Abstract:
:Palindromati, the massive host-edited synthetic palindromic contamination found in GenBank, is illustrated and exemplified. Millions of contaminated sequences with portions or tandems of such portions derived from the ZAP adaptor or related linkers are shown (1) by the 12-bp sequence reported elsewhere, exon Xb, 5' CCCGAATTCGGG 3', (2) by a 22-bp related sequence 5' CTCGTGCCGAATTCGGCACGAG 3', and (3) by a longer 44-bp related sequence: 5' CTCGTGCCGAATTCGGCACGAGCTCGTGCCGAATTCGGCACGAG 3'. Possible reasons for why those long contaminating sequences continue in the databases are presented here: (1) the recognition site for the plus strand (+) is single-strand self-annealed; (2) the recognition site for the minus strand (-) is not only single-strand self-annealed but also located far away from the single-strand self-annealed plus strand, rendering impossible the formation of the active EcoRI enzyme dimer to cut on 5' G/AATTC 3', its target sequence. As a possible solution, it is suggested to rely on at least two or three independent results, such as sequences obtained by independent laboratories with the use, preferably, of independent sequencing methodologies. This information may help to develop tools for bioinformatics capable to detect/remove these contaminants and to infer why some damaged sequences which cause genetic diseases escape detection by the molecular quality control mechanism of cells and organisms, being undesirably transferred unchecked through the generations.
journal_name
DNA Cell Bioljournal_title
DNA and cell biologyauthors
Castro-Chavez Fdoi
10.1089/dna.2011.1339subject
Has Abstractpub_date
2012-02-01 00:00:00pages
151-63issue
2eissn
1044-5498issn
1557-7430journal_volume
31pub_type
杂志文章abstract::Quantitative determination of T-cell receptor (TCR) V beta expression is necessary to define the changes in TCR-V beta subfamily expression that occur during T-cell maturation and selection and to detect alterations of the TCR-V beta repertoire that may be associated with human diseases. Here we describe and validate ...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.1993.12.217
更新日期:1993-04-01 00:00:00
abstract::Human T cells express HLA class II molecules upon activation. The factors that regulate the induction of expression of these molecules are for the most part unknown. Here we report preliminary results indicating that tumor necrosis factor-alpha (TNF-alpha) regulates the induction of cell-surface HLA-DR, DO, and DP mol...
journal_title:DNA and cell biology
pub_type: 杂志文章,评审
doi:10.1089/dna.1992.11.265
更新日期:1992-04-01 00:00:00
abstract::In an effort to develop a more effective genetic immunization strategy for HIV, we developed an HIV-2 env DNA vaccine and evaluated three adjuvant formulations. The gp140 gene from HIV-2(UC2 )was synthesized using mammalian codons and cloned into a plasmid vector that expresses eukaryotic genes at high levels. We foun...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/104454904322759911
更新日期:2004-02-01 00:00:00
abstract::Six identical cDNA clones corresponding to an RNA of 1685 nucleotides that is enriched in mouse sperm compared with testis were isolated from a mouse testis cDNA library. The sequence of these clones corresponds to the 16S mitochondrial RNA plus an inverted repeat of 120 bp covalently joined to the 5' end of the RNA. ...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/104454900439809
更新日期:2000-09-01 00:00:00
abstract::The human OZF gene encodes a protein consisting essentially of zinc finger motifs of the Krüppel type. Evolutionary studies revealed amplification of the bovine OZF gene in cattle. Domestic cattle includes two major subspecies: taurine (Bos primigenius taurus) and zebu (B. p. indicus). Amplified sequences were found i...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.1996.15.83
更新日期:1996-01-01 00:00:00
abstract::Peanut is an important crash crop worldwide, and it is often threatened by drought stress due to unexpected extreme weather events. In this work, NH5 and FH18 were selected as drought-tolerant and drought-sensitive varieties, respectively. Comparison of their physiological responses revealed that NH5 showed less wilti...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2020.6245
