Abstract：
:A reliable phylogenetic reconstruction of the evolutionary history of contemporary species depends on a robust identification of the universal common ancestor (UCA) at the root of the Tree of Life (ToL). That root polarizes the tree so that the evolutionary succession of ancestors to descendants is discernable. In effect, the root determines the branching order and the direction of character evolution. Typically, conventional phylogenetic analyses implement time-reversible models of evolution for which character evolution is un-polarized. Such practices leave the root and the direction of character evolution undefined by the data used to construct such trees. In such cases, rooting relies on theoretic assumptions and/or the use of external data to interpret unrooted trees. The most common rooting method, the outgroup method is clearly inapplicable to the ToL, which has no outgroup. Both here and in the accompanying paper (Harish and Kurland, 2017) we have explored the theoretical and technical issues related to several rooting methods. We demonstrate (1) that Genome-level characters and evolution models are necessary for species phylogeny reconstructions. By the same token, standard practices exploiting sequence-based methods that implement gene-scale substitution models do not root species trees; (2) Modeling evolution of complex genomic characters and processes that are non-reversible and non-stationary is required to reconstruct the polarized evolution of the ToL; (3) Rooting experiments and Bayesian model selection tests overwhelmingly support the earlier finding that akaryotes and eukaryotes are sister clades that descend independently from UCA (Harish and Kurland, 2013); (4) Consistent ancestral state reconstructions from independent genome samplings confirm the previous finding that UCA features three fourths of the unique protein domain-superfamilies encoded by extant genomes.
journal_name
Biochimiejournal_title
Biochimieauthors
Harish A,Kurland CGdoi
10.1016/j.biochi.2017.04.014subject
Has Abstractpub_date
2017-07-01 00:00:00pages
137-155eissn
0300-9084issn
1638-6183pii
S0300-9084(17)30109-8journal_volume
138pub_type
杂志文章相关文献
BIOCHIMIE文献大全abstract：:Pseudouridine [Ψ] is a frequent base modification in the ribosomal RNA [rRNA] and may be involved in the modulation of the conformational flexibility of rRNA helix-loop structures during protein synthesis. Helix 69 of 23S rRNA contains pseudouridines at the positions 1911, 1915 and 1917 which are formed by the helix 6...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2010.12.018
更新日期：2011-05-01 00:00:00
abstract：:We present here, a new method for coupling sulfhydryl groups (SH) to low-density lipoprotein (LDL) surface. This method uses homocysteine thiolactone (HCTL) which reacts with lysine residues in a very mild manner, and permits the selection of the number of SH bound per LDL. Under our experimental conditions (8 SH/LDL)...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/s0300-9084(86)80166-3
更新日期：1986-05-01 00:00:00
abstract：:Lipidomics is a subspecialty of metabolomics that focuses on water insoluble metabolites that form membrane barriers. Most lipidomic databases catalog lipids from common model organisms, like humans or Escherichia coli. However, model organisms' lipid profiles show surprisingly little overlap with those of specialized...
journal_title：Biochimie
pub_type： 杂志文章,评审
doi：10.1016/j.biochi.2012.08.012
更新日期：2013-01-01 00:00:00
abstract：:Posttranscriptional gene regulation by small RNAs and its crucial impact on development, apoptosis, stem cell self-renewal and differentiation gained tremendous scientific attention since the discovery of RNA interference (RNAi) and microRNAs (miRNAs). However, in the last few years, many more examples for regulatory ...
