Genomes and Genes
Summary: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
- Doukakis P, Hanner R, Shivji M, Bartholomew C, Chapman D, Wong E, et al. Applying genetic techniques to study remote shark fisheries in northeastern Madagascar. Mitochondrial DNA. 2011;22 Suppl 1:15-20 pubmed publisher..Conservation efforts should characterize species exploitation at present, create spatial and temporal fishing restrictions to protect endangered species, and restrict large mesh gillnets. ..
- Haubensak W, Kunwar P, Cai H, Ciocchi S, Wall N, Ponnusamy R, et al. Genetic dissection of an amygdala microcircuit that gates conditioned fear. Nature. 2010;468:270-6 pubmed publisher..This correspondence, together with behavioural data, defines an inhibitory microcircuit in CEl that gates CEm output to control the level of conditioned freezing. ..
- Fath S, Bauer A, Liss M, Spriestersbach A, Maertens B, Hahn P, et al. Multiparameter RNA and codon optimization: a standardized tool to assess and enhance autologous mammalian gene expression. PLoS ONE. 2011;6:e17596 pubmed publisher..This is the first large-scale study addressing the influence of multiparameter optimization on autologous human protein expression. ..
- Haynes K, Ceroni F, Flicker D, Younger A, Silver P. A sensitive switch for visualizing natural gene silencing in single cells. ACS Synth Biol. 2012;1:99-106 pubmed..Our studies extend the application of rationally designed synthetic switches to RNAi, providing a sensitive way to visualize the dynamics of RNAi activity rather than just the presence of miRNA molecules. ..
- Gomez E, Pérez Pascual D, Fernández L, Méndez J, Reimundo P, Navais R, et al. Construction and validation of a GFP-based vector for promoter expression analysis in the fish pathogen Flavobacterium psychrophilum. Gene. 2012;497:263-8 pubmed publisher..psychrophilum, by enabling the determination of gene expression both in vitro and in vivo. Furthermore, this would also open the possibility for studies on the location of this bacterium in the fish tissues...
- Titov D, Liu J. Identification and validation of protein targets of bioactive small molecules. Bioorg Med Chem. 2012;20:1902-9 pubmed publisher..A special emphasis is placed on target validation, including correlation analysis and genetic methods, as this area is often ignored despite its importance. ..
- Prabhu J, Wahi K, Korlimarla A, Correa M, Manjunath S, Raman N, et al. The epigenetic silencing of the estrogen receptor (ER) by hypermethylation of the ESR1 promoter is seen predominantly in triple-negative breast cancers in Indian women. Tumour Biol. 2012;33:315-23 pubmed publisher..The development of this assay also permits a rational approach to the selection of patients for clinical trials examining the efficacy of demethylating agents in the treatment of ER-negative breast cancer. ..
- Dai Q, Smibert P, Lai E. Exploiting Drosophila genetics to understand microRNA function and regulation. Curr Top Dev Biol. 2012;99:201-235 pubmed publisher..Overall, we hope that this exposition of Drosophila genetic techniques, well known to the legions of fly geneticists and used to study all genes, can inform the general miRNA ..
- White J, Gerdin A, Karp N, Ryder E, Buljan M, Bussell J, et al. Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes. Cell. 2013;154:452-64 pubmed publisher..Phenotypic data and more than 900 mutants are openly available for further analysis. PAPERCLIP: ..
- Zimmerman D. Thyroid carcinoma in children and adolescents: diagnostic implications of analysis of the tumor genome. Curr Opin Pediatr. 2013;25:528-31 pubmed publisher..A number of molecular techniques are available to identify patients with indeterminate cytology who can confidently be followed without surgery as the probability of malignancy is low. ..
- Kani S, Tanaka Y, Matsuura K, Watanabe T, Yatsuhashi H, Orito E, et al. Development of new IL28B genotyping method using Invader Plus assay. Microbiol Immunol. 2012;56:318-23 pubmed publisher..3%, and that of non-responders in the minor heterozygous/homozygous type was 72.5%. A convenient IL28B genotyping method using the Invader Plus assay could be useful to predict the treatment outcome in clinical practice. ..
- Parker V, Semple R. Genetics in endocrinology: genetic forms of severe insulin resistance: what endocrinologists should know. Eur J Endocrinol. 2013;169:R71-80 pubmed publisher..In particular, we draw distinctions among the biochemical subphenotypes of IR that arise from primary adipose tissue dysfunction or from primary insulin signalling defects and discuss the implications of this dichotomy for management. ..
- Liao H, Tsai I, Chen G, Kuo C, Wei M, Hwang T, et al. Simultaneous detection of single nucleotide polymorphisms and copy number variations in the CYP2D6 gene by multiplex polymerase chain reaction combined with capillary electrophoresis. Anal Chim Acta. 2013;763:67-75 pubmed publisher..Similar approach can be applied to simultaneous detection of SNPs and CNVs of other genes. ..
