Solution conformations of unmodified and A(37)N(6)-dimethylallyl modified anticodon stem-loops of Escherichia coli tRNA(Phe)

The modification of RNA nucleotide bases, a fundamental process in all cells, alters the chemical and physical properties of RNA molecules and broadly impacts the physiological properties of cells. tRNA molecules are by far the most diverse-modified RNA species within cells, containing as a group >80% of the known 96 chemically unique nucleic acid modifications. The greatest varieties of modifications are located on residue 37 and play a role in ensuring fidelity and efficiency of protein synthesis. The enzyme dimethylallyl (Delta(2)-isopentenyl) diphosphate:tRNA transferase catalyzes the addition of a dimethylallyl group to the exocyclic amine nitrogen (N6) of A(37) in several tRNA species. Using a 17 residue oligoribonucleotide corresponding to the anticodon arm of Escherichia coli tRNA(Phe), we have investigated the structural and dynamic changes introduced by the dimethylallyl group. The unmodified RNA molecule adopts stem-loop conformation composed of seven base-pairs and a compact three nucleotide loop. This conformation is distinctly different from the U-turn motif that characterizes the anticodon arm in the X-ray crystal structure of the fully modified yeast tRNA(Phe). The adoption of the tri-nucleotide loop by the purine-rich unmodified tRNA(Phe) anticodon arm suggests that other anticodon sequences, especially those containing pyrimidine bases, also may favor a tri-loop conformation. Introduction of the dimethylallyl modification increases the mobility of nucleotides of the loop region but does not dramatically alter the RNA conformation. The dimethylallyl modification may enhance ribosome binding through multiple mechanisms including destabilization of the closed anticodon loop and stabilization of the codon-anticodon helix.     

Functions of lumican and fibromodulin: lessons from knockout mice

Lumican and fibromodulin are collagen-binding leucine-rich proteoglycans widely distributed in interstitial connective tissues. The phenotypes of lumican-null (Lum ^–/–), Fibromodulin-null (Fmod ^–/–) and compound double-null (Lum ^–/– Fmod ^–/–) mice identify a broad range of tissues where these two proteoglycans have overlapping and unique roles in modulating the extracellular matrix and cellular behavior. The lumican-deficient mice have reduced corneal transparency and skin fragility. The Lum ^–/– Fmod ^–/– mice are smaller than their wildtype littermates, display gait abnormality, joint laxity and age-dependent osteoarthritis. Misaligned knee patella, severe knee dysmorphogenesis and extreme tendon weakness are the likely cause for joint-laxity. Fibromodulin deficiency alone leads to significant reduction in tendon stiffness in the Lum ^+/+ Fmod ^–/– mice, with further loss in stiffness in a lumican gene dose-dependent way. At the level of ultrastructure, the Lum ^–/– cornea, skin and tendon show irregular collagen fibril contours and increased fibril diameter. The Fmod ^–/– tendon contains irregular contoured collagen fibrils, with increased frequency of small diameter fibrils. The tendons of Lum ^–/– Fmod ^–/– have an abnormally high frequency of small and large diameter fibrils indicating a de-regulation of collagen fibril formation and maturation. In tissues like the tendon, where both proteoglycans are present, fibromodulin may be required early in collagen fibrillogenesis to stabilize small-diameter fibril-intermediates and lumican may be needed at a later stage, primarily to limit lateral growth of fibrils Published in 2003.     

Analysis of the nonsteroidal anti-inflammatory drug literature for potential developmental toxicity in rats and rabbits

