'Studying DNA methylation profiles in detail should be the first step in epigenetic research. Although sodium bisulfite modification of genomic DNA is the gold standard method for DNA methylation analysis, this method results in the loss of the majority of the DNA material. Whole genome amplification (WGA) of bisulfite-modified DNA ... More
Molecular detection and species identification of Alexandrium (Dinophyceae) causing harmful algal blooms along the Chilean coastline.
AuthorsJedlicki A, Fernández G, Astorga M, Oyarzún P, Toro JE, Navarro JM, Martínez V,
JournalAoB Plants
PubMed ID23259043
'On the basis of morphological evidence, the species involved in South American Pacific coast harmful algal blooms (HABs) has been traditionally recognized as Alexandrium catenella (Dinophyceae). However, these observations have not been confirmed using evidence based on genomic sequence variability. Our principal objective was to accurately determine the species of ... More
[DNA extraction from coagulated human blood for application in genotyping techniques for human leukocyte antigen and immunoglobulin-like receptors].
'The objective of this study was to standardize a method for extracting high-quality DNA from samples of coagulated blood. Forty-eight samples of human coagulated blood were used for DNA extraction by means of the EZ-DNA commercial kit (Biological Industries, Beit Haemek, Israel), the Neoscience column kit (One Lambda Inc., San ... More
PKCa is genetically linked to memory capacity in healthy subjects and to risk for posttraumatic stress disorder in genocide survivors.
Authorsde Quervain DJ, Kolassa IT, Ackermann S, Aerni A, Boesiger P, Demougin P, Elbert T, Ertl V, Gschwind L, Hadziselimovic N, Hanser E, Heck A, Hieber P, Huynh KD, Klarhöfer M, Luechinger R, Rasch B, Scheffler K, Spalek K, Stippich C, Vogler C, Vukojevic V, Stetak A, Papassotiropoulos A,
JournalProc Natl Acad Sci U S A
PubMed ID22586106
'Strong memory of a traumatic event is thought to contribute to the development and symptoms of posttraumatic stress disorder (PTSD). Therefore, a genetic predisposition to build strong memories could lead to increased risk for PTSD after a traumatic event. Here we show that genetic variability of the gene encoding PKCa ... More
Reflex: intramolecular barcoding of long-range PCR products for sequencing multiple pooled DNAs.
AuthorsCasbon JA, Slatter AF, Musgrave-Brown E, Osborne RJ, Lichtenstein CP, Brenner S,
JournalNucleic Acids Res
PubMed ID23580546
We present an intramolecular reaction, Reflex™, to derive shorter, sequencer-ready, daughter polymerase chain reaction products from a pooled population of barcoded long-range polymerase chain reaction products, whilst still preserving the cognate DNA barcodes. Our Reflex workflow needs only a small number of primer extension steps to rapidly enable uniform sequence ... More
Giving drought the cold shoulder: a relationship between drought tolerance and fall dormancy in an agriculturally important crop.
AuthorsPembleton KG, Sathish P,
Journal
PubMed ID24790133
The growth of fall dormant/freezing tolerant plants often surpasses the growth of non-fall dormant/non-freezing tolerant types of the same species under water-limited conditions, while under irrigated conditions non-fall dormant types exhibit superior yield performance. To investigate the mechanism behind this phenomenon, we exposed seven diverse alfalfa (Medicago sativa) cultivars to ... More
Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate Pseudomonas aeruginosa 96.
AuthorsXiong J, Alexander DC, Ma JH, Déraspe M, Low DE, Jamieson FB, Roy PH,
Journal
PubMed ID23716048
Pseudomonas aeruginosa 96 (PA96) was isolated during a multicenter surveillance study in Guangzhou, China, in 2000. Whole-genome sequencing of this outbreak strain facilitated analysis of its IncP-2 carbapenem-resistant plasmid, pOZ176. The plasmid had a length of 500,839 bp and an average percent G+C content of 57%. Of the 618 predicted ... More
Genetic mapping and exome sequencing identify 2 mutations associated with stroke protection in pediatric patients with sickle cell anemia.
