A note on distributions of times to coalescence,under time-dependent population size

Expressions for marginal distributions of times in the time-varying coalescence process are derived. The proposed method allows also for computation of joint probability distribution for pairs, triples, etc. of coalescence times. The expressions derived are useful for (1) extending several statistics from time constant to time-varying case, (2) increasing efficiency and accuracy of simulations in time-varying evolution, and (3) debugging coalescence simulation software.     

AccD6, a key carboxyltransferase essential for mycolic acid synthesis in Mycobacterium tuberculosis, is dispensable in a nonpathogenic strain

Acetyl coenzyme A carboxylase (ACC) is a key enzyme providing a substrate for mycolic acid biosynthesis. Although in vitro studies have demonstrated that the protein encoded by accD6 (Rv2247) may be a functional carboxyltransferase subunit of ACC in Mycobacterium tuberculosis, the in vivo function and regulation of accD6 in slow- and fast-growing mycobacteria remain elusive. Here, directed mutagenesis demonstrated that although accD6 is essential for M. tuberculosis, it can be deleted in Mycobacterium smegmatis without affecting its cell envelope integrity. Moreover, we showed that although it is part of the type II fatty acid synthase operon, the accD6 gene of M. tuberculosis, but not that of M. smegmatis, possesses its own additional promoter (P(acc)). The expression level of accD6(Mtb) placed only under the control of P(acc) is 10-fold lower than that in wild-type M. tuberculosis but is sufficient to sustain cell viability. Importantly, this limited expression level affects growth, mycolic acid content, and cell morphology. These results provide the first in vivo evidence for AccD6 as a key player in the mycolate biosynthesis of M. tuberculosis, implicating AccD6 as the essential ACC subunit in pathogenic mycobacteria and an excellent target for new antitubercular compounds. Our findings also highlight important differences in the mechanism of acetyl carboxylation between pathogenic and nonpathogenic mycobacterial species.     

A phylogeny reconstruction of the Dendrophylliidae (Cnidaria,Scleractinia) based on molecular and micromorphological criteria,and its ecological implications

Recent molecular phylogenetic studies have shown that most traditional families of zooxanthellate shallow‐water scleractinians are polyphyletic, whereas most families mainly composed of deep‐sea and azooxanthellate species are monophyletic. In this context, the family Dendrophylliidae (Cnidaria, Scleractinia) has unique features. It shows a remarkable variation of morphological and ecological traits by including species that are either colonial or solitary, zooxanthellate or azooxanthellate, and inhabiting shallow or deep water. Despite this morphological heterogeneity, recent molecular works have confirmed that this family is monophyletic. Nevertheless, what so far is known about the evolutionary relationships within this family, is predominantly based on skeleton macromorphology, while most of its species have remained unstudied from a molecular point of view. Therefore, we analysed 11 dendrophylliid genera, four of which were investigated for the first time, and 30 species at molecular, micromorphological and microstructural levels. We present a robust molecular phylogeny reconstruction based on two mitochondrial markers (COI and the intergenic spacer between COI and 16S) and one nuclear (rDNA), which is used as basis to compare micromorphogical and microstructural character states within the family. The monophyly of the Dendrophylliidae is well supported by molecular data and also by the presence of rapid accretion deposits, which are ca. 5 μm in diameter and arranged in irregular clusters, and fibres that thicken the skeleton organized in small patches of a few micrometres in diameter. However, all genera represented by at least two species are not monophyletic, Tubastraea excluded. They were defined by traditional macromorphological characters that appear affected by convergence, homoplasy and intraspecific variation. Micromorphogical and microstructural analyses do not support the distinction of clades, with the exception of the organization of thickening deposits for the Tubastraea clade.     

