INSECT PHYLOGENOMICS. Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

Tong et al. comment on the accuracy of the dating analysis presented in our work on the phylogeny of insects and provide a reanalysis of our data. They replace log-normal priors with uniform priors and add a "roachoid" fossil as a calibration point. Although the reanalysis provides an interesting alternative viewpoint, we maintain that our choices were appropriate.

Gold(III) compounds containing a chelating, dicarbanionic ligand derived from 4,4'-di-tert-butylbiphenyl.

An oligomeric gold(III) compound containing dicarbanionic chelating 4,4'-di-tert-butylbiphenyl was prepared via transmetallation using the corresponding organotin(IV) compound. The reactivity of the chloro-bridged oligomer with various species including neutral N-, P-, and C-donor ligands as well as monoanionic S- and Se-ligands was investigated. Some of the products were characterised by X-ray crystallography. The photophysical properties of two derivatives were studied.

Pyrolysing poultry litter reduces N2O and CO2 fluxes.

Application of poultry litter (PL) to soil can lead to substantial nitrous oxide (N2O) emissions due to the co-application of labile carbon (C) and nitrogen (N). Slow pyrolysis of PL to produce biochar may mitigate N2O emissions from this source, whilst still providing agronomic benefits. In a corn crop on ferrosol with similarly matched available N inputs of ca. 116 kg N/ha, PL-biochar plus urea emitted significantly less N2O (1.5 kg N2O-N/ha) compared to raw PL at 4.9 kg N2O-N/ha. Urea amendment without the PL-biochar emitted 1.2 kg N2O-N/ha, and the PL-biochar alone emitted only 0.35 kg N2O-N/ha. Both PL and PL-biochar resulted in similar corn yields and total N uptake which was significantly greater than for urea alone. Using stable isotope methodology, the majority (~80%) of N2O emissions were shown to be from non-urea sources. Amendment with raw PL significantly increased C mineralisation and the quantity of permanganate oxidisable organic C. The low molar H/C (0.49) and O/C (0.16) ratios of the PL-biochar suggest its higher stability in soil than raw PL. The PL-biochar also had higher P and K fertiliser value than raw PL. This study suggests that PL-biochar is a valuable soil amendment with the potential to significantly reduce emissions of soil greenhouse gases compared to the raw product. Contrary to other studies, PL-biochar incorporated to 100mm did not reduce N2O emissions from surface applied urea, which suggests that further field evaluation of biochar impacts, and methods of application of both biochar and fertiliser, are needed.

Chemical and structural analysis of enhanced biochars: thermally treated mixtures of biochar, chicken litter, clay and minerals.

In this study biochar mixtures comprising a Jarrah-based biochar, chicken litter (CL), clay and other minerals were thermally treated, via torrefaction, at moderate temperatures (180 and 220 °C). The objectives of this treatment were to reduce N losses from CL during processing and to determine the effect of both the type of added clay and the torrefaction temperature on the structural and chemical properties of the final product, termed as an enhanced biochar (EB). Detailed characterisation indicated that the EBs contained high concentrations of plant available nutrients. Both the nutrient content and plant availability were affected by torrefaction temperature. The higher temperature (220 °C) promoted the greater decomposition of organic matter in the CL and dissociated labile carbon from the Jarrah-based biochar, which produced a higher concentration of dissolved organic carbon (DOC). This DOC may assist to solubilise mineral P, and may also react with both clay and minerals to block active sites for P adsorption. This subsequently resulted in higher concentrations of plant available P. Nitrogen loss was minimised, with up to 73% of the initial total N contained in the feedstock remaining in the final EB. However, N availability was affected by both torrefaction temperature and the nature of the clay minerals added.

Parenting and the psychological development of a representative sample of triplets conceived by assisted reproduction.

