On Hill et al's conjecture for calculating the subtree prune and regraft distance between phylogenies

Background  

Recently, Hill et al. [1] implemented a new software package--called SPRIT--which aims at calculating the minimum number of horizontal gene transfer events that is needed to simultaneously explain the evolution of two rooted binary phylogenetic trees on the same set of taxa. To this end, SPRIT computes the closely related so-called rooted subtree prune and regraft distance between two phylogenies. However, calculating this distance is an NP-hard problem and exact algorithms are often only applicable to small- or medium-sized problem instances. Trying to overcome this problem, Hill et al. propose a divide-and-conquer approach to speed up their algorithm and conjecture that this approach can be used to compute the rooted subtree prune and regraft distance exactly.     

The C-terminal domains of ADAMTS-4 and ADAMTS-5 promote association with N-TIMP-3

We investigated whether the affinity of tissue inhibitor of metalloproteinases (TIMP)-3 for adamalysins with thrombospondin motifs (ADAMTS)-4 and ADAMTS-5 is affected by the non-catalytic ancillary domains of the enzymes. For this purpose, we first established a novel method of purifying recombinant FLAG-tagged TIMP-3 and its inhibitory N-terminal domain (N-TIMP-3) by treating transfected HEK293 cells with sodium chlorate to prevent heparan sulfate proteoglycan-mediated TIMP-3 internalization. TIMP-3 and N-TIMP-3 affinity for selected matrix metalloproteinases and forms of ADAMTS-4 and -5 lacking sequential C-terminal domains was determined. TIMP-3 and N-TIMP-3 displayed similar affinity for various matrix metalloproteinases as has been previously reported for E. coli-expressed N-TIMP-3. ADAMTS-4 and -5 were inhibited more strongly by N-TIMP-3 than by full-length TIMP-3. The C-terminal domains of the enzymes enhanced interaction with N-TIMP-3 and to a lesser extent with the full-length inhibitor. For example, N-TIMP-3 had 7.5-fold better K_i value for full-length ADAMTS-5 than for the catalytic and disintegrin domain alone. We propose that the C-terminal domains of the enzymes affect the structure around the active site, favouring interaction with TIMP-3.     

pH-dependent assembly of DNA-gold nanoparticles based on the i-motif

Oligonucleotides containing stretches of 2 '-deoxycytidine residues were immobilized on 15 nm gold nanoparticles. Under acidic pH conditions a reversible supramolecular assembly is formed, induced by the formation of the tetrameric i-motif structure. The replacement of 2 '-deoxycytidine by 5-propynyl-2 '-deoxycytidine (dC*) leads to novel i-motif structures. Oligonucleotides incorporating multiple residues of dC* were immobilized on 15 nm gold nanoparticles and are able to aggregate into i-motif structures even at non-optimal pH values.     

Chromosome banding in three species of <Emphasis Type="Italic">Hypsiboas</Emphasis> (Hylidae,Hylinae), with special reference to a new case of B-chromosome in anuran frogs and to the reduction of the diploid number of 2n = 24 to 2n = 22 in the genus

The chromosomes of hylids Hypsiboas albopunctatus, H. raniceps, and H. crepitans from Brazil were analyzed with standard and differential staining techniques. The former species presented 2n = 22 and 2n = 23 karyotypes, the odd diploid number is due to the presence of an extra element interpreted as B chromosome. Although morphologically very similar to the small-sized chromosomes of the A complement, the B was promptly recognized, even under standard staining, on the basis of some characteristics that are usually attributed to this particular class of chromosomes. The two other species have 2n = 24, which is the chromosome number usually found in the species of Hypsiboas karyotyped so far. This means that 2n = 22 is a deviant diploid number, resulted from a structural rearrangement, altering the chromosome number of 2n = 24 to 2n = 22. Based on new chromosome data, some possibilities were evaluated for the origin of B chromosome in Hypsiboas albopunctatus, as well as the karyotypic evolution in the genus, leading to the reduction in the diploid number of 2n = 24 to 2n = 22.     

Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study

Diversity of indigenous microbial consortia and natural occurrence of obligate hydrocarbon-degrading bacteria (OHCB) are of central importance for efficient bioremediation techniques. To investigate the microbial population dynamics and composition of oil-degrading consortia, we have established a series of identical oil-degrading mesocosms at three different locations, Bangor (Menai Straits, Irish Sea), Helgoland (North Sea) and Messina (Messina Straits, Mediterranean Sea). Changes in microbial community composition in response to oil spiking, nutrient amendment and filtration were assessed by ARISA and DGGE fingerprinting and 16Sr RNA gene library analysis. Bacterial and protozoan cell numbers were quantified by fluorescence microscopy. Very similar microbial population sizes and dynamics, together with key oil-degrading microorganisms, for example, Alcanivorax borkumensis, were observed at all three sites; however, the composition of microbial communities was largely site specific and included variability in relative abundance of OHCB. Reduction in protozoan grazing had little effect on prokaryotic cell numbers but did lead to a decrease in the percentage of A.?borkumensis 16S rRNA genes detected in clone libraries. These results underline the complexity of marine oil-degrading microbial communities and cast further doubt on the feasibility of bioaugmentation practices for use in a broad range of geographical locations.     

