Gene conversion homogenizes the CMT1A paralogous repeats

Background

Non-allelic homologous recombination between paralogous repeats is increasingly being recognized as a major mechanism causing both pathogenic microdeletions and duplications, and structural polymorphism in the human genome. It has recently been shown empirically that gene conversion can homogenize such repeats, resulting in longer stretches of absolute identity that may increase the rate of non-allelic homologous recombination.

Results

Here, a statistical test to detect gene conversion between pairs of non-coding sequences is presented. It is shown that the 24 kb Charcot-Marie-Tooth type 1A paralogous repeats (CMT1A-REPs) exhibit the imprint of gene conversion processes whilst control orthologous sequences do not. In addition, Monte Carlo simulations of the evolutionary divergence of the CMT1A-REPs, incorporating two alternative models for gene conversion, generate repeats that are statistically indistinguishable from the observed repeats. Bounds are placed on the rate of these conversion processes, with central values of 1.3 × 10^-4 and 5.1 × 10^-5 per generation for the alternative models.

Conclusions

This evidence presented here suggests that gene conversion may have played an important role in the evolution of the CMT1A-REP paralogous repeats. The rates of these processes are such that it is probable that homogenized CMT1A-REPs are polymorphic within modern populations. Gene conversion processes are similarly likely to play an important role in the evolution of other segmental duplications and may influence the rate of non-allelic homologous recombination between them.

     

Relation between the outer cover of the egg case of Argiope aurantia (Araneae: Araneidae) and the emergence of its spiderlings

To emerge from the egg case, Argiope aurantia spiderlings must penetrate a tightly woven outer cover composed primarily of large-diameter cylindrical gland fibers and small-diameter fibers, likely of aciniform gland origin. They accomplish this using enzymatic digestion and mastication to form a communal hole in the outer cover. The involvement of proteolytic enzymes in this process was demonstrated by zymography of spiderling homogenates and washes made from the edges of holes. The specific source(s) of the proteases is unknown, but histological examination of spiderling sections indicates that the digestive tract, venom glands, and gnathocoxal glands are all functioning at the time of emergence from the egg case. Observations on edges of holes indicate that spiderlings are able to solubilize the small-diameter fibers completely, but cylindrical gland fibers only partially. In the outer cover, cylindrical fibers are composed of numerous fibrils embedded within a matrix. Spiderlings appear to be unable to solubilize the fibrils, but digestion of the matrix allows the spiderlings to push the fibrils aside to create the opening.     

Adrenomedullin influences magnocellular and parvocellular neurons of paraventricular nucleus via separate mechanisms

We previously reported that adrenomedullin (AM) decreases blood pressure following microinjection into the paraventricular nucleus of the hypothalamus (PVN) of the rat. With the use of whole cell recordings in rat hypothalamic slice preparations, we characterized the effects of AM on electrophysiologically identified PVN neurons and described the membrane events underlying such actions. AM hyperpolarized magnocellular (type I) neurons in a dose-dependent manner, a response associated with an increase in the frequency and amplitude of inhibitory postsynaptic potentials. Blockade of action potentials with tetrodotoxin (TTX) abolished AM effects on membrane potential and synaptic activity in magnocellular neurons, suggesting direct actions on inhibitory interneurons. Furthermore, blockade of inhibitory synaptic transmission with the GABA(A) receptor antagonist bicuculline methiodide also abolished AM effects on membrane potential in magnocellular neurons. In contrast, parvocellular (type II) neurons depolarized following AM receptor activation. AM effects on parvocellular neurons were dose dependent and were maintained in the presence of TTX, indicating direct effects on this population of neurons. Voltage-clamp recordings from parvocellular neurons showed AM enhances a nonselective cationic conductance, suggesting a potential mechanism through which AM influences membrane potential. These observations show clear population-specific actions of AM on separate identified groups of PVN neurons. Such effects on magnocellular neurons likely contribute to the hypotensive actions of this peptide in PVN. Although the effects on parvocellular neurons may also contribute to such cardiovascular effects of AM, it is more likely that actions on this population of PVN neurons underlie the previously demonstrated activational effects of AM on the hypothalamic-pituitary-adrenal axis.     

