Dipeptides containing the alpha-aminoisobutyric residue (Aib) as ligands: preparation,spectroscopic studies and crystal structures of copper(II) complexes with H-Aib-X-OH (X=Gly,L-Leu,L-Phe)

Synthetic procedures are described that allow access to new copper(II) complexes with dipeptides containing the alpha-aminoisobutyric residue (Aib) as ligands. The solid complexes [Cu(H(-1)L(A))](n).nH(2)O (1) (L(A)H=H-Aib-Gly-OH), [Cu(H(-1)L(B))(MeOH)](n).nMeOH (2) (L(B)H=H-Aib-L-Leu-OH) and [Cu(H(-1)L(C))](n) (3) (L(C)H=H-Aib-L-Phe-OH) have been isolated and characterized by single-crystal X-ray crystallography, solid-state IR spectra and UV-Vis spectroscopy in solution (H(-1)L(2-) is the dianionic form of the corresponding dipeptide). Complexes 1 and 3 are three-dimensional coordination polymers with similar structures. The doubly deprotonated dipeptide behaves as a N(amino), N(peptide), O(carboxylate), O'(carboxylate), O(peptide) mu(3) ligand and binds to one Cu(II) atom at its amino and peptide nitrogens and at one carboxylate oxygen, to a second metal at the other carboxylate oxygen, while a third Cu(II) atom is attached to the peptide oxygen. The geometry around copper(II) is distorted square pyramidal with the peptide oxygen at the apex of the pyramid. The structure of 2 consists of zigzag polymeric chains, where the doubly deprotonated dipeptide behaves as a N(amino), N(peptide), O(carboxylate), O'(carboxylate) mu(2) ligand. The geometry at copper(II) is square pyramidal with the methanol oxygen at the apex. The IR data are discussed in terms of the nature of bonding and known structures. The UV-Vis spectra show that the solid-state structures of 1, 2 and 3 do not persist in H(2)O.     

Logit effect values and efficiency of significance tests when a noncollapsible variable is omitted

For linear models, randomization of the assignment to the levels of a variable A is a sufficient condition to obtain correct estimates of the effect of A on another variable B. For logit models, the omission of a relevant variable Z often results in invalid estimates of the effect of A and in a loss of power of the significance test. The values of this underestimation and of the loss of power are evaluated here asymptotically and from simulation studies. Consequences for practical use of logit models in randomized settings are underlined.     

Role for the pleckstrin homology domain-containing protein CKIP-1 in phosphatidylinositol 3-kinase-regulated muscle differentiation

In this work, we report the implication of the pleckstrin homology (PH) domain-containing protein CKIP-1 in phosphatidylinositol 3-kinase (PI3-K)-regulated muscle differentiation. CKIP-1 is upregulated during muscle differentiation in C2C12 cells. We show that CKIP-1 binds to phosphatidylinositol 3-phosphate through its PH domain and localizes to the plasma membrane in a PI3-K-dependent manner. Activation of PI3-K by insulin or expression of an active form of PI3-K p110 induces a rapid translocation of CKIP-1 to the plasma membrane. Conversely, expression of the 3-phosphoinositide phosphatase myotubularin or PI3-K inhibition by LY294002, wortmannin, or mutant p85 abolishes CKIP-1 binding to the membrane. Upon induction of differentiation in low-serum medium, CKIP-1 overexpression in C2C12 myoblasts first promotes proliferation and then stimulates the expression of myogenin and cell fusion in a manner reminiscent of the dual positive effect of insulin-like growth factors on muscle cells. Interference with the PI3-K pathway impedes the effect of CKIP-1 on C2C12 cell differentiation. Finally, silencing of CKIP-1 by RNA interference abolishes proliferation and delays myogenin expression. Altogether, these data strongly implicate CKIP-1 as a new component of PI3-K signaling in muscle differentiation.     

Expression and subcellular localization of a membrane protein related to Hsp30p in Saccharomyces cerevisiae

The Saccharomyces cerevisiae YDR033w gene product is homologous to Hsp30p and Yro2p, both of which are induced during heat shock. To investigate the subcellular localization of the YDR033w gene product, hemagglutinin (HA) epitope-tagged protein was expressed, detected on immunoblots, and localized by immunofluorescence to cell membranes, primarily the plasma membrane. A punctuate immunofluorescence pattern was observed within cell buds. The nuclear envelope, but not the vacuole or mitochondrial membranes, were also immunostained. We refer to YDR033w as MRH1 to denote that it encodes a membrane protein related to Hsp30p.     

How Diverse is Aquatic Biodiversity Research?

