Describing RNA structure by libraries of clustered nucleotide doublets

The rapidly increasing wealth of structural information on RNA and knowledge of its varying roles in biology have facilitated the study of RNA structure using computational methods. Here, we present a new method to describe RNA structure based on nucleotide doublets, where a doublet is any two nucleotides in a structure. We restrict our search to doublets that are close together in space, but not necessarily in sequence, and obtain doublet libraries of various sizes by clustering a large set of doublets taken from a data set of high-resolution RNA structures. We demonstrate that these libraries are able to both capture structural features present in RNA and fit local RNA structure with a high level of accuracy. Libraries ranging in size from ten to 100 doublets are examined, and a detailed analysis shows that a library with as few as 30 doublets is sufficient to capture the most common structural features, while larger libraries would be more appropriate for accurate modeling. We anticipate many uses for these libraries, from annotation to structure refinement and prediction.     

Socio-economic and ecological impacts of global protected area expansion plans

Several global strategies for protected area (PA) expansion have been proposed to achieve the Convention on Biological Diversity''s Aichi target 11 as a means to stem biodiversity loss, as required by the Aichi target 12. However, habitat loss outside PAs will continue to affect habitats and species, and PAs may displace human activities into areas that might be even more important for species persistence. Here we measure the expected contribution of PA expansion strategies to Aichi target 12 by estimating the extent of suitable habitat available for all terrestrial mammals, with and without additional protection (the latter giving the counterfactual outcome), under different socio-economic scenarios and consequent land-use change to 2020. We found that expanding PAs to achieve representation targets for ecoregions under a Business-as-usual socio-economic scenario will result in a worse prognosis than doing nothing for more than 50% of the world''s terrestrial mammals. By contrast, targeting protection towards threatened species can increase the suitable habitat available to over 60% of terrestrial mammals. Even in the absence of additional protection, an alternative socio-economic scenario, adopting progressive changes in human consumption, leads to positive outcomes for mammals globally and to the largest improvements for wide-ranging species.     

Segregation of all four major fibrillar collagen genes in the Marfan syndrome.

Linkage markers at or close to the genes encoding the three major fibrillar collagens were used to analyze the segregation of these loci in six pedigrees with dominantly inherited Marfan syndrome. Four pedigrees were discordant at one of the Type I collagen loci (COL1A2), and, of these, two were discordant at the other Type I locus (COL1A1). The Marfan syndrome also segregated independently of the structural loci for Type II and Type III collagen in these two families. This is evidence against the Marfan syndrome being, in general, due to mutations in the major fibrillar collagen genes.     

Scanning electron microscopy of Treponema pallidum (Nichols strain) attached to cultured mammalian cells.

This paper describes the attachment of Treponema pallidum (Nichols strain) to cultured mammalian cells as a visualized by scanning electron microscopy. Treponemes were incubated for 3 hr with cultured cells derived from normal rabbit testes or human skin epithelium, then fixed, processed with critical-point drying, and examined with a Cambridge Mark 2A scanning electron microscope. Large numbers of treponemes became attached to the cultured cells without altering the morphological integrity of the cultured cells. Attachment appeared to involve a very close physical proximity of treponemes to the cultured cells; at the site of attachment, no changes such as swelling or indentation of the cultured cell surface were observed. The addition of ruthenium red to the fixatives produced a treponemal-associated surface precipitate. This material, which is probably mucopolysaccharide and/or phospholipid, may be important in protecting the organisms against host defense mechanisms; in addition, it may be involved in the serological unresponsiveness of freshly prepared suspensions of T. pallidum.     

The CXCR3 binding chemokine IP-10/CXCL10: structure and receptor interactions

The structure of IP-10 was solved by NMR spectroscopy and represents the first structure from the class of agonists toward the receptor CXCR3. CXCR3 binding chemokines are unique in their ability to bind receptors from both the CC and CXC classes of chemokine receptors. An unusual structural feature of IP-10 was identified that may provide the basis for the ability of IP-10 to bind both CXCR3 and CCR3. The surface of IP-10 that interacts with the N-terminus of CXCR3 was defined by monitoring changes in the NMR spectrum of IP-10 upon addition of a CXCR3 N-terminal peptide. These studies indicated that the interaction involves a hydrophobic cleft, formed by the N-loop and 40s-loop region of IP-10, similar to the interaction surface observed for other chemokines such as IL-8. An additional region of interaction was observed that consists of a hydrophobic cleft formed by the N-terminus of IP-10 and 30s-loop of IP-10.     

Solution structure and basis for functional activity of stromal cell-derived factor-1; dissociation of CXCR4 activation from binding and inhibition of HIV-1.

The three-dimensional structure of stromal cell-derived factor-1 (SDF-1) was determined by NMR spectroscopy. SDF-1 is a monomer with a disordered N-terminal region (residues 1-8), and differs from other chemokines in the packing of the hydrophobic core and surface charge distribution. Results with analogs showed that the N-terminal eight residues formed an important receptor binding site; however, only Lys-1 and Pro-2 were directly involved in receptor activation. Modification to Lys-1 and/or Pro-2 resulted in loss of activity, but generated potent SDF-1 antagonists. Residues 12-17 of the loop region, which we term the RFFESH motif, unlike the N-terminal region, were well defined in the SDF-1 structure. The RFFESH formed a receptor binding site, which we propose to be an important initial docking site of SDF-1 with its receptor. The ability of the SDF-1 analogs to block HIV-1 entry via CXCR4, which is a HIV-1 coreceptor for the virus in addition to being the receptor for SDF-1, correlated with their affinity for CXCR4. Activation of the receptor is not required for HIV-1 inhibition.     