更新日期:2020-12-29 00:00:00
abstract::The rat D2 dopamine receptor gene is transcribed from a TATA-less promoter that has an initiator-like sequence and several putative Sp1 binding sites. We previously reported that a negative modulator is located between nucleotides -116 and -76 (D2Neg-B) in this gene and that Sp1 as well as another unknown factor bind ...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.1998.17.471
更新日期:1998-05-01 00:00:00
abstract::MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate mRNAs through a sequence-specific mechanism. By virtue of their structure and mechanism of action, computational methods have been devised to investigate the encoding of miRNA genes and the targets of miRNA action. A variety of assumptions have predic...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2006.0546
更新日期:2007-05-01 00:00:00
abstract::Liver-expressed chemokine (LEC) is a CC chemokine that is selectively expressed in the liver. We report here the structures of the human and mouse genes for LEC. The human LEC gene (SCYA16) was isolated from a bacterial artificial chromosome (BAC) clone that also contained CC chemokine genes for MPIF-1/Ckbeta8, HCC-2/...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/104454999315330
更新日期:1999-04-01 00:00:00
abstract::We evaluated the effects of administration of 1,25-dihydroxyvitamin D (1,25(OH)2D) during pregnancy on relieving adverse outcomes of preeclampsia and the pathologic and biochemical changes in reduction in uteroplacental perfusion (RUPP) model of rats. On day 1, 7, and 14 of pregnancy, rats in pregnant RUPP plus 1,25(O...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2015.2885
更新日期:2016-02-01 00:00:00
abstract::Long noncoding RNA host gene 16 (SNHG16) has a key role in a variety of cancer progression. However, the role and mechanism of SNHG16 in osteosarcoma (OS) remain unknown. In this study, we examined the functional role of SNHG16 in OS cells through knocked-down SNHG16 by using siRNA. We found that SNHG16 is overexpress...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2018.4424
更新日期:2019-02-01 00:00:00
abstract::Antibody-targeting therapy has drawn great interests to the hematologists and oncologists. 3A4, a novel antibody recognizing human CD45RA antigen, is a new target molecule for leukemias and holds a therapeutic potential for myeloid lineage leukemias. However, murine antibodies cannot be safely used in patients because...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2018.4199
更新日期:2018-09-01 00:00:00
abstract::Defective T cell receptor (TCR) signaling resulting in lower T cell function plays a crucial role in the pathogenesis of T cell immunodeficiency in leukemia. Previous studies have indicated that lower TCRζ levels are a common characteristic of patients with leukemia, and upregulating TCRζ could partially recover T cel...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2015.2810
更新日期:2015-07-01 00:00:00
abstract::The computer program, SIGSEQ2, was used to select heterologous signal peptides from a catalog of published sequences to express the echistatin gene in insect (Sf9) cells. S-values for each amino acid were determined to select empirically the site of cleavage between the signal peptide and mature echistatin. Five gene ...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.1990.9.453
更新日期:1990-07-01 00:00:00
abstract::Uterine corpus endometrial carcinoma (UCEC) is a common malignancy in the female reproductive system, associated with high morbidity and mortality. Despite the high prevalence of UCEC, molecular understanding of uterine endothelium tumorigenesis remains poorly understood. In this study, we reported that transcription ...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2017.4062
更新日期:2018-05-01 00:00:00
abstract::Host cell-derived danger-associated molecular patterns (DAMPs), such as the hemoglobin (Hb) can interact with the innate immune system either directly or through binding to pathogen-associated molecular patterns (PAMPs). Hemolysis occurs under various pathological conditions, leading to hemoglobinemia. In the extracel...