AuthorsFlanagan JM, Sheehan V, Linder H, Howard TA, Wang YD, Hoppe CC, Aygun B, Adams RJ, Neale GA, Ware RE,
JournalBlood
PubMed ID23422753
Stroke is a devastating complication of sickle cell anemia (SCA), occurring in 11% of patients before age 20 years. Previous studies of sibling pairs have demonstrated a genetic component to the development of cerebrovascular disease in SCA, but few candidate genetic modifiers have been validated as having a substantial effect ... More
Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas.
AuthorsBoyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus SJ, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher SD, Johnson S, Benning C, Pellegrini M, Grossman A, Merchant SS,
JournalJ Biol Chem
PubMed ID22403401
Algae have recently gained attention as a potential source for biodiesel; however, much is still unknown about the biological triggers that cause the production of triacylglycerols. We used RNA-Seq as a tool for discovering genes responsible for triacylglycerol (TAG) production in Chlamydomonas and for the regulatory components that activate the ... More
Automated extraction improves multiplex molecular detection of infection in septic patients.
AuthorsRegueiro BJ, Varela-Ledo E, Martinez-Lamas L, Rodriguez-Calviño J, Aguilera A, Santos A, Gomez-Tato A, Alvarez-Escudero J,
JournalPLoS One
PubMed ID20967222
Sepsis is one of the leading causes of morbidity and mortality in hospitalized patients worldwide. Molecular technologies for rapid detection of microorganisms in patients with sepsis have only recently become available. LightCycler SeptiFast test M(grade) (Roche Diagnostics GmbH) is a multiplex PCR analysis able to detect DNA of the 25 ... More
Isolation of a novel lipase from a metagenomic library derived from mangrove sediment from the south Brazilian coast.
A novel gene coding for a LipA-like lipase with 283 amino acids and a molecular mass of 32 kDa was isolated and characterized from a metagenomic library prepared from mangrove sediment from the south Brazilian coast. LipA was 52% identical to a lipolytic enzyme from an uncultured bacterium and shared ... More
DNA qualification workflow for next generation sequencing of histopathological samples.
AuthorsSimbolo M, Gottardi M, Corbo V, Fassan M, Mafficini A, Malpeli G, Lawlor RT, Scarpa A,
Journal
PubMed ID23762227
Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the ... More
Benchmarking the MinION: Evaluating long reads for microbial profiling.
AuthorsLeidenfrost RM, Pöther DC, Jäckel U, Wünschiers R
JournalSci Rep
PubMed ID32198413
'Nanopore based DNA-sequencing delivers long reads, thereby simplifying the decipherment of bacterial communities. Since its commercial appearance, this technology has been assigned several attributes, such as its error proneness, comparatively low cost, ease-of-use, and, most notably, aforementioned long reads. The technology as a whole is under continued development. As such, ... More
Accumulation of Cytoplasmic DNA Due to ATM Deficiency Activates the Microglial Viral Response System with Neurotoxic Consequences.
AuthorsSong X, Ma F, Herrup K
JournalJ Neurosci
PubMed ID31189575
'ATM (ataxia-telangiectasia mutated) is a PI3K-like kinase best known for its role in the DNA damage response (DDR), especially after double-strand breaks. Mutations in the ATM gene result in a condition known as ataxia-telangiectasia (A-T) that is characterized by cancer predisposition, radiosensitivity, neurodegeneration, sterility, and acquired immune deficiency. We show ... More
Limitations of methods for measuring the concentration of human genomic DNA and oligonucleotide samples.
AuthorsHe HJ, Stein EV, DeRose P, Cole KD
JournalBiotechniques
PubMed ID29571283
'We compared different methods (absorbance, fluorescent dye-binding, and digital PCR) for measuring the concentrations of human genomic DNA from cultured cells and absorbance measurements of a synthetic DNA oligonucleotide. NIST Standard Reference Material (SRM) 2082, a pathlength absorbance standard, was used to benchmark the absorbance measurements done with microvolume spectrophotometers ... More
Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples.
AuthorsPaskey AC, Frey KG, Schroth G, Gross S, Hamilton T, Bishop-Lilly KA
JournalBMC Genomics
PubMed ID30808306
'Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity ... More
Genome-Wide Analysis of Differential Gene Expression and Splicing in Excitatory Neurons and Interneuron Subtypes.