Ferulic acid antioxidant protection against hydroxyl and peroxyl radical oxidation in synaptosomal and neuronal cell culture systems in vitro: structure-activity studies

In this study, free radical scavenging abilities of ferulic acid in relation to its structural characteristics were evaluated in solution, cultured neurons, and synaptosomal systems exposed to hydroxyl and peroxyl radicals. Cultured neuronal cells exposed to the peroxyl radical initiator AAPH die in a dose-response manner and show elevated levels of protein carbonyls. The presence of ferulic acid or similar phenolic compounds, however, greatly reduces free radical damage in neuronal cell systems without causing cell death by themselves. In addition, synaptosomal membrane systems exposed to oxidative stress by hydroxyl and peroxyl radical generators show elevated levels of oxidation as indexed by protein oxidation, lipid peroxidation, and ROS measurement. Ferulic acid greatly attenuates these changes, and its effects are far more potent than those obtained for vanillic, coumaric, and cinnamic acid treatments. Moreover, ferulic acid protects against free radical mediated changes in conformation of synaptosomal membrane proteins as monitored by EPR spin labeling techniques. The results presented in this study suggest the importance of naturally occurring antioxidants such as ferulic acid in therapeutic intervention methodology against neurodegenerative disorders such as Alzheimer's disease in which oxidative stress is implicated.     

The combined impact of mechanical factors on the wall stress of the human ascending aorta – a finite elements study

Background

Biomechanical factors influence stress in the aortic wall. The aim of this study was to assess how the diameter and shape of the vessel, blood pressure and longitudinal systolic aortic stretching (SAS) caused by the contraction of the myocardium influence stress in the aortic wall.

Methods

Three computational models of the non-dilated aorta and aneurysms of the ascending aorta and aortic root were created. Then, finite elements analyses were carried out. The models were subjected to blood pressure (120 mmHg and 160 mmHg) and longitudinal systolic aortic stretching (0 mm, 5 mm, 10 mm and 15 mm). The influence of wall elasticity was examined too.

Results

Blood pressure had a smaller impact on the stress than the SAS. An increase in blood pressure from 120 mmHg to 160 mmHg increased the peak wall stress (PWS) on average by 0.1 MPa in all models. A 5 mm SAS caused a 0.1–0.2 MPa increase in PWS in all the models. The increase in PWS caused by a 10 mm and 15 mm SAS was 0.2 MPa and 0.4 MPa in the non-dilated aorta, 0.2–0.3 MPa and 0.3–0.5 MPa in the aneurysm of the ascending aorta, and 0.1–0.2 MPa and 0.2–0.3 MPa in the aortic root aneurysm model, respectively. The loss of elasticity of the aneurysmal wall resulted in an increase of PWS by 0.1–0.2 MPa.

Conclusions

Aortic geometry, wall stiffness, blood pressure and SAS have an impact on PWS. However, SAS had the biggest impact on wall stress. The results of this study may be useful in future patient-specific computational models used to assess the risk of aortic complications.

     

Meiotic maturation of the mouse oocyte requires an equilibrium between cyclin B synthesis and degradation

Among the proteins whose synthesis and/or degradation is necessary for a proper progression through meiotic maturation, cyclin B appears to be one of the most important. Here, we attempted to modulate the level of cyclin B1 and B2 synthesis during meiotic maturation of the mouse oocyte. We used cyclin B1 or B2 mRNAs with poly(A) tails of different sizes and cyclin B1 or B2 antisense RNAs. Oocytes microinjected with cyclin B1 mRNA showed two phenotypes: most were blocked in MI, while the others extruded the first polar body in advance when compared to controls. Moreover, these effects were correlated with the length of the poly(A) tail. Thus it seems that the rate of cyclin B1 translation controls the timing of the first meiotic M phase and the transition to anaphase I. Moreover, overexpression of cyclin B1 or B2 was able to bypass the dbcAMP-induced germinal vesicle block, but only the cyclin B1 mRNA-microinjected oocytes did not extrude their first polar body. Oocytes injected with the cyclin B1 antisense progressed through the first meiotic M phase but extruded the first polar body in advance and were unable to enter metaphase II. This suggested that inhibition of cyclin B1 synthesis only took place at the end of the first meiotic M phase, most likely because the cyclin B1 mRNA was protected. The injection of cyclin B2 antisense RNA had no effect. The life observation of the synthesis and degradation of a cyclin B1-GFP chimera during meiotic maturation of the mouse oocyte demonstrated that degradation can only occur during a given period of time once it has started. Taken together, our data demonstrate that the rates of cyclin B synthesis and degradation determine the timing of the major events taking place during meiotic maturation of the mouse oocyte.     

