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https://www.readbyqxmd.com/read/28647612/evolution-of-human-apolipoprotein-e-apoe-isoforms-gene-structure-protein-function-and-interaction-with-dietary-factors
#1
REVIEW
Patricia Huebbe, Gerald Rimbach
Apolipoprotein E (APOE) is a member of the vertebrate protein family of exchangeable apolipoproteins that is characterized by amphipathic α-helices encoded by multiple nucleotide tandem repeats. Its equivalent in flying insects - apolipophorin-III - shares structural and functional commonalities with APOE, suggesting the possibility of an evolutionary relationship between the proteins. In contrast to all other known species, human APOE is functionally polymorphic and possesses three major allelic variants (ε4, ε3 and ε2)...
June 21, 2017: Ageing Research Reviews
https://www.readbyqxmd.com/read/28640841/a-sorghum-sorghum-bicolor-mutant-with-altered-carbon-isotope-ratio
#2
Govinda Rizal, Shanta Karki, Vivek Thakur, Samart Wanchana, Hugo Alonso-Cantabrana, Jacque Dionora, John E Sheehy, Robert Furbank, Susanne von Caemmerer, William Paul Quick
Recent efforts to engineer C4 photosynthetic traits into C3 plants such as rice demand an understanding of the genetic elements that enable C4 plants to outperform C3 plants. As a part of the C4 Rice Consortium's efforts to identify genes needed to support C4 photosynthesis, EMS mutagenized sorghum populations were generated and screened to identify genes that cause a loss of C4 function. Stable carbon isotope ratio (δ13C) of leaf dry matter has been used to distinguishspecies with C3 and C4 photosynthetic pathways...
2017: PloS One
https://www.readbyqxmd.com/read/28629206/an-enhanced-vector-free-allele-exchange-vfae-mutagenesis-protocol-for-genome-editing-in-a-wide-range-of-bacterial-species
#3
Ahmed E Gomaa, Chen Zhang, Zhimin Yang, Liguo Shang, Shijie Jiang, Zhiping Deng, Yuhua Zhan, Wei Lu, Min Lin, Yongliang Yan
Vector-free allele exchange (VFAE) is a newly developed protocol for genome editing in Pseudomonas species. Although several parameters have been determined to optimize the procedures for obtaining a stable and high-frequency mutation, numerous false-positive clones still appear on the plate, which increases the difficulty of finding the desired mutants. It has also not been established whether this protocol can be used for genome editing in other bacterial species. In the current study, the protocol was modified to dramatically decrease the occurrence of false-positive colonies using Pseudomonas stutzeri A1501 as a model strain...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28613379/restoration-over-time-and-sustainability-of-schinus-terebinthifolius-raddi
#4
S V Álvares-Carvalho, R Silva-Mann, I B Gois, M F V Melo, A S Oliveira, R A Ferreira, L J Gomes
The success of recovery programs on degraded areas is dependent on the genetic material to be used, which should present heterozygosity and genetic diversity in native and recovered populations. This study was carried out to evaluate the model efficiency to enable the recovery of a degraded area of the Lower São Francisco, Sergipe, Brazil. The target species for this study was Schinus terebinthifolius Raddi. Three populations were analyzed, the recovered area, seed-tree source population, and native tree population border established to the recovered area...
May 31, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28611741/glycosylation-of-a-capsule-like-complex-clc-by-francisella-novicida-is-required-for-virulence-and-partial-protective-immunity-in-mice
#5
Kelly C Freudenberger Catanzaro, Anna E Champion, Nrusingh Mohapatra, Thomas Cecere, Thomas J Inzana
Francisella tularensis is a Gram-negative bacterium and the etiologic agent of tularemia. F. tularensis may appear encapsulated when examined by transmission electron microscopy (TEM), which is due to production of an extracellular capsule-like complex (CLC) when the bacterium is grown under specific environmental conditions. Deletion of two glycosylation genes in the live vaccine strain (LVS) results in loss of apparent CLC and attenuation of LVS in mice. In contrast, F. novicida, which is also highly virulent for mice, is reported to be non-encapsulated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28607459/the-arf6-activator-efa6-psd3-confers-regional-specificity-and-modulates-ethanol-consumption-in-drosophila-and-humans
#6
D A Gonzalez, T Jia, J H Pinzón, S F Acevedo, S A Ojelade, B Xu, N Tay, S Desrivières, J L Hernandez, T Banaschewski, C Büchel, A L W Bokde, P J Conrod, H Flor, V Frouin, J Gallinat, H Garavan, P A Gowland, A Heinz, B Ittermann, M Lathrop, J-L Martinot, T Paus, M N Smolka, A R Rodan, G Schumann, A Rothenfluh
Ubiquitously expressed genes have been implicated in a variety of specific behaviors, including responses to ethanol. However, the mechanisms that confer this behavioral specificity have remained elusive. Previously, we showed that the ubiquitously expressed small GTPase Arf6 is required for normal ethanol-induced sedation in adult Drosophila. Here, we show that this behavioral response also requires Efa6, one of (at least) three Drosophila Arf6 guanine exchange factors. Ethanol-naive Arf6 and Efa6 mutants were sensitive to ethanol-induced sedation and lacked rapid tolerance upon re-exposure to ethanol, when compared with wild-type flies...