BACKGROUND: Nonsteroidal anti‐inflammatory drugs (NSAIDs) are among the most commonly prescribed to pregnant women. Some case‐control studies have linked the NSAIDs aspirin and indomethacin with a risk of congenital abnormalities and low birthweight. High doses of aspirin produce developmental toxicity in rats (e.g., gastroschisis/umbilical hernia, diaphragmatic hernia [DH]) when administered during sensitive windows of development. Unlike other NSAIDs, aspirin irreversibly inhibits cyclooxygenases (COXs) 1 and 2. Hence, the developmental toxicity seen in rats after exposure to aspirin may be due to the irreversible inhibition of COX‐1 and/or COX‐2. If so, other NSAIDs, which act through a reversible inhibition of COX, may produce a weak developmental toxicity signal or no developmental toxicity signal when tested in preclinical models. To investigate this relationship, a comprehensive analysis of the NSAID developmental toxicity literature was undertaken to determine whether NSAIDs other than aspirin induce developmental anomalies similar to those elicited by aspirin. METHODS: Developmental toxicity studies were identified through literature searches of PubMed and TOXNET, and pregnancy outcome data were extracted and tabulated. By using a set of defined criteria, each study was evaluated for quality and assigned to one of five tiers. The relation between certain malformations and NSAID treatment was analyzed for the best studies (tiers 1–4) by using concurrent control data (Mantel–Haenszel and permutation tests) and by combining the concurrent control data with historical control data (χ² test and permutation tests). RESULTS: A qualitative analysis of these data led to a focus on three types of malformations: DH, ventricular septal defects (VSDs), and midline defects (MDs). In rats, the incidences of VSD and MD were increased among fetuses treated with NSAIDs when compared with the concurrent controls. The extent of the increase was attenuated when the data from the aspirin studies were excluded from the analysis. There were no qualifying (i.e., tiers 1–4) aspirin studies conducted in rabbits, but the incidences of the three defects were increased over control incidences among non‐aspirin NSAID‐treated animals. Statistical analysis of these data was subsequently conducted. When tiers 1–4 were combined and compared with concurrent controls plus the most appropriate historical control database, the strongest associations were between NSAID treatment and VSD in rats, VSD in rabbits, and MD in rabbits. There also was some suggestion of an association between NSAID treatment and DH in rabbits. CONCLUSIONS: This analysis of the non‐clinical NSAID literature demonstrated a possible association between exposure to NSAIDs and developmental anomalies. The anomalies were similar for aspirin and for other NSAIDs, but effects occurred at a much lower incidence with non‐aspirin NSAIDs than previously reported with aspirin. Such a finding is consistent with the concept that reversible inhibition of COX‐1 and/or COX‐2 by other NSAIDs would produce weaker developmental toxicity signals than aspirin. However, there were limitations of the evaluated studies: (1) there were very few robust International Conference on Harmonization–compliant studies conducted with NSAIDs in the published literature; (2) many of the studies were conducted at doses well below the maximum tolerated dose (MTD), where effects are rarely seen; and (3) numerous studies were conducted above the MTD, where reduced numbers of fetuses hampered detection of low‐incidence findings. Although weak associations were observed, these limitations prevented us from definitively determining the presence or absence of a developmental toxicity signal from the existing body of NSAID data. Further exploration of this hypothesis will require assessing the potential association in animal models by using dose levels centered around the MTD. Birth Defects Research (Part B) 68:5–26, 2003. © 2003 Wiley‐Liss, Inc.     

Birth order and relationships

Previous studies (Salmon 1999; Salmon and Daly 1998) have found that sex and birth order are strong predictors of familial sentiments. Middleborns tend to be less family-oriented than firstborns or lastborns, while sex differences seem to focus on the utility of kin in certain domains. If this is a reflection of middleborns receiving a lesser degree of support from kin (particularly in terms of parental investment), are middleborns turning to reciprocal alliances outside the family, becoming friendship specialists? Are there comparable birth order differences with respect to mating strategies? In this study, the impact of birth order on attitudes toward family, friends, and mating were examined. Two hundred and forty-five undergraduates completed a questionnaire relating to their attitudes toward friends and family as well as some aspects of mating behavior. Birth order did have a significant impact in several areas. Middleborns expressed more positive views toward friends and less positive opinions of family in general. They were less inclined to help family in need than firstborns or lastborns. Mating strategies also appeared to be influenced by birth order, most notably in the area of infidelity, with middleborns being the least likely birth order to cheat on a sexual partner.     

Application of Preserved Human Amniotic Membrane for Corneal Surface Reconstruction

Objective: To evaluate the efficacy of preserved human amniotic membrane transplantation for reconstruction of the corneal surface diseases. Methods: Preserved human amniotic membrane transplantations were performed in 84 eyes of 78 patients for corneal surface reconstruction. The indications were limbal stem cell deficiency from Steven–Johnson syndrome, chemical burn and herpes keratitis (27 eyes), bullous keratopathy (26 eyes), persistent epithelial defect and dellen (17 eyes), band keratopathy (11 eyes), preparing for prosthesis (1 eye), corneal ulcer (1 eye) and acute chemical burn (1 eye). Results: Success was noted in 83.3% (70/84) eyes, partial success in 13.1% (11/84) eyes, and failure in 3.6% (3/84) eyes for an average follow-up of 10.5 months (3 – 29 months). No patient developed major immediate post-operative complications. Conclusion: Amniotic membrane transplantation can reduce inflammation, promote corneal epithelial healing, and decrease irritation in corneal surface problems.     

