当前位置： SCI文献检索 > BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS期刊下所有文献 > On the methodological weakness of 'the effective number of codons': a reply to Marashi and Najafabadi.

On the methodological weakness of 'the effective number of codons': a reply to Marashi and Najafabadi.

Abstract：

:In a recent publication [Biochem. Biophys. Res. Commun. 317 (2004) 957] it was proposed that the 'effective number of codons' (Nc) in a gene should be calculated by summing the individual amino acid Nc's using rounding whenever the codon homozygosities are lower than the reciprocal value of the number of members of the synonymous families. This led Marashi and Najafabadi to examine the consequences of individual re-adjustment when comparing observed Nc with the expected Nc under assumptions of no selection, and C=G and A=T [Biochem. Biophys. Res. Commun. 324 (2004) 1]. Clearly, the present methodology has some weaknesses; in this work, I discuss these in relation to the observations by Marashi and Najafabadi, and finally an alternative method for the calculation of Nc is introduced with the purpose of eliminating the need for re-adjustments.

journal_name

Biochem Biophys Res Commun

journal_title

Biochemical and biophysical research communications

authors

Fuglsang A

doi

10.1016/j.bbrc.2004.11.133

subject

Has Abstract

pub_date

2005-02-04 00:00:00

pages

1-3

issue

1

eissn

0006-291X

issn

1090-2104

pii

S0006-291X(04)02716-0

journal_volume

327

pub_type

评论,杂志文章

相关文献

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS文献大全
  • Rpg1p/Tif32p, a subunit of translation initiation factor 3, interacts with actin-associated protein Sla2p.

    abstract：:The yeast two-hybrid system was used to screen for proteins that interact in vivo with Saccharomyces cerevisiae Rpg1p/Tif32p, the large subunit of the translation initiation factor 3 core complex (eIF3). Eight positive clones encoding portions of the SLA2/END4/MOP2 gene were isolated. They overlapped in the region of ...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1006/bbrc.2001.4721

    authors： Palecek J,Hasek J,Ruis H

    更新日期：2001-04-20 00:00:00

  • A novel role for earthworm peptide Lumbricusin as a regulator of neuroinflammation.

    abstract：:Recently, we reported that Lumbricusin, an antimicrobial peptide isolated from earthworm Lumbricus terrestris, enhanced neuronal proliferation and ameliorated motor dysfunction and dopaminergic neurodegeneration. Accumulating evidence suggests that neurodegeneration is the primary pathological feature of acute or chro...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2017.06.154

    authors： Seo M,Lee JH,Baek M,Kim MA,Ahn MY,Kim SH,Yun EY,Hwang JS

    更新日期：2017-08-26 00:00:00

  • Melanoregulin is stably targeted to the melanosome membrane by palmitoylation.

    abstract：:In mammals, pigments are made by melanocytes within a specialized organelle, the melanosome. Mature, pigment-laden melanosomes are then transferred to keratinocytes to drive the visible pigmentation of the animal's hair and skin. The dilute suppressor (dsu) locus encodes an extragenic suppressor of the pigmentation de...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2012.08.064

    authors： Wu XS,Martina JA,Hammer JA 3rd

    更新日期：2012-09-21 00:00:00

  • IFN-gamma acts as anti-angiogenic cytokine in the human cornea by regulating the expression of VEGF-A and sVEGF-R1.

    abstract：:Inflammatory processes within the cornea are known to be associated with corneal neovascularization (CN). We examined the effects of inflammatory mediators on the expression of angiogenic factors by corneal cells. TNF-alpha and IL-1 induced VEGF-A secretion by corneal fibroblasts (HCRF) and this was inhibited signific...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2008.07.042

    authors： Kommineni VK,Nagineni CN,William A,Detrick B,Hooks JJ

    更新日期：2008-09-26 00:00:00

  • The use of monoclonal antibodies in the study of the interaction between adrenal medullary cell membranes and chromaffin granules.