The use of the term ‘biodiversity’ in the aquatic bibliography has expanded during the last 10 years at an almost exponential rate. A quantitative analysis of the bibliography addressing the issue of biodiversity showed that it is mainly dominated by reviews or policy-oriented articles rather than articles referring to field data or models. The scientific effort is largely biased in terms of geographic distribution of the areas studied, country of origin of the first author and the biota studied. The number of institutions using the term ‘biodiversity’ in their title also increased dramatically with time after 1992. The proportion of references using molecular or genetic approaches to study aquatic biodiversity changed little during the last decade and ranged between 4 and 10% of the total. Our current perception of the earth’s aquatic biodiversity has been formed mainly from research carried out in the developed countries of the Northern Hemisphere. Most publications refer to commercial, charismatic or large size species, as well as to taxa of well known taxonomy; this is perhaps more compatible with traditional views of conservation of K-selection species rather than with concepts linking biodiversity to ecosystem function.     

High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection

There are at least 31 families of human endogenous retroviruses (HERVs), each derived from an independent infection by an exogenous virus. Using evidence of purifying selection on HERV genes, we have shown previously that reinfection by replication-competent elements was the predominant mechanism of copying in some families. Here we analyze the evolution of 17 HERV families using d(N)/d(S) ratios and find a positive relationship between copy number and the use of additional copying mechanisms. All families with more than 200 elements have also used one or more of the following mechanisms: (1) complementation in trans (elements copied by other elements of the same family; HERV-H and ERV-9), (2) retrotransposition in cis (elements copying themselves) within germ-line cells (HERV-K(HML3)), and (3) being copied by non-HERV machinery (HERV-W). We discuss why these other mechanisms are rare in most families and suggest why complementation in trans is significant only in the larger families.     

Structural requirements for the stabilization of metarhodopsin II by the C terminus of the alpha subunit of transducin

The retinal receptor rhodopsin undergoes a conformational change upon light excitation to form metarhodopsin II (Meta II), which allows interaction and activation of its cognate G protein, transducin (G(t)). A C-terminal 11-amino acid peptide from transducin, G(talpha)-(340-350), has been shown to both bind and stabilize the Meta II conformation, mimicking heterotrimeric G(t). Using a combinatorial library we identified analogs of G(talpha)-(340-350) that bound light-activated rhodopsin with high affinity (Martin, E. L., Rens-Domiano, S., Schatz, P. J., and Hamm, H. E. (1996) J. Biol. Chem. 271, 361-366). We have made peptides with key substitutions either on the background of the native G(talpha)-(340-350) sequence or on the high affinity sequences and used the stabilization of Meta II as a tool to determine which amino acids are critical in G protein-rhodopsin interaction. Removal of the positive charge at the N termini by acylation or delocalization of the charge by K to R substitution enhances the affinity of the G(talpha)-(340-350) peptides for Meta II, whereas a decrease was observed following C-terminal amidation. Cys-347, a residue conserved in pertussis toxin-sensitive G proteins, was shown to interact with a hydrophobic site in Meta II. These studies provide further insight into the mechanism of interaction between the G(talpha) C terminus and light-activated rhodopsin.     

Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved

About 8% of the human genome is made up of endogenous retroviruses (ERVs). Though most human endogenous retroviruses (HERVs) are thought to be irrelevant to our biology notable exceptions include members of the HERV-H family that are necessary for the correct functioning of stem cells. ERVs are commonly found in two forms, the full-length proviral form, and the more numerous solo-LTR form, thought to result from homologous recombination events. Here we introduce a phylogenetic framework to study ERV insertion and solo-LTR formation. We then apply the framework to site patterns sampled from a set of long alignments covering six primate genomes. Studying six categories of ERVs we quantitatively recapitulate patterns of insertional activity that are usually described in qualitative terms in the literature. A slowdown in most ERV groups is observed but we suggest that HERV-K activity may have increased in humans since they diverged from chimpanzees. We find that the rate of solo-LTR formation decreases rapidly as a function of ERV age and that an age dependent model of solo-LTR formation describes the history of ERVs more accurately than the commonly used exponential decay model. We also demonstrate that HERV-H loci are markedly less likely to form solo-LTRs than ERVs from other families. We conclude that the slower dynamics of HERV-H suggest a host role for the internal regions of these exapted elements and posit that in future it will be possible to use the relationship between full-length proviruses and solo-LTRs to help identify large scale co-options in distant vertebrate genomes.     

The design of stirred reactors with hollow fiber catalysts for Michaelis-Menten kinetics

A method of calculating the conversion in Rony's hollow fiber reactor is outlined. It, is assumed that, the kinetics are of Michaelis-Menten type and that diffusion within the hollow fiber, as well as through its wall, should be taken into account. The normalization of the Thiele modulus suffices to unify the treatment of internal diffusion and the pseudosteady state hypothesis is found to be valid under almost all conditions.