Reduction of hypoxic pulmonary vasoconstriction during trichloroethylene anesthesia.

A double-lumen tube was inserted into the trachea of dogs anesthetized with intravenous pentobarbital (30-40 mg/kg). Blood flow/unit lung volume in each lung was measured with 133Xe. Both lungs were initially ventilated with oxygen and measurements of pulmonary blood flow, CO2 output, cardiac output, and blood gases were made. When nitrogen was administered to one lung blood flow was diverted to the opposite lung. The diversion of flow was reduced by the inhalation of 1% trichloroethylene but returned after withdrawal of the anesthetic. There were no significant changes in cardiac output. Changes in CO2 output and arterial Po2 were compatible with the xenon results. It is concluded that trichloroethylene may increase arterial hypoxemia by reducing vasoconstriction in hypoxic areas of lung.     

Mapping of the Interaction Site between Sortilin and the p75 Neurotrophin Receptor Reveals a Regulatory Role for the Sortilin Intracellular Domain in p75 Neurotrophin Receptor Shedding and Apoptosis

Neurotrophins comprise a group of neuronal growth factors that are essential for the development and maintenance of the nervous system. However, the immature pro-neurotrophins promote apoptosis by engaging in a complex with sortilin and the p75 neurotrophin receptor (p75^NTR). To identify the interaction site between sortilin and p75^NTR, we analyzed binding between chimeric receptor constructs and truncated p75^NTR variants by co-immunoprecipitation experiments, surface plasmon resonance analysis, and FRET. We found that complex formation between sortilin and p75^NTR relies on contact points in the extracellular domains of the receptors. We also determined that the interaction critically depends on an extracellular juxtamembrane 23-amino acid sequence of p75^NTR. Functional studies further revealed an important regulatory function of the sortilin intracellular domain in p75^NTR-regulated intramembrane proteolysis and apoptosis. Thus, although the intracellular domain of sortilin does not contribute to p75^NTR binding, it does regulate the rates of p75^NTR cleavage, which is required to mediate pro-neurotrophin-stimulated cell death.     

Enhancing the activity of a beta-helical antifreeze protein by the engineered addition of coils

The effectiveness of natural antifreeze proteins in inhibiting the growth of a seed ice crystal seems to vary with protein size. Here we have made use of the extreme regularity of the beta-helical antifreeze protein from the beetle Tenebrio molitor to explore systematically the relationship between antifreeze activity and the area of the ice-binding site. Each of the 12-amino acid, disulfide-bonded central coils of the beta-helix contains a Thr-Xaa-Thr ice-binding motif. By adding coils to, and deleting coils from, the seven-coil parent antifreeze protein, we have made a series of constructs with 6-11 coils. Misfolded forms of these antifreezes were removed by ice affinity purification to accurately compare the specific activity of each construct. There was a 10-100-fold gain in activity upon going from six to nine coils, depending on the concentration that was compared. Activity was maximal for the nine-coil construct, which gave a freezing point depression of 6.5 C degrees at 0.7 mg/mL, but actually decreased for the 10- and 11-coil constructs. This small loss in activity might result from the accumulation of a slight mismatch between the spacing of the ice-binding threonine residues and the O atoms of the ice lattice.     

Brain serotonin determines maternal behavior and offspring survival

Maternal care is an indispensable component of offspring survival and development in all mammals and necessary for reproductive success. Although brain areas regulating maternal behaviors are innervated by serotonergic afferents, very little is known about the role of this neurotransmitter in these behaviors. To evaluate the contribution of serotonin to maternal care, we used mice with a null mutation in the gene for tryptophan hydroxylase‐2 (TPH2), which results in a genetic depletion of brain serotonin, and tested them in a wide range of maternal behavior paradigms. We found that litters born to and reared by TPH2^?/? mothers showed decreased survival, lower weaning weights and increased cannibalization. In addition, TPH2^?/? mothers performed poorly in pup retrieval, huddling, nest construction and high‐arched back nursing. Aggression in TPH2^?/? dams was not triggered by lactation and was steadily high. Survival and weaning weight deficits of TPH2^?/? pups were rescued by cross‐fostering and in litters of mixed genotype (TPH2^?/? and TPH2^?/+). However, the maternal behaviors of TPH2^?/? dams did not improve when rearing either TPH2^+/+ pups or mixed‐genotype litters. In addition, TPH2^?/? pups significantly worsened the behavior of TPH2^+/+ dams with respect to cannibalism, weaning weight and latency to attack. Olfactory and auditory functions of TPH2^?/? females or anxiety‐like behaviors did not account for these maternal alterations as they were equal to their TPH2^+/+ counterparts. These findings illustrate a profound influence of brain serotonin on virtually all elements of maternal behavior and establish that TPH2^?/? pups can engender maladaptive mothering in dams of both genotypes.