Polarization of cinnamoyl-CoA substrates bound to enoyl-CoA hydratase: correlation of (13)C NMR with quantum mechanical calculations and calculation of electronic strain energy

When alpha,beta-unsaturated substrates bind to the active site of enoyl-CoA hydratase, large spectral changes can be observed [D'Ordine, R. L., et al. (1994) Biochemistry 33, 12635-12643]. The differences in the isotropic magnetic shieldings of the free and active site-bound forms of the carbonyl, alpha-, and beta-carbons of the substrates, hexadienoyl-CoA, cinnamoyl-CoA, and (N,N-dimethyl-p-amino)cinnamoyl-CoA have been experimentally determined. The carbonyl and beta-carbons are all deshielded, while the alpha-carbons show increased shielding. These chemical shift perturbations are interpreted to suggest that the pi-electrons of the enoyl thiolester are polarized when bound at the active site. Using the crystal structure of (N,N-dimethyl-p-amino)cinnamoyl-CoA bound at the enzyme active site, the shielding tensors were calculated at three different levels of theory, up to a density functional theory model that included all of the contiguous active site residues. These calculations successfully reproduced the observed spectral changes and permitted the electronic polarization of the substrate to be quantified as an electron density difference map. The calculated electron density difference confirms the loss of electrons at the electrophilic beta-carbon and carbonyl carbon, while a slight increase in electron density at the alpha-carbon where proton donation occurs during the hydration reaction and a larger increase in electron density at the carbonyl oxygen are predicted. The energy required to polarize the electrons to the observed extent was calculated to be 3.2 kcal/mol. The force that provides the requisite energy for the polarization is the interaction of the electric field generated by the protein at the enzyme active site with the polarizable electrons of the substrate. Because the induced electronic polarization is along the predicted reaction pathway, the extent of substrate activation by the induced electronic strain is catalytically relevant.     

Gene Finding on the Y: Fruitful Strategy in Drosophila does not Deliver in Anopheles

The Anopheles gambiae genome project yielded almost complete sequences for the autosomes and for a large part of the X chromosome, however, no information for the Y chromosome was obtained. Yet, by design, fragmented Y chromosome sequences should be present in the resulting assembly. Here we report the search for Anopheles Y chromosome genes using a strategy successfully applied for identification of Y genes in Drosophila. A complete set of the unmapped scaffolds was targeted in a broad TBLASTN search using both A. gambiae predicted genes and all proteins from nr database as query sequences. After filtering of the BLAST report, we selected 181 scaffolds possibly containing fragments of Y chromosome genes to experimentally test their Y-linkage. Surprisingly, none of the tested sequences appeared to originate from the Y chromosome. Several factors could account for the failure to detect Y genes, including their different organization in A. gambiae compared to Drosophila and the suboptimal quality of the assembly and annotation of the Anopheles genome. Regardless of the cause, our results illuminate problems associated with the genome analysis of outbred organisms.     

Molecular mechanisms of autosomal recessive hypercholesterolemia

PURPOSE OF REVIEW: Autosomal recessive hypercholesterolemia (ARH) is a rare Mendelian dyslipidemia characterized by markedly elevated plasma LDL levels, xanthomatosis, and premature coronary artery disease. LDL receptor function is normal, or only moderately impaired in fibroblasts from ARH patients, but their cultured lymphocytes show increased cell-surface LDL binding, and impaired LDL degradation, consistent with a defect in LDL receptor internalization. Recently, the disorder was shown to be caused by mutations in a phosphotyrosine binding domain protein, ARH, which is required for internalization of low density lipoproteins in the liver. This review summarizes the findings of new investigations into the pathophysiology and molecular genetics of ARH. RECENT FINDINGS: All mutations that have been characterized to date preclude the synthesis of a full-length protein. GST-pulldown experiments indicate that the phosphotyrosine binding domain of ARH interacts with the internalization sequence (NPVY) in the cytoplasmic tail of LDLR, and that conserved motifs in the C-terminal portion of the protein bind to clathrin and to the beta2-adaptin subunit of AP-2. SUMMARY: The available data suggest that ARH functions as an adaptor protein that couples LDLR to the endocytic machinery.