- van der Weerd K, Dik W, Schrijver B, Bogers A, Maat A, van Nederveen F, et al. Combined TCRG and TCRA TREC analysis reveals increased peripheral T-lymphocyte but constant intra-thymic proliferative history upon ageing. Mol Immunol. 2013;53:302-12 pubmed publisher..This novel TREC assay approach could prove valuable in immune status monitoring in a variety of conditions. ..
- Weber T, Renzland I, Baur M, Mönks S, Herrmann E, Huppert V, et al. Tetracycline inducible gene manipulation in serotonergic neurons. PLoS ONE. 2012;7:e38193 pubmed publisher..This will allow precise delineation of serotonergic gene functions during development and adulthood. ..
- Puthucheary S, Puah S, Chua K. Molecular characterization of clinical isolates of Aeromonas species from Malaysia. PLoS ONE. 2012;7:e30205 pubmed publisher..Different combinations of the virulence genes present in the isolates indicate their probable role in the pathogenesis of Aeromonas infections. ..
- Devers E, Teply J, Reinert A, Gaude N, Krajinski F. An endogenous artificial microRNA system for unraveling the function of root endosymbioses related genes in Medicago truncatula. BMC Plant Biol. 2013;13:82 pubmed publisher..The endogenous amiR system demonstrated here presents a novel and highly efficient tool to unravel gene functions during root endosymbioses. ..
- Sch fer M, Br tting C, Gase K, Reichelt M, Baldwin I, Meldau S. 'Real time' genetic manipulation: a new tool for ecological field studies. Plant J. 2013;76:506-18 pubmed publisher..As the arena of most ecological interactions is highly constrained in time and space, these tools will advance the genetic analysis of dynamic traits that matter for plant performance in nature...
- Lammers Y, Kremer D, Brakefield P, Groenenberg D, Pirovano W, Schilthuizen M. SNP genotyping for detecting the 'rare allele phenomenon' in hybrid zones. Mol Ecol Resour. 2013;13:237-42 pubmed publisher..We test this approach on a hybrid zone in the land snail Albinaria hippolyti from Greece. ..
- Wang G, Gaddis S, Vasquez K. Methods to detect replication-dependent and replication-independent DNA structure-induced genetic instability. Methods. 2013;64:67-72 pubmed publisher..We also describe a new web-based search engine to identify potential intramolecular triplex (H-DNA) and left-handed Z-DNA-forming motifs in entire genomes or at selected sequences of interest. ..
- Funabashi K, Barcelos D, Visoná I, E Silva M, E Sousa M, de Franco M, et al. DNA extraction and molecular analysis of non-tumoral liver, spleen, and brain from autopsy samples: the effect of formalin fixation and paraffin embedding. Pathol Res Pract. 2012;208:584-91 pubmed publisher..The data provided here should be used in other molecular studies in FFPE samples. ..
- Yamaguchi T, Hamanaka S, Kamiya A, Okabe M, Kawarai M, Wakiyama Y, et al. Development of an all-in-one inducible lentiviral vector for gene specific analysis of reprogramming. PLoS ONE. 2012;7:e41007 pubmed publisher..All these findings suggest that the Ai-LV system enables us to generate a panel of iPSC clones derived from various tissues with the same genetic background, and thus provides an invaluable tool for iPSC research. ..
- López Muñoz E, Méndez Montes M. Markers of circulating breast cancer cells. Adv Clin Chem. 2013;61:175-224 pubmed..Also discussed are methods for CTC enrichment using molecular strategies. The clinical application of CTC in the metastatic disease process is also summarized. ..
- Candelli A, Modesti M, Peterman E, Wuite G. Single-molecule views on homologous recombination. Q Rev Biophys. 2013;46:323-48 pubmed publisher..Here, we survey important recent developments in this field of research and provide an outlook on future developments. ..
- Holst Jensen A, Bertheau Y, De Loose M, Grohmann L, Hamels S, Hougs L, et al. Detecting un-authorized genetically modified organisms (GMOs) and derived materials. Biotechnol Adv. 2012;30:1318-35 pubmed publisher..Emphasis is put on exemplifying practical detection of un-authorized GMOs. Although this paper has a European (EU) bias when examples are given, the contents have global relevance. ..
- Bassett A, Liu J. CRISPR/Cas9 and genome editing in Drosophila. J Genet Genomics. 2014;41:7-19 pubmed publisher..We discuss the recent techniques that apply the CRISPR/Cas9 system to Drosophila, highlight potential uses for this technology and speculate upon the future of genome engineering in this model organism. ..
- Neumann H. Rewiring translation - Genetic code expansion and its applications. FEBS Lett. 2012;586:2057-64 pubmed publisher..Here, I review these recent developments emphasizing their tremendous potential to facilitate biochemical and cell biological studies. ..
- Claassen S, du Toit E, Kaba M, Moodley C, Zar H, Nicol M. A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples. J Microbiol Methods. 2013;94:103-110 pubmed publisher..DGGE and T-RFLP produced the highest diversity scores for DNA extracted using kit Z (H'=2.30 and 1.27) and kit QS (H'=2.16 and 0.94), which also extracted the highest DNA yields compared to the other kits assessed. ..