    abstract：:Simultaneous incubation of bovine adrenal medullary plasma membranes (PM) with chromaffin granules (CG) resulted in the release of the soluble granular content. The molecular mechanism of this process was studied with several monoclonal antibodies (mAb) raised against different plasma membrane components. Specific inh...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/0006-291x(85)91236-7

    authors： Bohner K,Boons J,Gheuens J,Konings F,De Potter WP

    更新日期：1985-12-31 00:00:00

  • Characterization of a competitive and reversible ligand to E2 conformation of Na, K ATPase molecule.

    abstract：:The binding of cardiac glycosides to the E2 conformation of Na, K ATPase suggests that this conformation may represent a potential regulatory site for an endogenous ligand. To examine this hypothesis, delipidated and desalted, ethanolic extracts were prepared from plasma. Plasma extracts produced displacement of 3H-ou...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/0006-291x(88)90441-x

    authors： Rauch AL,Buckalew VM Jr

    更新日期：1988-01-29 00:00:00

  • Different receptors mediate stimulation of nitric oxide-dependent cyclic GMP formation in neurons and astrocytes in culture.

    abstract：:The ability of various compounds to stimulate cyclic GMP accumulation was studied in neuronal and astrocyte-enriched primary cultures from rat cerebrum. Glutamate was the only agonist eliciting a response in neurons whereas several agonists had an effect in astrocytes but only those due to norepinephrine and glutamate...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/0006-291x(92)91883-r

    authors： Agulló L,García A

    更新日期：1992-02-14 00:00:00

  • Human alpha-fetoprotein binds to primary macrophages.

    abstract：:We have previously reported that alpha-fetoprotein (AFP) inhibits infection of human monocyte-derived macrophages (MDM) by R5-HIV-1 strains and that a peptide mimicking the clade B HIV-1 gp120 consensus V3 domain (V3Cs) binds to CCR5. We demonstrate here that AFP binds high- and low-affinity binding sites of MDM, char...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/s0006-291x(02)00909-9

    authors： Atemezem A,Mbemba E,Marfaing R,Vaysse J,Pontet M,Saffar L,Charnaux N,Gattegno L

    更新日期：2002-08-23 00:00:00

  • Cloning, sequencing and expression of the human thyrotropin (TSH) receptor: evidence for binding of autoantibodies.

    abstract：:A human thyroid cDNA library was screened by hybridization with a dog thyrotropin receptor (TSHr) cDNA. Sequencing of the resulting clones identified a 2292 residue open reading frame encoding a 744 amino acid mature polypeptide presenting 90.3% similarity with the dog TSHr. Two major transcripts (4.6 and 4.4 kilobase...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/0006-291x(89)92736-8

    authors： Libert F,Lefort A,Gerard C,Parmentier M,Perret J,Ludgate M,Dumont JE,Vassart G

    更新日期：1989-12-29 00:00:00

  • Major role of the histones H3-H4 in the folding of the chromatin fiber.

    abstract：:We have characterized the hydrodynamic behavior of nucleosome arrays in which the N- and C-terminal "tails" of the histone H2A-H2B and H3-H4 domains have been selectively removed by digestion with immobilized trypsin. The sedimentation coefficient of the polynucleosome fibers lacking the histone H2A-H2B tails exhibite...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1006/bbrc.1996.5903

    authors： Moore SC,Ausió J

    更新日期：1997-01-03 00:00:00

  • Probing the catalytic mechanism of bovine pancreatic deoxyribonuclease I by chemical rescue.

    abstract：:Previous structural and mutational studies of bovine pancreatic deoxyribonuclease I (bpDNase I) have demonstrated that the active site His134 and His252 played critical roles in catalysis. In our present study, mutations of these two His residues to Gln, Ala or Gly reduced the DNase activity by a factor of four to fiv...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2006.11.078

    authors： Chen WJ,Lai PJ,Lai YS,Huang PT,Lin CC,Liao TH

    更新日期：2007-01-19 00:00:00

  • Association of Shc, Cbl, Grb2, and Sos following treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin in primary rat hepatocytes.