AuthorsHuntley MA, Srinivasan K, Friedman BA, Wang TM, Yee AX, Wang Y, Kaminker JS, Sheng M, Hansen DV, Hanson JE
JournalJ Neurosci
PubMed ID31831521
'Cortical circuit activity is shaped by the parvalbumin (PV) and somatostatin (SST) interneurons that inhibit principal excitatory (EXC) neurons and the vasoactive intestinal peptide (VIP) interneurons that suppress activation of other interneurons. To understand the molecular-genetic basis of functional specialization and identify potential drug targets specific to each neuron subtype, ... More
RNA sequencing by direct tagmentation of RNA/DNA hybrids.
AuthorsDi L, Fu Y, Sun Y, Li J, Liu L, Yao J, Wang G, Wu Y, Lao K, Lee RW, Zheng G, Xu J, Oh J, Wang D, Xie XS, Huang Y, Wang J
JournalProc Natl Acad Sci U S A
PubMed ID31988135
'Transcriptome profiling by RNA sequencing (RNA-seq) has been widely used to characterize cellular status, but it relies on second-strand complementary DNA (cDNA) synthesis to generate initial material for library preparation. Here we use bacterial transposase Tn5, which has been increasingly used in various high-throughput DNA analyses, to construct RNA-seq libraries ... More
Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.
AuthorsRanjan R, Rani A, Metwally A, McGee HS, Perkins DL
JournalBiochem Biophys Res Commun
PubMed ID26718401
'The human microbiome has emerged as a major player in regulating human health and disease. Translational studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have ... More
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.
AuthorsLagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R
JournalNat Genet
PubMed ID29106417
'Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE ... More
Sensitive tumour detection and classification using plasma cell-free DNA methylomes.
AuthorsShen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, Kis O, Zhao Z, Spreafico A, Medina TDS, Wang Y, Roulois D, Ettayebi I, Chen Z, Chow S, Murphy T, Arruda A, O'Kane GM, Liu J, Mansour M, McPherson JD, O'Brien C, Leighl N, Bedard PL, Fleshner N, Liu G, Minden MD, Gallinger S, Goldenberg A, Pugh TJ, Hoffman MM, Bratman SV, Hung RJ, De Carvalho DD
JournalNature
PubMed ID30429608
The use of liquid biopsies for cancer detection and management is rapidly gaining prominence
AuthorsChen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA
JournalScience
PubMed ID29449511
CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind and cut DNA as components of bacterial adaptive immune systems. Like CRISPR-Cas9, Cas12a has been harnessed for genome editing on the basis of its ability to generate targeted, double-stranded DNA breaks. Here we show that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA ... More
Germline-Encoded TCR-MHC Contacts Promote TCR V Gene Bias in Umbilical Cord Blood T Cell Repertoire.
AuthorsGao K, Chen L, Zhang Y, Zhao Y, Wan Z, Wu J, Lin L, Kuang Y, Lu J, Zhang X, Tian L, Liu X, Qiu X
JournalFront Immunol
PubMed ID31543879
T cells recognize antigens as peptides bound to major histocompatibility complex (MHC) proteins through T cell receptors (TCRs) on their surface. To recognize a wide range of pathogens, each individual possesses a substantial number of TCRs with an extremely high degree of variability. It remains controversial whether germline-encoded TCR repertoire ... More
Tumor suppressor MCPH1 regulates gene expression profiles related to malignant conversion and chromosomal assembly.
AuthorsTervasmäki A, Mantere T, Eshraghi L, Laurila N, Tuppurainen H, Ronkainen VP, Koivuluoma S, Devarajan R, Peltoketo H, Pylkäs K
JournalInt J Cancer
PubMed ID30809794
Strong inherited predisposition to breast cancer is estimated to cause about 5-10% of all breast cancer cases. As the known susceptibility genes, such as BRCA1 and BRCA2, explain only a fraction of this, additional predisposing genes and related biological mechanisms are actively being searched for. We have recently identified a ... More