. S., Ding, X.-Q. Inhibition of thyroid hormone receptor locally in the retina is a therapeutic strategy for retinal degeneration. ..
- Singh M, Kim K, Kwak G, Baek S, Kim H. Methionine sulfoxide reductase A protects against lipopolysaccharide-induced septic shock via negative regulation of the proinflammatory responses. Arch Biochem Biophys. 2017;631:42-48 pubmed publisher..Taken together, our results suggest that MsrA protects against LPS-induced septic shock, and negatively regulates proinflammatory responses via inhibition of the ROS-MAPK-NF-ÎºB signaling pathways. ..
- Liu X, Zhang L, Ruan M, Liu T, Zhang J, Liu F, et al. [Significance of PAX5 deletion in childhood B-lineage acute lymphoblastic leukemia without reproducible chromosomal abnormalities]. Zhongguo Dang Dai Er Ke Za Zhi. 2016;18:287-91 pubmed..128). The Cox analysis showed that PAX5 deletion was a risk factor for DFS (P=0.03). PAX5 deletion is an independent risk factor for DFS in B-ALL children without reproducible chromosomal abnormalities. ..
- Curtis P. Stalk formation of Brevundimonas and how it compares to Caulobacter crescentus. PLoS ONE. 2017;12:e0184063 pubmed publisher..subvibrioides stalk. In summary, this work begins to address how much the C. crescentus model for this unusual morphological adaptation can be extended to related organisms. ..
- Hoefler B, Stubbendieck R, Josyula N, Moisan S, Schulze E, Straight P. A Link between Linearmycin Biosynthesis and Extracellular Vesicle Genesis Connects Specialized Metabolism and Bacterial Membrane Physiology. Cell Chem Biol. 2017;24:1238-1249.e7 pubmed publisher..Our results reveal integration of linearmycin biosynthesis with production of extracellular vesicles, suggesting a deep connection between specialized metabolism and bacterial membrane physiology. ..
- Bröer A, Rahimi F, Broer S. Deletion of Amino Acid Transporter ASCT2 (SLC1A5) Reveals an Essential Role for Transporters SNAT1 (SLC38A1) and SNAT2 (SLC38A2) to Sustain Glutaminolysis in Cancer Cells. J Biol Chem. 2016;291:13194-205 pubmed publisher..Silencing of GCN2 in the ASCT2(-/-) background reduced cell growth, showing that a combined targeted approach would inhibit growth of glutamine-dependent cancer cells. ..
- Ray S, Maitra A, Biswas A, Panjikar S, Mondal J, Anand R. Functional insights into the mode of DNA and ligand binding of the TetR family regulator TylP from Streptomyces fradiae. J Biol Chem. 2017;292:15301-15311 pubmed publisher..Collectively, the structure along with corroborating biochemical studies provided insights into the novel mode of regulation of TetRs in antibiotic-producing organisms. ..
- Guo H, Kazadaeva Y, Ortega F, Manjunath N, Desai T. Trinucleotide repeat containing 6c (TNRC6c) is essential for microvascular maturation during distal airspace sacculation in the developing lung. Dev Biol. 2017;430:214-223 pubmed publisher..These results imply a complex and indirect mode of regulation of sacculation by TNRC6c, mediated in part by dynamic transcriptional repression of an inhibitor of TGF? family gene expression. ..
- Salazar S, Gallardo C, Kaufman A, Herber C, Haas L, Robinson S, et al. Conditional Deletion of Prnp Rescues Behavioral and Synaptic Deficits after Disease Onset in Transgenic Alzheimer's Disease. J Neurosci. 2017;37:9207-9221 pubmed publisher..This study underscores the therapeutic potential of PrPC deletion given that patients already present symptoms at the time of diagnosis. ..
- Gangaiah D, Raterman E, Wu H, Fortney K, Gao H, Liu Y, et al. Both MisR (CpxR) and MisS (CpxA) Are Required for Neisseria gonorrhoeae Infection in a Murine Model of Lower Genital Tract Infection. Infect Immun. 2017;85: pubmed publisher..Provided the MisR is constitutively phosphorylated in the misS mutant, the data suggest that controlled but not constitutive activation is required for gonococcal infection in mice. ..
- Striebinger H, Funk C, Raschbichler V, Bailer S. Subcellular Trafficking and Functional Relationship of the HSV-1 Glycoproteins N and M. Viruses. 2016;8:83 pubmed publisher..We propose that gN functions in gM-dependent as well as gM-independent processes during which it is complemented by other viral factors. ..