journal_title:DNA and cell biology
pub_type: 杂志文章,评审
doi:10.1089/dna.2012.1897
更新日期:2013-02-01 00:00:00
abstract::CXXC finger protein 1 (CFP1) is a component of the Setd1A and Setd1B methyltransferase complexes, localizes to euchromatic regions of the genome, and specifically binds unmethylated CpG dinucleotides in DNA. Murine embryos lacking CFP1 exhibit peri-implantation lethality, a developmental time that correlates with glob...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2007.0714
更新日期:2008-10-01 00:00:00
abstract::The globally distributed American cockroach (Periplaneta americana) is considered a pest, but it has been widely used in traditional Chinese medicine. In the past, the American cockroach's genome and transcriptomes were sequenced, but the differential expression transcripts between developmental stages were unavailabl...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2018.4578
更新日期:2019-10-01 00:00:00
abstract::Zidovudine (AZT) is widely used in the treatment of human immunodeficiency virus (HIV) infection because of its ability to act as a false substrate for the viral reverse transcriptase. AZT in the clinical setting has also been shown to produce significant hematologic and other toxicity, even though prior reports in th...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.1996.15.363
更新日期:1996-05-01 00:00:00
abstract::We cloned and sequenced a 1378 bp BamHI satellite DNA fraction from the water buffalo Bubalus bubalis and have studied its expression in different tissues. The GC-rich sequences of the resultant contig pDS5 crosshybridize only with bovid DNA and are not conserved evolutionarily. Typing of buffalo genomic DNA using pDS...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/104454901317095007
更新日期:2001-09-01 00:00:00
abstract::Xenotransplantation from pigs to human beings is viewed as a potential solution for the acute organ shortage. However, consequent xenorejection induced by Gal alpha 1,3 Gal (a Gal, Gal antigen) prevents xenotransplantation from clinical application. Thus, the most attracting attempt to prevent xenorejection is the eli...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2005.24.235
更新日期:2005-04-01 00:00:00
abstract::Parkinson's disease (PD) is a serious neurodegenerative disorder that lacks effective therapeutic methods. In this research, expressions of PPARα, RXRα, and miR-21 were evaluated in PD patients and normal controls. To investigate the effects of miR-21, docosahexaenoic acid (DHA) and aspirin (ASA) on PD, as well as the...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2017.3643
更新日期:2017-06-01 00:00:00
abstract::The abnormal function of O(6)-methylguanine-DNA methyltransferase (MGMT) is reported to be associated with the occurrence of various tumors and malignant tumor progression. However, little evidence is available to describe its role in esophageal carcinogenesis. To address this issue, we constructed a stable MGMT-silen...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2011.1318
更新日期:2012-05-01 00:00:00
abstract::Gallbladder carcinoma (GBC) is a leading cause of cancer deaths in north India. Evidence has highlighted the role of abnormal DNA methylation patterns on inappropriate gene expression in development and progression of various cancers. 5,10-Methylenetetrahydrofolate reductase (MTHFR) plays a major role in provision of ...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2007.0679
更新日期:2008-03-01 00:00:00
abstract::Long noncoding RNAs (lncRNAs) may serve as potential molecular diagnostic markers to improve the capacity of earlier and more accurate diagnosis of dilated cardiomyopathy (DCM). We integrated five independent transcriptomic datasets (n = 504) from Gene Expression Omnibus for systematic identification of lncRNA-based d...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2020.5670
更新日期:2020-11-03 00:00:00
abstract::A recombinant baculovirus vAc beta hCG-luc was constructed that carried the cDNAs encoding firefly luciferase (luc) and beta-subunit of human chorionic gonadotropin (beta hCG) placed under the transcriptional control of individual copies of the baculovirus polyhedrin gene promoter. The simple, rapid, and sensitive det...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.1994.13.275
更新日期:1994-03-01 00:00:00
abstract::To investigate the contribution of de novo variants to Tourette disorder (TD) probands in China. Whole-exome sequencing (WES) conducted on 15 child-parent trios (45 samples) detected 25 coding de novo variants, including 2 de novo Likely Gene Disrupting (LGD) variants and 6 Missense3 variants. The de novo LGD variants...
journal_title:DNA and cell biology
pub_type: 杂志文章
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更新日期:2020-01-01 00:00:00
abstract::Interstitial lung disease (ILD) is the main reason of death in patients with systemic sclerosis (SSc). The potential microRNA (miRNA)-messenger RNA (mRNA) interaction networks of SSc-ILD from a systematic biological perspective are unclear. To characterize differentially expressed miRNAs (DE-miRNAs) and differentially...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2019.4780
更新日期:2019-09-01 00:00:00
abstract::DNA methylation plays an essential role in carcinogenesis. Promoter hypermethylation can result in transcriptional silencing of specific genes, such as tumor suppressors. Thus far, few reports have investigated the effect of curcumin, an active component of the perennial herb Curcuma longa, on DNA methylation. In the ...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2013.2042
更新日期:2013-06-01 00:00:00
abstract::FOXO3 is a member of the Forkhead box class O (FOXO) transcription factor family that modulates the transcription of target genes in a variety of cellular functions in lower animals to mammals. It has been implicated in the attenuation of insulin-signaling pathways, including having a potential role in lifespan contro...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2010.1193
更新日期:2011-07-01 00:00:00