Molecular changes in the d-bifunctional protein cDNA sequence in australasian patients belonging to the bifunctional protein complementation group

The cDNA sequence for the human d-bifunctional protein (D-BP: 17β-hydroxysteroid dehydrogenase IV) was investigated in patients with peroxisomal disorders belonging to the BP complementation group (CG). In three cases, analysis of polymerase chain reaction products generated from the patients' cDNA indicated the presence of a deletion within the region corresponding to nucleotides 209–537 of the normal cDNA sequence. Subsequent sequencing revealed that, in two of the patients, 47 base pairs were missing, with the deletion corresponding to nucleotides 302/3–349/50 of the normal sequence. In the third patient, a smaller deletion of 22 bp (nucleotides 280/1–302/3) was characterized. Only the mutant sequence was detected in each of these cases, consistent with parental consanguinity. Both deletions cause a frameshift, and would lead to premature termination of the BP. Available family members were also investigated, and the findings conformed with expectations for an autosomal recessive disorder. In addition to the deletions, a number of other base changes have been identified in this series of patients. In particular, one patient, whose parents were also consanguineous, was homozygous for a base change, which results in a nonconservative substitution of serine 177 with a phenylalanine residue. The functional significance of this amino acid substitution, as well as the other identified changes, is still to be determined. Nevertheless, our data provide strong support for the hypothesis that defects in the gene for the D-BP are responsible for the β-oxidation defect in patients belonging to the BP CG.     

Bmp2 and Bmp4 genetically interact to support multiple aspects of mouse development including functional heart development

Bone morphogenetic proteins (BMPs) have multiple roles during embryogenesis. Current data indicate that the dosage of BMPs is tightly regulated for normal development in mice. Since Bmp2 or Bmp4 homozygous mutant mice show early embryonic lethality, we generated compound heterozygous mice for Bmp2 and Bmp4 to explore the impact of lowered dosage of these BMP ligands. Genotyping pups bred between Bmp2 and Bmp4 heterozygous mice revealed that the ratio of adult compound heterozygous mice for Bmp2 and Bmp4 is much lower than expected. During embryogenesis, the compound heterozygous embryos showed several abnormalities, including defects in eye formation, body wall closure defects, and ventricular septal defects (VSD) in the heart. However, the ratio of the compound heterozygous embryos was the same as expected. Caesarean sections at E18.5 revealed that half of the compound heterozygotes died soon after birth, and the majority of the dead individuals exhibited VSD. Survivors were able to grow to adults, but their body weight was significantly lower than control littermates. They demonstrated progressive abnormalities in the heart, eventually showing a branched leaflet in atrioventricular valves. These results suggest that the dosage of both BMP2 and 4 is critical for functional heart formation during embryogenesis and after birth. genesis 47:374–384, 2009. © 2009 Wiley‐Liss, Inc.     

Phosphodiesterase inhibitor 3-isobutyl-methyl-xanthine stimulates reproduction in rabbit females

The aim of our study was to examine the influence of 3-isobutyl-1-methyl-xanthine (IBMX), an inhibitor of cyclic adenosine monophosphate and cyclic guanosine monophosphate phosphodiesterases, on the reproductive efficiency of gonadotropin-stimulated rabbits (Oryctolagus cuniculus, Leporidae, Lagomorpha). The ovarian cycle and ovulation of control rabbits was induced by pregnant mare serum gonadotropin (PMSG) followed by administration of human chorionic gonadotropin (hCG; first series of experiments) or gonadotropin-releasing hormone (GnRH; second series of experiments). Experimental animals received PMSG and hCG together with IBMX (at 5 or 25 μg/animal) or GnRH together with IBMX (at 50 or 500 μg/animal). After ovulation and mating, in the first series of experiments, animals were killed; the pronuclear-stage eggs were flushed from the oviducts and cultured up to blastocyst cell stage. Numbers of ovarian corpora lutea, ovulated oocytes, and oocyte-derived embryos reaching blastocyst stage were determined. In the second series of experiments, all the animals were kept until parturition, when the pregnancy and birth rate, litter size, and number, viability, and body weight of pups were recorded. IBMX injections at doses of 5 or 25 μg/animal significantly increased the number of ovulations/corpora lutea, harvested zygotes, and embryos derived from these zygotes. Administration of IBMX at doses of 500 μg/animal or 50 μg/animal to nulliparous young animals (4.5 mo of age) significantly increased their pregnancy rate and birth rate, litter size, and litter weight. In multiparous old animals (2 yr of age), IBMX at a dose of 50 μg/animal, but not 500 μg/animal, significantly increased their pregnancy rate and litter size, but not the birth rate, number of pups per female, or litter weight. These data demonstrate that (1) IBMX can enhance the stimulatory effect of GnRH/gonadotropins on rabbit ovulation, oocyte maturation, embryo yield and development, pregnancy and birth rate, and number, viability, and body weight of pups; (2) nulliparous young females (4.5 mo of age) are more sensitive to IBMX treatments than the multiparous old animals (2 yr of age); and (3) cyclic nucleotides-dependent intracellular mechanisms are involved in control of rabbit reproductive functions and IBMX, an activator of these mechanisms, can be a stimulator of reproduction and fertility.