    abstract：:c-Src kinases and p21 Ras are known to be implicated in 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-mediated signal transduction. However, the effects of TCDD on the molecular interaction of adaptor complex in the protein tyrosine kinase signaling cascade have not been reported. The present study is designed to clarify...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1006/bbrc.1998.9816

    authors： Park R,Kim DH,Kim MS,So HS,Chung HT,Kwon KB,Ryu DG,Kim BR

    更新日期：1998-12-30 00:00:00

  • Tissue targeting and plasma clearance of cobra venom factor in mice.

    abstract：:The tissue targeting and rate of clearance of cobra venom factor (CVF) from the circulation was studied in mice by intravenous or intraperitoneal injection of radioiodinated CVF. In both modes of administrations, CVF was targeted mainly to liver. CVF injected directly into the blood was cleared from the circulation wi...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1006/bbrc.1997.6078

    authors： Fu Q,Satyaswaroop PG,Gowda DC

    更新日期：1997-02-13 00:00:00

  • HDC gene polymorphisms are associated with age at natural menopause in Caucasian women.

    abstract：:Histidine decarboxylase gene (HDC) encodes histidine decarboxylase which is the crucial enzyme for the biosynthesis of histidine. Studies have shown that histamine is likely to be involved in the regulation of reproduction system. To find the possible correlation between HDC gene and AANM (age at natural menopause), w...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2006.08.008

    authors： Zhang F,Xiong DH,Wang W,Shen H,Xiao P,Yang F,Recker RR,Deng HW

    更新日期：2006-10-06 00:00:00

  • Afrikander cattle congenital goiter: size heterogeneity in thyroglobulin mRNA.

    abstract：:The mRNA coding for thyroglobulin in cattle homozygous for an autosomal recessive defect of thyroglobulin synthesis was investigated using a recombinant plasmid containing bovine mRNA coding sequence. Total RNA preparations from goiter contained one third of the thyroglobulin mRNA sequences found in normal thyroid tis...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/0006-291x(85)90597-2

    authors： Ricketts MH,Vandenplas S,van der Walt M,van Jaarsveld PP,Bester AJ,Boyd CD

    更新日期：1985-01-16 00:00:00

  • Alteration in L-type pyruvate kinase gene expression is not associated with the LF-B1 mRNA level.

    abstract：:The relation of expression of the LF-B1 gene with the L-type pyruvate kinase (L-PK) mRNA level in rat liver and hepatoma cells was investigated. The L-PK mRNA level in rat liver changed after partial hepatectomy, during development and on intake of a high carbohydrate diet, while the level of LF-B1 mRNA remained uncha...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/0006-291x(91)90393-l

    authors： Imai E,Noguchi T,Takenaka M,Yamada K,Matsuda T,Monaci P,Nicosia A,Tanaka T

    更新日期：1991-05-15 00:00:00

  • Ubiquitin-specific protease 14 promotes prostate cancer progression through deubiquitinating the transcriptional factor ATF2.

    abstract：:Activating Transcription Factor 2 (ATF2) is a member of the ATF/CREB bZIP family of transcription factors and an oncogene in prostate cancer. ATF2 has been reported to be a critical substrate of the CUL3-SPOP-RBX1 E3 ubiquitin ligase complex and the recurrent somatic mutation of SPOP has been believed to be a key feat...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2019.12.128

    authors： Geng L,Chen X,Zhang M,Luo Z

    更新日期：2020-03-26 00:00:00

  • Fructose 2,6-bisphosphate, a potent regulator of carbohydrate metabolism, inhibits trehalose phosphorylase from protist Euglena gracilis.

