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  • 1
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    High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment [Medical Sciences] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-12-28
    Description: The primary cause of poor outcome following allogeneic hematopoietic cell transplantation (HCT) for chronic lymphocytic leukemia (CLL) is disease recurrence. Detection of increasing minimal residual disease (MRD) following HCT may permit early intervention to prevent clinical relapse; however, MRD quantification remains an uncommon diagnostic test because of logistical and financial barriers to widespread use. Here we describe a method for quantifying CLL MRD using widely available consensus primers for amplification of all Ig heavy chain (IGH) genes in a mixture of peripheral blood mononuclear cells, followed by high-throughput sequencing (HTS) for disease-specific IGH sequence quantification. To achieve accurate MRD quantification, we developed a systematic bioinformatic methodology to aggregate cancer clone sequence variants arising from systematic and random artifacts occurring during IGH-HTS. We then compared the sensitivity of IGH-HTS, flow cytometry, and allele-specific oligonucleotide PCR for MRD quantification in 28 samples collected from 6 CLL patients following allogeneic HCT. Using amplimer libraries generated with consensus primers from patient blood samples, we demonstrate the sensitivity of IGH-HTS with 454 pyrosequencing to be 10−5, with a high correlation between quantification by allele-specific oligonucleotide PCR and IGH-HTS (r = 0.85). From the same dataset used to quantify MRD, IGH-HTS also allowed us to profile IGH repertoire reconstitution after HCT—information not provided by the other MRD methods. IGH-HTS using consensus primers will broaden the availability of MRD quantification in CLL and other B cell malignancies, and this approach has potential for quantitative evaluation of immune diversification following transplant and nontransplant therapies.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-04
    Description: Estimates of the total number of bacterial species indicate that existing DNA sequence databases carry only a tiny fraction of the total amount of DNA sequence space represented by this division of life. Indeed, environmental DNA samples have been shown to encode many previously unknown classes of proteins and RNAs. Bioinformatics searches of genomic DNA from bacteria commonly identify new noncoding RNAs (ncRNAs) such as riboswitches. In rare instances, RNAs that exhibit more extensive sequence and structural conservation across a wide range of bacteria are encountered. Given that large structured RNAs are known to carry out complex biochemical functions such as protein synthesis and RNA processing reactions, identifying more RNAs of great size and intricate structure is likely to reveal additional biochemical functions that can be achieved by RNA. We applied an updated computational pipeline to discover ncRNAs that rival the known large ribozymes in size and structural complexity or that are among the most abundant RNAs in bacteria that encode them. These RNAs would have been difficult or impossible to detect without examining environmental DNA sequences, indicating that numerous RNAs with extraordinary size, structural complexity, or other exceptional characteristics remain to be discovered in unexplored sequence space.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140389/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140389/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weinberg, Zasha -- Perreault, Jonathan -- Meyer, Michelle M -- Breaker, Ronald R -- P01 GM022778/GM/NIGMS NIH HHS/ -- RR19895-02/RR/NCRR NIH HHS/ -- Canadian Institutes of Health Research/Canada -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Dec 3;462(7273):656-9. doi: 10.1038/nature08586.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, New Haven, Connecticut 06520-8103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19956260" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*genetics/metabolism ; Base Sequence ; Gene Expression Regulation, Bacterial ; Genome, Bacterial/*genetics ; *Genomics ; Molecular Sequence Data ; *Nucleic Acid Conformation ; RNA, Bacterial/*chemistry/*genetics ; RNA, Untranslated/chemistry/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Riboswitches in eubacteria sense the second messenger cyclic di-GMP (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-19
    Description: Cyclic di-guanosine monophosphate (di-GMP) is a circular RNA dinucleotide that functions as a second messenger in diverse species of bacteria to trigger wide-ranging physiological changes, including cell differentiation, conversion between motile and biofilm lifestyles, and virulence gene expression. However, the mechanisms by which cyclic di-GMP regulates gene expression have remained a mystery. We found that cyclic di-GMP in many bacterial species is sensed by a riboswitch class in messenger RNA that controls the expression of genes involved in numerous fundamental cellular processes. A variety of cyclic di-GMP regulons are revealed, including some riboswitches associated with virulence gene expression, pilus formation, and flagellum biosynthesis. In addition, sequences matching the consensus for cyclic di-GMP riboswitches are present in the genome of a bacteriophage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sudarsan, N -- Lee, E R -- Weinberg, Z -- Moy, R H -- Kim, J N -- Link, K H -- Breaker, R R -- GM 068819/GM/NIGMS NIH HHS/ -- HV28186/HV/NHLBI NIH HHS/ -- R33 DK07027/DK/NIDDK NIH HHS/ -- RR19895-02/RR/NCRR NIH HHS/ -- T32GM007223/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):411-3. doi: 10.1126/science.1159519.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635805" target="_blank"〉PubMed〈/a〉