Expression of different forms of transglutaminases by immature cells of Helianthus tuberosus sprout apices

Immature cells of etiolated apices of sprouts growing from Helianthus tuberosus (H. t.) tubers showed Ca²⁺-dependent transglutaminase (TG, EC 2.3.2.13) activity on fibronectin (more efficiently) and dimethylcasein as substrates. Three main TG bands of about 85, 75 and 58 kDa were isolated from the 100,000×g apices supernatant through a DEAE-cellulose column at increasing NaCl concentrations and immuno-identified by anti-TG K and anti-rat prostate gland TG antibodies. These three fractions had catalytic activity as catalyzed polyamine conjugation to N-benzyloxycarbonyl-L-γ-glutaminyl-L-leucine (Z-L-Gln-L-Leu) and the corresponding glutamyl-derivatives were identified. The amino acid composition of these TG proteins was compared with those of several sequenced TGs of different origin. The composition of the two larger bands presented great similarities with annotated TGs; in particular, the 75 kDa form was very similar to mammalian inactive EPB42. The 58 kDa form shared a low similarity with other TGs, including a maize sequence of similar molecular mass, which, however, did not present the catalytic triad in the position of all annotated TGs. A 3D model of the H. t. TGs was built adopting TG2 as template. These novel plant TGs are hypothesized to be constitutive and discussed in relation to their possible roles in immature cells. These data suggest that in plants, multiple TG forms are active in the same organ and that plant and animal enzymes probably are very close not only for their catalytic activity but also structurally.     

Monitoring ovarian cycles and pregnancy in brown brocket deer (Mazama gouazoubira) by measurement of fecal progesterone metabolites

In the present study, pregnancy and the estrous cycle were monitored in captive brown brocket deer (Mazama gouazoubira) by measuring fecal progestagens with a commercial enzyme immunoassay (EIA), along with behavioral data. Fecal samples were collected twice a week during pregnancy and daily during the estrous cycle and post-partum period. It was possible to distinguish between inter-luteal and luteal phases of the estrous cycle. Behavioral estrus corresponded with low concentrations of fecal progestagens. Samples from two consecutive cycles were available from five hinds, and the mean estrous cycle (n=10) was 26.9+/-1.7 d (mean+/-S.E.M.). However, when two extreme cycles (34 and 37 d) were deleted, the mean estrous cycle was 24.7+/-1.2 d. Three animals became pregnant (gestation ranged from 208 to 215 d). After fertile breeding, progestagen concentration in these hinds remained among luteal phase concentrations throughout pregnancy, with the exception of a few peaks. Within 4 d post-partum, two hinds reached interluteal phase values, while one hind maintained luteal concentrations for at least 1 week.     

The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of BRASSINOSTEROID INSENSITIVE1 in Arabidopsis

Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptor-mediated endocytosis.     

Replication of Simian Virus 40 Deoxyribonucleic Acid: Analysis of the One-Step Growth Cycle

The time course of replication of simian virus 40 deoxyribonucleic acid (DNA) was investigated in growing monolayer cultures of subcloned CV1 cells. At multiplicities of infection of 30 to 60 plaque-forming units (PFU)/cell, first progeny DNA molecules (component 1) were detected by 10 hr after infection. During the following 10 to 12 hr, accumulation of virus DNA proceeded at ever increasing rates, albeit in a non-exponential fashion. The rate of synthesis then remained constant, until approximately the 40th hour postinfection, when DNA replication stopped. Under these conditions, the duration of the virus growth cycle was approximately 50 hr. The time needed for the synthesis of one DNA molecule was found to be approximately 15 min. At multiplicities of infection of 1 or less than 1 PFU/cell, the onset of the linear phase of DNA accumulation was delayed, but the final rate of DNA synthesis was the same, independent of the input multiplicity. This was taken as a proof that templates for the synthesis of viral DNA multiply in the cell during the early phase of replication. However, the probability for every replicated DNA molecule to become in turn replicative decreased constantly during that phase. This could be accounted for by assuming a limited number of replication sites in the infected cell.