- Fan J, Wang Y, Liu L, Zhang H, Zhang F, Shi L, et al. cTAGE5 deletion in pancreatic ? cells impairs proinsulin trafficking and insulin biogenesis in mice. J Cell Biol. 2017;216:4153-4164 pubmed publisher..Together our data provide more insight into the underlying mechanism of the proinsulin trafficking pathway. ..
- Chitrala K, Guan H, Singh N, Busbee B, Gandy A, Mehrpouya Bahrami P, et al. CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice. Eur J Immunol. 2017;47:1188-1199 pubmed publisher..In conclusion, our results demonstrate that the attenuation of EAE seen following CD44 gene deletion in mice may result from alterations in the gut microbiota and SCFAs...
- Bouthier de La Tour C, Mathieu M, Meyer L, Dupaigne P, Passot F, Servant P, et al. In vivo and in vitro characterization of DdrC, a DNA damage response protein in Deinococcus radiodurans bacterium. PLoS ONE. 2017;12:e0177751 pubmed publisher..DdrC might also be an accessory protein that participates in a single strand annealing pathway whose importance in DNA repair becomes apparent when DNA is heavily damaged. ..
- Zhang S, Ito M, Skerker J, Arkin A, Rao C. Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation. Appl Microbiol Biotechnol. 2016;100:9393-9405 pubmed..61 g/L/h during fed-batch growth on glucose. These results further establish R. toruloides as a platform organism for the production of lipids and potentially other lipid-derived compounds from sugars. ..
- Olson A, Rico A, Wang Z, Delhon G, Wiebe M. Deletion of the Vaccinia Virus B1 Kinase Reveals Essential Functions of This Enzyme Complemented Partly by the Homologous Cellular Kinase VRK2. J Virol. 2017;91: pubmed publisher..As a result, we have discovered that B1 and VRK2 target a common set of substrates vital to productive infection of this large cytoplasmic DNA virus. ..
- Parisot J, Flore G, Bertacchi M, Studer M. COUP-TFI mitotically regulates production and migration of dentate granule cells and modulates hippocampal Cxcr4 expression. Development. 2017;144:2045-2058 pubmed publisher..Together, our results indicate that COUP-TFI is required predominantly in DG progenitors for modulating expression of the Cxcr4 receptor during granule cell neurogenesis and migration. ..
- Luongo T, Lambert J, Gross P, Nwokedi M, Lombardi A, Shanmughapriya S, et al. The mitochondrial Na+/Ca2+ exchanger is essential for Ca2+ homeostasis and viability. Nature. 2017;545:93-97 pubmed publisher..These results demonstrate the essential nature of mCa2+ efflux in cellular function and suggest that augmenting mCa2+ efflux may be a viable therapeutic strategy in disease. ..
- Shafer M, Nguyen A, Tremblay M, Viala S, Béland M, Bertos N, et al. Lineage Specification from Prostate Progenitor Cells Requires Gata3-Dependent Mitotic Spindle Orientation. Stem Cell Reports. 2017;8:1018-1031 pubmed publisher..Collectively, these results identify a critical role for GATA3 in prostate lineage specification, and further highlight the importance of regulating spindle orientation for hierarchical cell lineage organization. ..
- Isaka M, Tatsuno I, Maeyama J, Matsui H, Zhang Y, Hasegawa T. The YvqE two-component system controls biofilm formation and acid production in Streptococcus pyogenes. APMIS. 2016;124:574-85 pubmed publisher..This study shows that at low environmental pH, biofilm formation in S. pyogenes is mediated by YvqE and suggests that regulation of pilus expression by environmental acidification could be directly under the control of YvqE. ..
- Afzal M, Kuipers O, Shafeeq S. Niacin-mediated Gene Expression and Role of NiaR as a Transcriptional Repressor of niaX, nadC, and pnuC in Streptococcus pneumoniae. Front Cell Infect Microbiol. 2017;7:70 pubmed publisher..The putative operator site of NiaR (5'-TACWRGTGTMTWKACASYTRWAW-3') in the promoter regions of niaX, nadC, and pnuC is predicted and further confirmed by promoter mutational experiments. ..
- Ciesielska K, Roelants S, Van Bogaert I, de Waele S, Vandenberghe I, Groeneboer S, et al. Characterization of a novel enzyme-Starmerella bombicola lactone esterase (SBLE)-responsible for sophorolipid lactonization. Appl Microbiol Biotechnol. 2016;100:9529-9541 pubmed..We therefore propose that SBLE operates via the common serine hydrolase mechanism in which the catalytic serine residue is assisted by a His/Asp pair. ..