BACKGROUND: The aim of the study was to examine the quality of parenting and the psychological development of three-year-old children in IVF/ICSI families with triplets. METHODS: Comparisons were carried out between a representative sample of 10 families with triplets and matched groups of 15 families with twins and 30 families with singletons. The families were recruited from Follow-Up, a national organization in France that was established to study children conceived by assisted reproduction. Standardized measures of the mother's psychological well-being (parenting stress, depression and quality of marriage) and standardized measures of the child's psychological development (emotional/behavioural problems and general development) were completed by the mother. RESULTS: Mothers with a multiple birth were found to experience greater difficulties in parenting than mothers of singletons, with no differences between mothers of triplets and mothers of twins. Regarding the children, there were no differences in emotional or behavioural problems between triplets, twins and singletons. However, there were indications of mild delay among triplets and twins in some aspects of language development in comparison with the singleton children. CONCLUSIONS: The birth of triplets or twins does appear to cause difficulties for parents in the early years, however, the children themselves do not seem to experience markedly raised levels of psychological or developmental problems.

Non-genetic and non-gestational parenthood: consequences for parent-child relationships and the psychological well-being of mothers, fathers and children at age 3.

BACKGROUND: Findings are presented of the third phase of a longitudinal study of children conceived by assisted reproduction procedures involving surrogacy and/or donor conception. METHODS: At the time of the child's third birthday, 34 surrogacy families, 41 donor insemination families and 41 oocyte donation families were compared with 67 natural conception families on standardized interview and questionnaire measures of the psychological well-being of the parents, mother-child relationships and the psychological well-being of the child. RESULTS: The differences found between family types reflected higher levels of warmth and interaction between mothers and their 3-year-old children in assisted reproduction families than in families with a naturally conceived child. A higher proportion of surrogacy parents than donor conception parents had told their children about the nature of their birth. CONCLUSIONS: It appears that the absence of a genetic and/or gestational link between parents and their child does not have a negative impact on parent-child relationships or the psychological well-being of mothers, fathers or children at age 3.

A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7.

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.

The European study of assisted reproduction families: the transition to adolescence.

BACKGROUND: Findings are presented of the second phase of a European longitudinal study of families created by assisted reproduction. The present investigation reports on data obtained during the child's transition to adolescence. METHODS: A total of 102 IVF families, 94 donor insemination (DI) families, 102 adoptive families, and 102 families with a naturally conceived child were compared on standardized interview and questionnaire measures of parenting and children's psychological well-being. RESULTS: The assisted reproduction families were similar to the adoptive and natural conception families for many of the measures of the quality of parent-child relationships. To the extent that differences were found between the assisted reproduction families and the other family types, these reflected mainly more positive functioning among the assisted reproduction families, with the possible exception of the overinvolvement with their children of a small proportion of assisted reproduction mothers and fathers. The assisted reproduction children were functioning well and did not differ from the adoptive or naturally conceived children on any of the measures of psychological adjustment. However, only 8.6% had been told about their genetic origins. CONCLUSIONS: IVF and DI families with an early adolescent child appear to be functioning well.

Structural insights into the hydrolysis of cellular nitric oxide synthase inhibitors by dimethylarginine dimethylaminohydrolase.

Nitric oxide synthase is inhibited by asymmetric NG-methylated derivatives of arginine whose cellular levels are controlled in part by dimethylarginine dimethylaminohydrolase (DDAH, EC 3.5.3.18). Levels of asymmetric NG,NG-dimethylarginine (ADMA) are known to correlate with certain disease states. Here, the first structure of a DDAH shows an unexpected similarity to arginine:glycine amidinotransferase (EC 2.1.4.1) and arginine deiminase (EC 3.5.3.6), thus defining a superfamily of arginine-modifying enzymes. The identification of a Cys-His-Glu catalytic triad and the structures of a Cys to Ser point mutant bound to both substrate and product suggest a reaction mechanism. Comparison of the ADMA-DDAH and arginine-amidinotransferase complexes reveals a dramatic rotation of the substrate that effectively maintains the orientation of the scissile bond of the substrate with respect to the catalytic residues. The DDAH structure will form a basis for the rational design of selective inhibitors, which are of potential use in modulating NO synthase activity in pathological settings.

The role of tyrosine residues in fibroblast growth factor receptor 1 signaling in PC12 cells. Systematic site-directed mutagenesis in the endodomain.