    Keywords: Aptamers, Nucleotide/*metabolism ; Bacillus cereus/genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacteriophages/genetics ; Base Sequence ; Clostridium difficile/genetics/metabolism ; Cyclic GMP/*analogs & derivatives/metabolism ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Ligands ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Bacterial/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; Regulon ; *Second Messenger Systems ; Vibrio cholerae/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Widespread genetic switches and toxicity resistance proteins for fluoride (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-12-24
    Description: Most riboswitches are metabolite-binding RNA structures located in bacterial messenger RNAs where they control gene expression. We have discovered a riboswitch class in many bacterial and archaeal species whose members are selectively triggered by fluoride but reject other small anions, including chloride. These fluoride riboswitches activate expression of genes that encode putative fluoride transporters, enzymes that are known to be inhibited by fluoride, and additional proteins of unknown function. Our findings indicate that most organisms are naturally exposed to toxic levels of fluoride and that many species use fluoride-sensing RNAs to control the expression of proteins that alleviate the deleterious effects of this anion.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140402/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140402/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Jenny L -- Sudarsan, Narasimhan -- Weinberg, Zasha -- Roth, Adam -- Stockbridge, Randy B -- Breaker, Ronald R -- GM022778/GM/NIGMS NIH HHS/ -- P01 GM022778/GM/NIGMS NIH HHS/ -- R01 DE022340/DE/NIDCR NIH HHS/ -- RR19895-02/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):233-5. doi: 10.1126/science.1215063. Epub 2011 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, Box 208103, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194412" target="_blank"〉PubMed〈/a〉
    Keywords: Anion Transport Proteins/genetics/metabolism ; Aptamers, Nucleotide ; Bacterial Proteins/*genetics/metabolism ; Calcium/metabolism ; *Drug Resistance, Bacterial ; Escherichia coli/genetics/growth & development/metabolism ; Fluorides/metabolism/*pharmacology ; *Gene Expression Regulation, Bacterial ; Ion Channels/genetics/metabolism ; Nucleic Acid Conformation ; Pseudomonas syringae/drug effects/*genetics/metabolism ; RNA, Bacterial/chemistry/genetics/metabolism ; *Riboswitch ; Sodium Fluoride/metabolism/pharmacology ; Transformation, Bacterial
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    A glycine-dependent riboswitch that uses cooperative binding to control gene expression (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: We identified a previously unknown riboswitch class in bacteria that is selectively triggered by glycine. A representative of these glycine-sensing RNAs from Bacillus subtilis operates as a rare genetic on switch for the gcvT operon, which codes for proteins that form the glycine cleavage system. Most glycine riboswitches integrate two ligand-binding domains that function cooperatively to more closely approximate a two-state genetic switch. This advanced form of riboswitch may have evolved to ensure that excess glycine is efficiently used to provide carbon flux through the citric acid cycle and maintain adequate amounts of the amino acid for protein synthesis. Thus, riboswitches perform key regulatory roles and exhibit complex performance characteristics that previously had been observed only with protein factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mandal, Maumita -- Lee, Mark -- Barrick, Jeffrey E -- Weinberg, Zasha -- Emilsson, Gail Mitchell -- Ruzzo, Walter L -- Breaker, Ronald R -- New York, N.Y. -- Science. 2004 Oct 8;306(5694):275-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, Post Office Box 208103, New Haven, CT 06520-8103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472076" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions/chemistry/*metabolism ; Allosteric Regulation ; Allosteric Site ; Bacillus subtilis/*genetics/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; *Gene Expression Regulation, Bacterial ; Glycine/*metabolism ; Ligands ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Operon ; RNA, Bacterial/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; Transcription, Genetic ; Vibrio cholerae/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    An allosteric self-splicing ribozyme triggered by a bacterial second messenger (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-08-14
    Description: Group I self-splicing ribozymes commonly function as components of selfish mobile genetic elements. We identified an allosteric group I ribozyme, wherein self-splicing is regulated by a distinct riboswitch class that senses the bacterial second messenger c-di-GMP. The tandem RNA sensory system resides in the 5' untranslated region of the messenger RNA for a putative virulence gene in the pathogenic bacterium Clostridium difficile. c-di-GMP binding by the riboswitch induces folding changes at atypical splice site junctions to modulate alternative RNA processing. Our findings indicate that some self-splicing ribozymes are not selfish elements but are harnessed by cells as metabolite sensors and genetic regulators.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538695/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538695/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Elaine R -- Baker, Jenny L -- Weinberg, Zasha -- Sudarsan, Narasimhan -- Breaker, Ronald R -- P01 GM022778/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Aug 13;329(5993):845-8. doi: 10.1126/science.1190713.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20705859" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Aptamers, Nucleotide/chemistry ; Base Pairing ; Base Sequence ; Clostridium difficile/*genetics/metabolism/pathogenicity ; Codon, Initiator ; Cyclic GMP/*analogs & derivatives/metabolism ; Exons ; Genes, Bacterial ; Guanosine Triphosphate/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Splicing ; RNA, Bacterial/chemistry/*genetics/metabolism ; RNA, Catalytic/chemistry/genetics/*metabolism ; RNA, Messenger/chemistry/genetics/metabolism ; *Regulatory Sequences, Ribonucleic Acid ; *Second Messenger Systems
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
    Electronic Resource
    Electronic Resource