- Gassner C, BrÃ¶nnimann C, Merki Y, Mattle Greminger M, Sigurdardottir S, Meyer E, et al. Stepwise partitioning of Xp21: a profiling method for XK deletions causative of the McLeod syndrome. Transfusion. 2017;57:2125-2135 pubmed publisher..1 is pragmatic and cost-efficient in comparison to other diagnostic techniques such as "massive parallel sequencing" given the rarity of MLS. All males with suspected MLS should be considered for molecular XK profiling. ..
- Quintas A, PÃ©rez NÃºÃ±ez D, SÃ¡nchez E, Nogal M, Hentze M, CastellÃ³ A, et al. Characterization of the African Swine Fever Virus Decapping Enzyme during Infection. J Virol. 2017;91: pubmed publisher..Here, we demonstrate that ASFV-DP is a novel RNA-binding protein implicated in the regulation of mRNA metabolism during infection, making it a good target for vaccine development. ..
- Kamphorst A, Wieland A, Nasti T, Yang S, Zhang R, Barber D, et al. Rescue of exhausted CD8 T cells by PD-1-targeted therapies is CD28-dependent. Science. 2017;355:1423-1427 pubmed publisher..Conditional gene deletion showed a cell-intrinsic requirement of CD28 for CD8 T cell proliferation after PD-1 blockade...
- Landry Truchon K, Houde N, Boucherat O, Joncas F, Dasen J, Philippidou P, et al. HOXA5 plays tissue-specific roles in the developing respiratory system. Development. 2017;144:3547-3561 pubmed publisher..Thus, Hoxa5 possesses tissue-specific functions that differentially contribute to the morphogenesis of the respiratory tract. ..
- Matsumura R, Akashi M. Multiple circadian transcriptional elements cooperatively regulate cell-autonomous transcriptional oscillation of Period3, a mammalian clock gene. J Biol Chem. 2017;292:16081-16092 pubmed publisher..These results indicate that three E box-like and two D box-like elements cooperatively and redundantly regulate cell-autonomous transcriptional oscillation of Per3. ..
- Peng C, Engle S, Yan Y, Weera M, Berry J, Arvin M, et al. Altered nicotine reward-associated behavior following ?4 nAChR subunit deletion in ventral midbrain. PLoS ONE. 2017;12:e0182142 pubmed publisher..These results reveal that attenuation of ?4* nAChR function in reward-related brain circuitry of adult animals may increase nicotine intake by enhancing the rewarding effects and/or reducing the aversive effects of nicotine. ..
- Birot A, Eguienta K, Vazquez S, Claverol S, Bonneu M, Ekwall K, et al. A second Wpl1 anti-cohesion pathway requires dephosphorylation of fission yeast kleisin Rad21 by PP4. EMBO J. 2017;36:1364-1378 pubmed publisher..These results reveal that Wpl1 antagonizes sister chromatid cohesion by a novel pathway regulated by the phosphorylation status of the cohesin kleisin subunit. ..
- Li L, Jiang W, Lu Y. A Novel Two-Component System, GluR-GluK, Involved in Glutamate Sensing and Uptake in Streptomyces coelicolor. J Bacteriol. 2017;199: pubmed publisher..To the best of our knowledge, this is the first report describing a TCS signal transduction pathway for glutamate sensing and uptake in actinobacteria. ..
- Cech D, Markin K, Woodard R. Identification of a d-Arabinose-5-Phosphate Isomerase in the Gram-Positive Clostridium tetani. J Bacteriol. 2017;199: pubmed publisher..We have speculated a regulatory role for this API in C. tetani, an organism that does not produce lipopolysaccharide. ..
- Baxley T, Johnson D, Pinto J, Chalovich J. Troponin C Mutations Partially Stabilize the Active State of Regulated Actin and Fully Stabilize the Active State When Paired with Î”14 TnT. Biochemistry. 2017;56:2928-2937 pubmed publisher..Because Ca2+ gives full activation, in this situation, troponin must be capable of positioning tropomyosin in the active M state without the need for rigor myosin binding. ..
- Loddeke M, Schneider B, Oguri T, Mehta I, Xuan Z, Reitzer L. Anaerobic Cysteine Degradation and Potential Metabolic Coordination in Salmonella enterica and Escherichia coli. J Bacteriol. 2017;199: pubmed publisher..For these and other reasons, cysteine and sulfide concentrations must be controlled, and this work shows that cysteine catabolism contributes to this control. ..
- Mason A, Garza R, McCormick M, Patel B, Kennedy B, Pillus L, et al. The replicative lifespan-extending deletion of SGF73 results in altered ribosomal gene expression in yeast. Aging Cell. 2017;16:785-796 pubmed publisher..These findings implicate altered ribosomal protein expression in sgf73Δ yeast RLS and highlight altered acetylation as a pathway of relevance for SCA7 neurodegeneration. ..