journal_title：Biochimie
pub_type： 杂志文章,评审
doi：10.1016/j.biochi.2011.07.032
更新日期：2011-11-01 00:00:00
abstract：:Purified chromatin from pig lymph nodes has been prepared and used for the isolation of chromatin proteins and non-histine proteins. Saccharose nuclei from this tissue have been used for the preparation of nuclear phenol-soluble phosphoproteins. The isolated proteins have been compared by analytical electrophoresis in...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/s0300-9084(76)80391-4
更新日期：1976-01-01 00:00:00
abstract：:Azelaic acid (AzA), a C9 linear α,ω-dicarboxylic acid, is found in whole grains namely wheat, rye, barley, oat seeds and sorghum. The study was performed to investigate whether AzA exerts beneficial effect on hepatic key enzymes of carbohydrate metabolism in high fat diet (HFD) induced type 2 diabetic C57BL/6J mice. C...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2013.01.018
更新日期：2013-06-01 00:00:00
abstract：:The bovine oxytocin precursor was expressed in Escherichia coli as a fusion protein by cloning the hormone encoding cDNA in frame behind the replicase gene of the RNA phage MS2. By step-wise extraction with different urea concentrations, the fusion protein was enriched in the 7 M urea fraction and further purified by ...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/0300-9084(88)90165-4
更新日期：1988-01-01 00:00:00
abstract：:Explants from 7, 8, 9, 11, 13-day chick embryonic skin incorporating (3H) Uridine for different periods 1 hr, 3 or 4 hr and a chase with actinomycin) are studied with respect to free (F) or membrane bound (B) cytoplasmic polysomes and to RNA extracted from them. Polysome specific activity decreases at older stages but...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/s0300-9084(76)80226-x
更新日期：1976-01-01 00:00:00
abstract：:The inhibitory action on rat liver phosphoglycerate kinase of structural analogs of the two substrates of this enzyme (beta,gamma- methyleneadenosine 5'-triphosphate for ATP and 2-phosphoglycerate for 3-phosphoglycerate) was studied. In the direction of ADP utilization, the inhibition patterns obtained with beta,gamma...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/s0300-9084(86)80201-2
更新日期：1986-04-01 00:00:00
abstract：:Neuropeptides and hormones, in contrast to constitutive secretory proteins, are sorted to and stored in secretory granules and released upon a stimulus. During the last two decades, signals and mechanisms involved in their sorting to the regulated pathway of protein secretion have been addressed in numerous studies. T...
journal_title：Biochimie
pub_type： 杂志文章,评审
doi：10.1016/s0300-9084(00)00195-4
更新日期：2000-04-01 00:00:00
abstract：:Our study highlights the tight relationship between protein binding to monolayers and the phase-state of the phospholipids. Interaction of mitochondrial creatine kinase with phospholipidic membranes was analysed using a two-phase monolayer system containing anionic phospholipids under chain mismatch conditions. Monola...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2009.03.014
更新日期：2009-06-01 00:00:00
abstract：:Peptides with hormonal or neuronal activity are derived by enzymatic processing from pro-hormones, which by themselves are biologically inert. Processing and other enzymatic conversions may occur step-wise, leading to the formation of a cascade of biologically active (or inactive) peptides. The neurokin in substance P...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/0300-9084(88)90159-9
更新日期：1988-01-01 00:00:00
abstract：:Fanconi anemia (FA) is a rare and complex inherited blood disorder of the child. At least 15 genes are associated with the disease. The highest frequency of mutations belongs to groups A, C and G. Genetic instability and cytokine hypersensitivity support the selection of leukemic over non-leukemic stem cells. FA cellu...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2013.06.006
更新日期：2013-10-01 00:00:00
abstract：:Disappearance of 7-ethylguanine and O6-ethylguanine lesions from nuclear DNA is observed on incubation of isolated rat liver nuclei previously treated with ethylnitrosourea. Free 7-ethylguanine but no free O6-ethylguanine is released in the medium. Incubation of methylated or ethylated DNA with chromatin proteins lead...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/s0300-9084(82)80132-6
更新日期：1982-08-01 00:00:00
abstract：:A high level of subcellular compartmentalization is a hallmark of eukaryotic cells. This intricate internal organization was present already in the common ancestor of all extant eukaryotes, and the determination of the origins and early evolution of the different organelles remains largely elusive. Organellar proteome...
journal_title：Biochimie
pub_type： 杂志文章,评审
doi：10.1016/j.biochi.2015.03.021
更新日期：2015-12-01 00:00:00
abstract：:The hydrolysis of trioctanoin and of monoolein by rat intestinal homogenates, catalyzed by the previously described "trioctanoin hydrolase" and "monoglyceride lipase" [Ref. 6 and 11], was shown to be entirely due to the action of the intestinal glycerol-ester hydrolase [Ref. 1 and 2] and to contaminating pancreatic li...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/s0300-9084(77)80320-9
更新日期：1977-01-01 00:00:00
abstract：:Glutaredoxins (Grxs), redox-active proteins with a typical -CPYC motif at their active sites, are involved in redox-regulatory processes and antioxidant defenses. The human malarial parasite Plasmodium falciparum possess a classical glutaredoxin (PfGrx) as well as a number of Grx-like proteins. In the present study, w...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2009.12.003
更新日期：2010-03-01 00:00:00
abstract：:Kinetic parameters characterizing the catalytic activities of enzymes are typically investigated in dilute solutions. However, in reality, these reactions occur in cells that, in addition to water and ions, are full of other macromolecules including proteins, nucleic acids, lipids, and metabolites. Such a crowded envi...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2020.07.009
更新日期：2020-09-01 00:00:00
abstract：:Microalgae are single-cell, photosynthetic organisms whose biodiversity places them at the forefront of biological producers of high-value molecules including lipids and pigments. Some of these organisms particular are capable of synthesizing n-3 very long chain polyunsaturated fatty acids (VLC-PUFAs), known to have b...