    A note on ensiling safflower forage (2002)
    Oxford, UK : Blackwell Science Ltd
    Grass and forage science 57 (2002), S. 0 
    Details
    ISSN: 1365-2494
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The ensiling characteristics of safflower (Carthamus tinctorius) wilted to 290 and 411 g dry matter (DM) kg−1 fresh material were studied in 1·5 l glass jars. The experiment included a control and the application of Lactobacillus plantarum at 3·3 × 105 colony-forming units (cfu) per g of crop. After 60 days of ensiling, the pH of safflower silages was 4·6 and 4·0 in the control and inoculated silages respectively, with corresponding values for lactic acid, the major fermentation product, of 20 and 45 g kg−1 DM. The silages from the anaerobic jars were stable upon aerobic exposure. It is concluded the safflower silage has potential as an alternative fodder in semiarid regions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2494.2002.00314.x
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  • 8
    Electronic Resource
    Electronic Resource
    Ensiling peas, ryegrass and wheat with additives of lactic acid bacteria (LAB) and cell wall degrading enzymes (1993)
    Oxford, UK : Blackwell Publishing Ltd
    Grass and forage science 48 (1993), S. 0 
    Details
    ISSN: 1365-2494
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: The effect of applying a commercial inoculum (at 1.5 × 105 cfu g-1) containing Streptococcus faecium (Lacticil M74®. Medipharm, Sweden), and cell wall degrading enzymes (Celluclast® and Viscozyme®, Novo, Denmark) to pea, ryegrass and wheat silages was studied under laboratory conditions. Celluclast was applied at 0.03 Novo Cellulose Units (NCU) and Viscozyme at 0.024 Fungal β-glucanase (FBG) per g fresh crop. The peas and wheat used were at three stages of maturity, and the ryegrass used was either direct-cut or wilted. This yielded a wide range of dry matter (DM) and fibre content.Inoculum use improved the ensiling process of most of the forages tested, as indicated by a faster and greater decrease in pH, and by a faster and larger build-up of lactic acid. Inoculum, however, lowered the aerobic stability of wheat silages. The addition of the enzymes alone did not affect the ensiling process. In silages of peas and wheat at the flowering stage, the combination of inoculum and enzymes resulted in a improvement to the ensiling process, as compared with inoculum only.The combined treatment of inoculum and enzymes resulted in a lower percentage of neutral detergent fibre (NDF) and acid detergent fibre (ADF) in the silages of the flowering peas and of the direct-cut ryegrass. The NDF and ADF contents in the inoculum plus enzyme-treated pea silages made at the flowering stage were 322 and 296 g kg-1, compared with 365 and 327 g kg-1 in the control silages. The NDF and ADF contents in the silages made from the direct-cut ryegrass were 312 and 205 (treated with inoculum plus enzymes) vs 383 and 257 g kg-1 (control). However, the DM rumen digestibility of the silages was not improved by any of the treatments.It is concluded that a suitable inoculum could be beneficial to the ensiling process. The benefit expected from the application of cell wall degrading enzymes to silages is as yet unclear.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2494.1993.tb01838.x
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  • 9
    Electronic Resource
    Electronic Resource
    Investigation of the SiO2-induced substrate current in silicon field-effect transistors (1985)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 57 (1985), S. 443-452 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: An experimental investigation is presented for the substrate current (holes) appearing in n-channel field-effect transistors having SiO2 as their gate insulator. In these experiments, the gate is biased by a high and positive voltage, causing an electron current to be injected from the device channel into the oxide. This current is accompanied by the substrate current whose origin is not clear. The experiments were performed by application of short pulses (400 μsec) to the gate. It is shown that the substrate current is too large to be explained by simple electron tunneling from the silicon valence band into the oxide. Temperature-dependence measurements, down to 20 K, show that some of the data are not consistent with models for hole transport from the oxide into the silicon valence band. It is argued that the substrate current may be related to the energy loss experienced by hot electrons as they traverse the oxide. It is further argued that the same mechanism responsible for the substrate current may produce positive charge at the injecting electrode and thus lead to breakdown in thin oxide devices.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.334771
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  • 10
    Electronic Resource
    Electronic Resource
    The effect of gate metal and SiO2 thickness on the generation of donor states at the Si-SiO2 interface (1985)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 57 (1985), S. 418-425 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Two experimental observations are reported concerning the degradation of the Si–SiO2 interface during electron injection in metal-oxide-semiconductor structures. First, the generation of the interfacial positive charge during avalanche injection can be strongly inhibited by employing magnesium, instead of aluminum, as gate metal, or enhanced by employing gold. This correlates with the different work functions of the metals. Second, during negative bias high-field injection in Al-gate capacitors with thin oxides ((approximately-less-than)100 A(ring)), a threshold in gate voltage, of 7–8 V, is found for the generation of the positive charge. Both observations are consistent with a model which assumes that holes generated in the anode by hot electrons, via emission of surface plasmons, are injected into the SiO2 and are subsequently trapped at the Si–SiO2 interface. Other possible mechanisms are also discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.334767
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