Pelvic and hindlimb musculature of Tyrannosaurus rex (Dinosauria: Theropoda)

In this article, we develop a new reconstruction of the pelvic and hindlimb muscles of the large theropod dinosaur Tyrannosaurus rex. Our new reconstruction relies primarily on direct examination of both extant and fossil turtles, lepidosaurs, and archosaurs. These observations are placed into a phylogenetic context and data from extant taxa are used to constrain inferences concerning the soft-tissue structures in T. rex. Using this extant phylogenetic bracket, we are able to offer well-supported inferences concerning most of the hindlimb musculature in this taxon. We also refrain from making any inferences for certain muscles where the resulting optimizations are ambiguous. This reconstruction differs from several previous attempts and we evaluate these discrepancies. In addition to providing a new and more detailed understanding of the hindlimb morphology of T. rex--the largest known terrestrial biped--this reconstruction also helps to clarify the sequence of character-state change along the line to extant birds.     

Peroxisome proliferators compete and ameliorate Hcy-mediated endocardial endothelial cell activation

To determine whether homocysteine(Hcy)-mediated activation of endocardial endothelial (EE) cells isameliorated by peroxisome proliferator-activated receptor (PPAR), weisolated EE cells from mouse endocardium. Matrix metalloproteinase(MMP) activity and intercellular adhesion molecule (ICAM)-1 in EE cellswere measured in the presence and absence of Hcy, and ciprofibrate (CF;PPAR- agonist) or 15-deoxy-^12,14-prostaglandinJ₂ (PGJ₂; PPAR- agonist) by zymography andWestern blot analyses, respectively. Results suggest that Hcy-mediated MMP activation and ICAM-1 expression are ameliorated by CF and PGJ₂. To test the hypothesis that Hcy competes with otherligands for binding to PPAR and -, we prepared cardiac nuclearextracts. Extracts were loaded onto an Hcy-cellulose affinity column.Bound proteins were eluted with CF and PGJ₂. To determineconformational changes in PPAR upon binding to Hcy, we measured PPARfluorescence at 334 nm. Dose-dependent increase in PPAR fluorescencedemonstrated a primary binding affinity of 0.32 ± 0.06 µM. There wasdose-dependent quenching of PPAR fluorescence byfluorescamine-homocysteine (F-Hcy). PPAR- fluorescence quenching wasabrogated by the addition of CF but not by PGJ₂. PPAR-fluorescence quenching was abrogated by the addition ofPGJ₂ but not by CF. These results suggest that Hcy competeswith CF and PGJ₂ for binding to PPAR- and -,respectively, indicating a role of PPAR in amelioration of Hcy-mediatedEE dysfunction.

     

Dysgonomonas mossii sp. nov., from human sources

Phenotypic and phylogenetic studies were performed on seven unidentified gram-negative, facultatively anaerobic, coccobacillus-shaped organisms isolated from human clinical specimens. Comparative 16S rRNA gene sequencing demonstrated that four of the strains corresponded to Dysgonomonas capnocytophagoides whereas the remaining three isolates represent a new sub-line within the genus Dysgonomonas, displaying greater than 5% sequence divergence with Dysgonomonas capnocytophagoides and Dysgonomonas gadei. The three novel isolates were readily distinguished from D.capnocytophagoides and D. gadei by biochemical tests. The DNA base composition of the novel species was consistent with its assignment to the genus Dysgonomonas. Based on phylogenetic and phenotypic evidence it is proposed that the unknown species, be classified as Dysgonomonas mossii sp. nov. The type strain of Dysgonomonas mossii is CCUG 43457T (= CIP 107079T).     

Fanconi anemia protein complex is a novel target of the IKK signalsome

Fanconi anemia (FA), a genetic disorder predisposing to aplastic anemia and cancer, is characterized by hypersensitivity to DNA-damaging agents and oxidative stress. Five of the cloned FA proteins (FANCA, FANCC, FANCE, FANCF, FANCG) appear to be involved in a common functional pathway that is required for the monoubiquitination of a sixth gene product, FANCD2. Here, we report that FANCA associates with the IkappaB kinase (IKK) signalsome via interaction with IKK2. Components of the FANCA complex undergo rapid, stimulus-dependent changes in phosphorylation, which are blocked by kinase-inactive IKK2 (IKK2 K > M). When exposed to mitomycin C, cells expressing IKK2 K > M develop a cell cycle abnormality characteristic of FA. Thus, FANCA may function to recruit IKK2, thus providing the cell a means of rapidly responding to stress.