journal_title：Biochimie
pub_type： 杂志文章,评审
doi：10.1016/j.biochi.2020.04.022
更新日期：2020-11-01 00:00:00
abstract：:The iron absorption by duodenal enterocytes is a key step of its homeostasis. But the control of this absorption is complex and cannot be fully explicated with present knowledge. In a global transcriptome approach, we identified 60 genes over-expressed in hemin (iron) overload in Caco-2 cells, an in vitro model of duo...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2008.01.002
更新日期：2008-04-01 00:00:00
abstract：:Developing a logical and rational methodology for obtaining vaccines, especially against the main parasite causing human malaria (P. falciparum), consists of blocking receptor-ligand interactions. Conserved peptides derived from proteins involved in invasion and having high red blood cell binding ability have thus bee...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2005.07.006
更新日期：2006-02-01 00:00:00
abstract：:The multisubunit Mediator is an evolutionary conserved transcriptional coregulatory complex in eukaryotes. It is needed for the transcriptional regulation of gene expression in general as well as in a gene specific manner. Mediator complex subunits interact with different transcription factors as well as components of...
journal_title：Biochimie
pub_type： 杂志文章,评审
doi：10.1016/j.biochi.2017.10.012
更新日期：2018-01-01 00:00:00
abstract：:Despite its biological importance, iron is a pro-oxidant element and its accumulation results in tissue injury. Iron overload diseases such as thalassemia and hereditary hemochromatosis are commonly associated with liver tissue injury. Glutamyl cysteine (GC) is a dipeptide with antioxidant properties owing to its cyst...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2015.06.006
更新日期：2015-08-01 00:00:00
abstract：:Sphingolipids are degraded by sphingomyelinase and ceramidase in the gut to ceramide and sphingosine, which may inhibit cell proliferation and induce apoptosis, and thus have anti-tumour effects in the gut. Although previous rodent studies including experiments on knockout mice indicate a role of neutral ceramidase in...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2007.03.009
更新日期：2007-08-01 00:00:00
abstract：:The biosynthesis of the beta-lactam antibiotic penicillin is an excellent model for the study of secondary metabolites produced by filamentous fungi due to the good background knowledge on the biochemistry and molecular genetics of the beta-lactam producing microorganisms. The three genes (pcbAB, pcbC, penDE) encoding...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2008.09.004
更新日期：2009-02-01 00:00:00
abstract：:The considerable affinity of tissue transglutaminase for heparin was the basis for use of heparin-based affinity matrices for enzyme purification. Interaction of transglutaminase with heparin might mimic the physiological binding to membrane heparan sulfates, accounting for the limited but significant fraction of enzy...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2005.01.012
更新日期：2005-06-01 00:00:00
abstract：:The issue of whether histone H1 possesses specificity of binding to certain nucleotide sequences in DNA is of fundamental importance to the suggested role of the linker histone in the regulation of gene transcription. The purpose of the present study was to reinvestigate the specificity of binding of histone H1 to the...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/0300-9084(93)90116-a
更新日期：1993-01-01 00:00:00
abstract：:Sphingosine is a natural sphingolipid found in membranes of all eukaryotic cells. In addition to its functions in cell signaling, sphingosine has broad-spectrum antimicrobial properties. Sphingosine's role as an antimicrobial is important in tissues such as the skin and respiratory epithelium. Reduction in the normal ...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/j.biochi.2017.03.014
更新日期：2017-10-01 00:00:00
abstract：:mRNAs extracted from human pheochromocytoma were translated in vitro in a lysate of a rabbit reticulocytes. Two enzymes of the biosynthetic pathway of the catecholamines, tyrosine-hydroxylase (TH) and dopamine-beta-hydroxylase (DBH), were characterized as translation products after immunoprecipitation by specific anti...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/s0300-9084(85)80198-x
更新日期：1985-06-01 00:00:00
abstract：:An apparatus for chemi- and bioluminescence measurements is described. The main features are in high sensitivity: for example, 5 10(-12) M adenosine triphosphate, 5 10(-7) M glucose, 2 10(-9) M perhydrol and 4 10(-13) M peroxidase are easily detected; its fast mixing time and the possibility of injecting a reactant, a...
journal_title：Biochimie
pub_type： 杂志文章
doi：10.1016/s0300-9084(80)80061-7
更新日期：1980-01-01 00:00:00