    abstract：:Partially purified trehalose phosphorylase (EC 2.4.1.64) from Euglena gracilis SM-ZK was inhibited by fructose 2,6-bisphosphate in both synthetic and degradative directions. Ki value for trehalose phosphorolysis was 1.2 microM and that for trehalose synthesis was 0.5 microM. Functions of fructose 2,6-bisphosphate in E...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/0006-291x(84)91176-8

    authors： Miyatake K,Kuramoto Y,Kitaoka S

    更新日期：1984-08-16 00:00:00

  • Study of multi-drug resistant mechanisms in a taxol-resistant hepatocellular carcinoma QGY-TR 50 cell line.

    abstract：:Cancer chemotherapy with taxol often fails due to acquired resistance of cancer cells, which is frequently associated with an overexpression of P-gp and alterations of beta-tubulin. A taxol-resistant cell line, QGY-TR50, derived from a human hepatocellular carcinoma (HCC) QGY-7703 cell line was used to investigate the...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1006/bbrc.2001.4268

    authors： Zhou J,Cheng SC,Luo D,Xie Y

    更新日期：2001-02-09 00:00:00

  • Hypoxia is a strong inducer of vascular endothelial growth factor mRNA expression in the heart.

    abstract：:Vascular endothelial growth factor (VEGF) is a potent and specific mitogen for vascular endothelial cells. A 3.9 kb VEGF transcript is expressed by all cardiac tissues from rat, mouse and guinea pig examined. VEGF expression was not developmentally regulated. The major form of VEGF mRNAs expressed by cardiac tissues c...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1006/bbrc.1993.2144

    authors： Ladoux A,Frelin C

    更新日期：1993-09-15 00:00:00

  • Ex vivo expansion of hematopoietic stem cell by fusion protein TAT-Zfx.

    abstract：:The relative inability of hemopoietic stem cells (HSCs) to reproduce themselves (self-renew) ex vivo imposes substantial limitations on the current use of HSC transplantation. Recently, the transcription factor Zfx has been demonstrated that played an important in controlling the self-renewal of hematopoietic stem cel...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章,收录出版

    doi：10.1016/j.bbrc.2008.12.125

    authors： Xu C,Zhang Y,Jiang H

    更新日期：2009-02-13 00:00:00

  • TT virus is distributed in various leukocyte subpopulations at distinct levels, with the highest viral load in granulocytes.

    abstract：:When TT virus (TTV) DNA was quantitated in whole blood and plasma aliquots from 27 viremic individuals by real-time detection PCR that can detect essentially all TTV genotypes, the TTV load was 6.9 +/- 3.5 (mean +/- standard deviation)-fold higher in the whole blood than in the plasma samples [P < 0.002 (paired t test...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1006/bbrc.2001.6183

    authors： Takahashi M,Asabe S,Gotanda Y,Kishimoto J,Tsuda F,Okamoto H

    更新日期：2002-01-11 00:00:00

  • LncRNA PCAT6 promotes tumor progression in osteosarcoma via activation of TGF-β pathway by sponging miR-185-5p.

    abstract：:Long noncoding RNAs (lncRNAs) play crucial roles in tumor development of osteosarcoma (OS). LncRNA PCAT6 was involved in the progression of multiple human cancers. However, the biological function of PCAT6 in OS remains largely unknown. We found that PCAT6 was elevated in OS tissues relative to that in their adjacent ...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2019.10.136

    authors： Zhu C,Huang L,Xu F,Li P,Li P,Hu F

    更新日期：2020-01-08 00:00:00

  • Differential gene expression in retinoic acid-induced differentiation of acute promyelocytic leukemia cells, NB4 and HL-60 cells.

    abstract：:Acute promyelocytic leukemia (APL) is characterized by a specific chromosome translocation t(15;17), which results in the fusion of the promyelocytic leukemia gene (PML) and retinoic acid receptor alpha gene (RARalpha). APL can be effectively treated with the cell differentiation inducer all-trans retinoic acid (ATRA)...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/s0006-291x(02)02043-0

    authors： Lee KH,Chang MY,Ahn JI,Yu DH,Jung SS,Choi JH,Noh YH,Lee YS,Ahn MJ

    更新日期：2002-09-06 00:00:00

  • Interactions of a designed peptide with lipopolysaccharide: Bound conformation and anti-endotoxic activity.