June 13, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28602864/nckx3-was-compensated-by-calcium-transporting-genes-and-bone-resorption-in-a-nckx3-ko-mouse-model
#7
Hyun Yang, Changhwan Ahn, Eun-Kyeong Shin, Ji-Sun Lee, Beum-Soo An, Eui-Bae Jeung
Gene knockout is the most powerful tool for determination of gene function or permanent modification of the phenotypic characteristics of an animal. Existing methods for gene disruption are limited by their efficiency, time required for completion and potential for confounding off-target effects. In this study, a rapid single-step approach to knockout of a targeted gene in mice using zinc-finger nucleases (ZFNs) was demonstrated for generation of mutant (knockout; KO) alleles. Specifically, ZFNs to target the sodium/calcium/potassium exchanger3 (NCKX3) gene in C57bl/6j were designed using the concept of this approach...
June 7, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28600642/characterization-and-comparison-of-genetic-variation-in-cotesia-flavipes-hymenoptera-braconidae-mass-reared-for-biological-pest-control-using-microsatellite-markers
#8
F C Freitas, A C Morales-Corrêa E Castro, N C C P Barbosa, O A Fernandes
The larval parasitoid Cotesia flavipes (Cameron) (Hymenoptera: Braconidae) is an important biological control agent of the sugarcane borer, Diatraea saccharalis (Fabricius) (Lepidoptera: Crambidae). This exotic parasitoid has been mass reared for field release since its introduction in the 1970s. Insects are exchanged between labs or introduced from the field, but without basic studies or criteria. Thus, the objective of this study was to evaluate the genetic variability of insects from six Brazilian States (São Paulo, Minas Gerais, Paraná, Goiás, Maranhão, and Alagoas) using microsatellites...
June 9, 2017: Neotropical Entomology
https://www.readbyqxmd.com/read/28597825/fungal-sex-the-basidiomycota
#9
Marco A Coelho, Guus Bakkeren, Sheng Sun, Michael E Hood, Tatiana Giraud
Fungi of the Basidiomycota, representing major pathogen lineages and mushroom-forming species, exhibit diverse means to achieve sexual reproduction, with particularly varied mechanisms to determine compatibilities of haploid mating partners. For species that require mating between distinct genotypes, discrimination is usually based on both the reciprocal exchange of diffusible mating pheromones, rather than sexes, and the interactions of homeodomain protein signals after cell fusion. Both compatibility factors must be heterozygous in the product of mating, and genetic linkage relationships of the mating pheromone/receptor and homeodomain genes largely determine the complex patterns of mating-type variation...
June 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28596255/thrombotic-thrombocytopenic-purpura-associated-with-pegylated-interferon-alfa-2a-use-in-a-patient-with-polycythemia-vera
#10
Radhika Gangaraju, Soo J Kim, Jing-Fei Dong, Sabina Swierczek, Josef T Prchal
Pegylated interferon alfa-2a (pegIFNa) is being increasingly used for treatment of myeloproliferative neoplasms; however, its side effects, including autoimmune complications, are not unusual. We report on a 47-year-old woman with polycythemia vera (PV) treated with pegIFNa and in complete hematologic remission who developed thrombotic thrombocytopenic purpura (TTP). To our knowledge, thrombotic microangiopathy has been reported as a side effect of interferon (IFN) use in patients with hepatitis and chronic myeloid leukemia, but not in those with PV...