To assess the contribution of the intracellular domain tyrosine residues to the signaling capacity of fibroblast growth factor receptor 1 (FGFR1), stably transfected chimeras bearing the ectodomain of the platelet-derived growth factor receptor (PDGFR) and the endodomain of FGFR1 were systematically altered by a tyrosine to phenylalanine bloc and individual conversions. The 15 tyrosine residues of the endodomain of this construct (PFR1) were divided into four linear segments (labeled A, B, C, and D) that contained 4, 4, 2, and 5 tyrosine residues, respectively. When stimulated by platelet-derived growth factor, derivatives in which the A, B, or A + B blocs of tyrosines were mutated were about two-thirds as active as the unmodified chimera at 48 h but achieved full activity by 96 h in a neurite outgrowth assay in transfected PC12 cells. Elimination of only the two activation loop tyrosines (C bloc) also inactivated the receptor. All derivatives in which 4 (or 5) of the D bloc tyrosines were mutated were inactive in producing differentiation but showed low levels of kinase activity in in vitro assays. Derivatives in which 1, 2, or 3 tyrosines of the D bloc in different combinations were systematically changed demonstrated that 2 residues (Tyr(677) and Tyr(701), using hFGFR1 numbering) were essential for bioactivity, but the remaining 3 residues, including Tyr(766), the previously identified site for phospholipase C gamma (PLC gamma) activation, were not. Differentiation activity was paralleled by the activation (phosphorylation) of FRS2, SOS, and ERK1/2. PLC gamma activity was dependent on the presence of Tyr(766) but also required Tyr(677) and/or Tyr(701). Although fully active chimeras did not require PLC gamma, the responses of chimeras showing reduced activation of FRS2 were significantly enhanced by this activity. These results establish that PFR1 does not utilize any tyrosine residues, phosphorylated or not, to activate FRS2. However, it does require Tyr(677) and/or Tyr(701), which may function to stabilize the active conformation directly or indirectly.

Nucleic acids. Sequences and topology Web alert.

A selection of World Wide Web sites relevant to reviews published in this issue of Current Opinion in Structural Biology.

Macromolecular assemblages. Theory and simulation.

A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Structural Biology.

Structure-activity relationship of the p55 TNF receptor death domain and its lymphoproliferation mutants.

Upon stimulation with tumor necrosis factor (TNF), the TNF receptor (TNFR55) mediates a multitude of effects both in normal and in tumor cells. Clustering of the intracellular domain of the receptor, the so-called death domain (DD), is responsible for both the initiation of cell killing and the activation of gene expression. To characterize this domain further, TNFR55 DD was expressed and purified as a thioredoxin fusion protein in Escherichia coli. Circular dichroism, steady-state and time-resolved fluorescence spectroscopy were used to compare TNFR55 DD with DDs of the Fas antigen (Fas), the Fas-associating protein with DD (FADD) and p75 nerve growth factor receptor, for which the 3-dimensional structure are already known. The structural information derived from the measurements strongly suggests that TNFR55 DD adopts a similar fold in solution. This prompted a homology modeling of the TNFR DD 3-D structure using FADD as a template. In vivo studies revealed a difference between the two lymphoproliferation (lpr) mutations. Biophysical techniques were used to analyze the effect of changing Leu351 to Ala and Leu351 to Asn on the global structure and its impact on the overall stability of TNFR55 DD. The results obtained from these experiments in combination with the modeled structure offer an explanation for the in vivo observed difference.

Web alert. Proteins catalysis and regulation.

A selection of World Wide Web sites relevant to reviews published in this issue of Current Opinion in Structural Biology.

The role of brothers and sisters in the gender development of preschool children.

The study examined whether the sex of older siblings influences the gender role development of younger brothers and sisters of age 3 years. Data on the Pre-School Activities Inventory, a measure of gender role behavior that discriminates within as well as between the sexes, were obtained in a general population study for 527 girls and 582 boys with an older sister, 500 girls and 561 boys with an older brother, and 1665 singleton girls and 1707 singleton boys. It was found that boys with older brothers and girls with older sisters were more sex-typed than same-sex singletons who, in turn, were more sex-typed than children with other-sex siblings. Having an older brother was associated with more masculine and less feminine behavior in both boys and girls, whereas boys with older sisters were more feminine but not less masculine and girls with older sisters were less masculine but not more feminine.