- Akerblom M, Sachdeva R, Quintino L, Wettergren E, Chapman K, Manfre G, et al. Visualization and genetic modification of resident brain microglia using lentiviral vectors regulated by microRNA-9. Nat Commun. 2013;4:1770 pubmed publisher..The microRNA-9-regulated vectors described here are a straightforward and powerful tool that facilitates functional studies of resident microglia. ..
- Mor O, Grossman Z, Avidor B, Turner D. [Relevance of HIV resistance testing for treatment decisions]. Harefuah. 2013;152:230-4, 245-6 pubmed..Consequently, we will be able to improve treatment strategy and life quality and increase Life expectancy of HIV carriers. ..
- Chen Q, Shi Q. [The genetic safety of induced pluripotent stem (iPS) cells]. Yi Chuan. 2012;34:260-8 pubmed..Hopefully, this review is helpful to improve the induction of iPS cells and obtain genetically safe iPS cells. ..
- You X, Zhang Z, Fan J, Cui Z, Zhang X. Functionally orthologous viral and cellular microRNAs studied by a novel dual-fluorescent reporter system. PLoS ONE. 2012;7:e36157 pubmed publisher..These findings also expand upon our current knowledge of functional homology and imply that a more general phenomenon of orthologous relationships exists between viral and cellular miRNAs. ..
- Tapia P, Flores F, Covarrubias P, Acuña L, Holmes D, Quatrini R. Complete genome sequence of temperate bacteriophage AcaML1 from the extreme acidophile Acidithiobacillus caldus ATCC 51756. J Virol. 2012;86:12452-3 pubmed publisher..Here, we announce the genome sequence of AcaML1 and report major findings from its annotation. ..
- Lambin M, Nicolas E, Oger C, Nguyen N, Prozzi D, Hallet B. Separate structural and functional domains of Tn4430 transposase contribute to target immunity. Mol Microbiol. 2012;83:805-20 pubmed publisher..The data are discussed with respect to alternative models in which TnpA acts as a specific determinant to both establish and respond to immunity. ..
- Kachapati K, Adams D, Bednar K, Ridgway W. The non-obese diabetic (NOD) mouse as a model of human type 1 diabetes. Methods Mol Biol. 2012;933:3-16 pubmed publisher..We describe how genetic approaches to identifying causative gene variants can be adapted to identify novel therapeutic agents for reversing new-onset T1D. ..
- Staton A, Giraldez A. Use of target protector morpholinos to analyze the physiological roles of specific miRNA-mRNA pairs in vivo. Nat Protoc. 2011;6:2035-49 pubmed publisher..Depending on the biological context, this set of experiments can be completed in 6-8 weeks. ..
- Park H, Noh E, Chung H, Kang M, Kim E, Park S. Efficient generation of virus-free iPS cells using liposomal magnetofection. PLoS ONE. 2012;7:e45812 pubmed publisher..LMF may represent a superior technique for the generation of virus-free or integration-free iPS cell lines that could lead to enhanced stem cell therapy in the future. ..
- Antunes R, Alonso N, Paula R. Importance of early diagnosis of Stickler syndrome in newborns. J Plast Reconstr Aesthet Surg. 2012;65:1029-34 pubmed publisher..The study aims to investigate a possible correlation between the main clinical and ophthalmological characteristics, age and Robin sequence in patients with the Stickler syndrome...
- Mosqueda J, Olvera Ramírez A, Aguilar Tipacamú G, Canto G. Current advances in detection and treatment of babesiosis. Curr Med Chem. 2012;19:1504-18 pubmed..In this review, we will present the current advances in detection and treatment of babesiosis in cattle and other animals, with additional reference to several apicomplexan parasites. ..
- Park H, Carmel J. Selective Manipulation of Neural Circuits. Neurotherapeutics. 2016;13:311-24 pubmed publisher..We also review the genetic techniques that allow gain- and loss-of-function within specific neural circuits...
- Mornkham T, Wangsomnuk P, Wangsomnuk P, Jogloy S, Pattanothai A, Fu Y. Comparison of five DNA extraction methods for molecular analysis of Jerusalem artichoke (Helianthus tuberosus). Genet Mol Res. 2012;11:572-81 pubmed publisher..The quality of the extracted DNA was confirmed by sequence-related amplified polymorphism. This information will be useful for molecular analyses of Jerusalem artichoke and other related Helianthus species. ..
- Ergul Y, Nisli K, Kayserili H, Karaman B, Basaran S, Koca B, et al. Cardiovascular abnormalities in Williams syndrome: 20 years'experience in Istanbul. Acta Cardiol. 2012;67:649-55 pubmed..Although surgery was performed in more patients with SVAS than with PAS, SVAS was minimal or mild in most patients and improved in few cases. ..