June 2017: Journal of the National Comprehensive Cancer Network: JNCCN
https://www.readbyqxmd.com/read/28594944/development-and-evaluation-of-a-core-genome-multilocus-typing-scheme-for-whole-genome-sequence-based-typing-of-acinetobacter-baumannii
#11
Paul G Higgins, Karola Prior, Dag Harmsen, Harald Seifert
We have employed whole genome sequencing to define and evaluate a core genome multilocus sequence typing (cgMLST) scheme for Acinetobacter baumannii. To define a core genome we downloaded a total of 1,573 putative A. baumannii genomes from NCBI as well as representative isolates belonging to the eight previously described international A. baumannii clonal lineages. The core genome was then employed against a total of fifty-three carbapenem-resistant A. baumannii isolates that were previously typed by PFGE and linked to hospital outbreaks in eight German cities...
2017: PloS One
https://www.readbyqxmd.com/read/28587902/involvement-of-charcot-marie-tooth-disease-gene-mitofusin-2-expression-in-paclitaxel-induced-mechanical-allodynia-in-rats
#12
Yuta Yamashita, Keiichi Irie, Akane Kochi, Nami Kimura, Toshinobu Hayashi, Koichi Matsuo, Takayuki Myose, Kazunori Sano, Takafumi Nakano, Yumi Takase, Yoshihiko Nakamura, Tomomitsu Satho, Kenji Mishima, Kenichi Mishima
Paclitaxel induces peripheral neuropathy, which is dose-limiting and results in loss of quality of life. Therefore, the prevention and treatment of paclitaxel-induced peripheral neuropathy are major concerns in clinical cancer therapy. However, the detailed mechanisms have not been fully elucidated. It has recently been reported that allelic variability in the Charcot-Marie-Tooth disease (CMT) genes, mitofusin 2 (MFN2), Rho guanine nucleotide exchange factor 10 (ARHGEF10), and periaxin (PRX), affected paclitaxel-induced peripheral neuropathy in clinical cases...
June 3, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28585695/the-rhogap-myo9b-promotes-bone-growth-by-mediating-osteoblastic-responsiveness-to-igf-1
#13
Brooke K McMichael, Yong-Hoon Jeong, Justin A Auerbach, Cheol-Min Han, Ryan Sedlar, Vikram Shettigar, Martin Bähler, Sudha Agarwal, Do-Gyoon Kim, Beth S Lee
The RhoA subfamily of Rho GTPases regulates actin-based cellular functions in bone such as differentiation, migration, and mechanotransduction. Polymorphisms or genetic ablation of RHOA and some of its regulatory guanine exchange factors (GEFs) have been linked to poor bone health in humans and mice, but the effects of RhoA-specific GTPase-activating proteins (GAPs) on bone quality have not yet been identified. Therefore, we examined the consequences of RhoGAP Myo9b gene knockout on bone growth, phenotype and cellular activity...
June 6, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28582546/the-contribution-of-homology-arms-to-nuclease-assisted-genome-engineering
#14
Oliver Baker, Sarah Tsurkan, Jun Fu, Barbara Klink, Andreas Rump, Mandy Obst, Andrea Kranz, Evelin Schröck, Konstantinos Anastassiadis, A Francis Stewart
Designer nucleases like CRISPR/Cas9 enable fluent site-directed damage or small mutations in many genomes. Strategies for their use to achieve more complex tasks like regional exchanges for gene humanization or the establishment of conditional alleles are still emerging. To optimize Cas9-assisted targeting, we measured the relationship between targeting frequency and homology length in targeting constructs using a hypoxanthine-guanine phosphoribosyl-transferase assay in mouse embryonic stem cells. Targeting frequency with supercoiled plasmids improved steeply up to 2 kb total homology and continued to increase with even longer homology arms, thereby implying that Cas9-assisted targeting efficiencies can be improved using homology arms of 1 kb or greater...
June 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28580238/rapid-breeding-and-varietal-replacement-are-critical-to-adaptation-of-cropping-systems-in-the-developing-world-to-climate-change
#15
REVIEW
Gary N Atlin, Jill E Cairns, Biswanath Das
Plant breeding is a key mechanism for adaptation of cropping systems to climate change. Much discussion of breeding for climate change focuses on genes with large effects on heat and drought tolerance, but phenology and stress tolerance are highly polygenic. Adaptation will therefore mainly result from continually adjusting allele frequencies at many loci through rapid-cycle breeding that delivers a steady stream of incrementally improved cultivars. This will require access to elite germplasm from other regions, shortened breeding cycles, and multi-location testing systems that adequately sample the target population of environments...