    abstract：:Designed peptides that would selectively interact with lipopolysaccharide (LPS) or endotoxin and fold into specific conformations could serve as important scaffolds toward the development of antisepsis compounds. Here, we describe solution structure of a designed amphipathic peptide, H(2)N-YVKLWRMIKFIR-CONH(2) (YW12D)...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2008.02.105

    authors： Bhunia A,Chua GL,Domadia PN,Warshakoon H,Cromer JR,David SA,Bhattacharjya S

    更新日期：2008-05-09 00:00:00

  • Transplantation of human umbilical cord blood cells improves glycemia and glomerular hypertrophy in type 2 diabetic mice.

    abstract：:Recent in vitro and in vivo studies have shown that either animal- or human-derived embryonic stem cells can differentiate into insulin-secreting cells and lower blood glucose levels. However, studies utilizing human umbilical cord blood (HUCB) mononuclear cells to improve blood glucose levels in diabetic animals have...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2004.06.121

    authors： Ende N,Chen R,Reddi AS

    更新日期：2004-08-13 00:00:00

  • Single cell analysis of changes in cytosolic calcium induced by vitamin D3 metabolites in cultured rat mesangial cells.

    abstract：:The acute effects of 1,25-Dihydroxy-vitamin D3 [1,25(OH)2D3] on the concentration of cytoplasmic ionized calcium [Ca2+] of cultured rat mesangial cells were studied at the single cell level by microspectrofluorometry of fura-2-loaded cells. Addition of 1,25(OH)2D3 produced an immediate increase of [Ca2]+. This rise in...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/s0006-291x(05)81140-4

    authors： Boland RL,de Boland AR,Nobiling R,Weinreich T,Ritz E

    更新日期：1991-10-31 00:00:00

  • The stimulation of prostaglandin production by transforming growth factor-alpha and 12-O-tetradecanoyl-phorbol-13-acetate or 1-oleoyl-2-acetyl-glycerol is synergistic.

    abstract：:Stimulation of prostaglandin production in C-9 rat liver cells by transforming growth factor (TGF)-alpha was synergistic with that of the tumor promoter 12-O-tetradecanoyl-phorbol-13-acetate (TPA). TGF-alpha and TPA synergized the release of radiolabelled compounds from [3H]arachidonic acid prelabelled C-9 cells. 1-Ol...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/0006-291x(85)90389-4

    authors： Levine L,Xiao DM,Worth N,Lilley WE

    更新日期：1985-07-16 00:00:00

  • Effects of polyamine analogs on the extent and fidelity of in vitro polypeptide synthesis.

    abstract：:A series of polyamine analogs has been examined for their ability to support protein synthesis in an in vitro rabbit reticulocyte translation system. Diamines were found to stimulate protein synthesis to the greatest extent (8-12 fold). Triamines, tetraamines and pentaamines only stimulated 2-4 fold under these condit...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/0006-291x(91)90440-i

    authors： Snyder RD,Edwards ML

    更新日期：1991-05-15 00:00:00

  • Acid-sensing by the T cell death-associated gene 8 (TDAG8) receptor cloned from rat brain.

    abstract：:The T cell death-associated gene 8 (TDAG8) is a pH-sensing GPCR with a reported immune-specific expression profile. Here, we demonstrate pH-induced activation of TDAG8 receptor cloned from rodent brain (rTDAG8). Cloned rTDAG8 transcript showed 88-95% homology with human and mouse transcripts of lymphoid origin. RT-PCR...

    journal_title：Biochemical and biophysical research communications

    pub_type： 杂志文章

    doi：10.1016/j.bbrc.2009.05.133

    authors： McGuire J,Herman JP,Ghosal S,Eaton K,Sallee FR,Sah R

    更新日期：2009-08-28 00:00:00