March 2017: Global Food Security
https://www.readbyqxmd.com/read/28566233/expanding-the-genetic-cause-of-multiple-sulfatase-deficiency-a-novel-sumf1-variant-in-a-patient-displaying-a-severe-late-infantile-form-of-the-disease
#16
Ilona Jaszczuk, Lars Schlotawa, Thomas Dierks, Andreas Ohlenbusch, Dominique Koppenhöfer, Mariusz Babicz, Monika Lejman, Karthikeyan Radhakrishnan, Agnieszka Ługowska
Multiple sulfatase deficiency (MSD) is a rare inherited metabolic disease caused by defective cellular sulfatases. Activity of sulfatases depends on post-translational modification catalyzed by formylglycine-generating enzyme (FGE), encoded by the SUMF1 gene. SUMF1 pathologic variants cause MSD, a syndrome presenting with a complex phenotype. We describe the first Polish patient with MSD caused by a yet undescribed pathologic variant c.337G>A [p.Glu113Lys] (i.e. p.E113K) in heterozygous combination with the known deletion allele c...
May 22, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28559318/a-mechanism-for-lipid-binding-to-apoe-and-the-role-of-intrinsically-disordered-regions-coupled-to-domain-domain-interactions
#17
Carl Frieden, Hanliu Wang, Chris M W Ho
Relative to the apolipoprotein E (apoE) E3 allele of the APOE gene, apoE4 strongly increases the risk for the development of late-onset Alzheimer's disease. However, apoE4 differs from apoE3 by only a single amino acid at position 112, which is arginine in apoE4 and cysteine in apoE3. It remains unclear why apoE3 and apoE4 are functionally different. Described here is a proposal for understanding the functional differences between these two isoforms with respect to lipid binding. A mechanism is proposed that is based on the full-length monomeric structure of the protein, on hydrogen-deuterium exchange mass spectrometry data, and on the role of intrinsically disordered regions to control protein motions...
May 30, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28553286/assessment-of-spanish-panel-reactive-antibody-calculator-and-potential-usefulness
#18
Esther Asensio, Marcos López-Hoyos, Íñigo Romón, Jesús Ontañón, David San Segundo
BACKGROUND AND OBJECTIVES: The calculated panel reactive of antibodies (cPRAs) necessary for kidney donor-pair exchange and highly sensitized programs are estimated using different panel reactive antibody (PRA) calculators based on big enough samples in Eurotransplant (EUTR), United Network for Organ Sharing (UNOS), and Canadian Transplant Registry (CTR) websites. However, those calculators can vary depending on the ethnic they are applied. Here, we develop a PRA calculator used in the Spanish Program of Transplant Access for Highly Sensitized patients (PATHI) and validate it with EUTR, UNOS, and CTR calculators...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28544176/interactions-between-calcium-intake-and-polymorphisms-in-genes-essential-for-calcium-reabsorption-and-risk-of-colorectal-neoplasia-in-a-two-phase-study
#19
Jing Zhao, Xiangzhu Zhu, Martha J Shrubsole, Reid M Ness, Elizabeth A Hibler, Qiuyin Cai, Jirong Long, Zhi Chen, Ming Jiang, Edmond K Kabagambe, Bing Zhang, Lifang Hou, Walter E Smalley, Todd L Edwards, Edward L Giovannucci, Wei Zheng, Qi Dai
The SLC8A1 (solute carrier family 8, member 1) gene, encoding Na(+) /Ca(2+) exchanger, is essential in regulating calcium reabsorption and homeostasis. Calcium homeostasis plays a key role in cell proliferation and apoptosis. We hypothesized that polymorphisms in five calcium-regulating genes (SLC8A1, ATP2B1, CALB1, CALB2, and CABP1) interact with calcium intake in relation to the risk of colorectal neoplasia. A two-phase (discovery and replication) study was conducted within the Tennessee Colorectal Polyp Study, including a total of 1275 cases and 2811 controls...
May 23, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28539926/gene-specific-substitution-profiles-describe-the-types-and-frequencies-of-amino-acid-changes-during-antibody-somatic-hypermutation
#20
Zizhang Sheng, Chaim A Schramm, Rui Kong, James C Mullikin, John R Mascola, Peter D Kwong, Lawrence Shapiro
Somatic hypermutation (SHM) plays a critical role in the maturation of antibodies, optimizing recognition initiated by recombination of V(D)J genes. Previous studies have shown that the propensity to mutate is modulated by the context of surrounding nucleotides and that SHM machinery generates biased substitutions. To investigate the intrinsic mutation frequency and substitution bias of SHMs at the amino acid level, we analyzed functional human antibody repertoires and developed mGSSP (method for gene-specific substitution profile), a method to construct amino acid substitution profiles from next-generation sequencing-determined B cell transcripts...
2017: Frontiers in Immunology
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