Unrelated to phenylalanine: Feeding studies provide new insight into salicylic acid biosynthesis

<正>How plants produce the important defense hormone salicylic acid(SA) has been studied for almost 50 years. The current understanding is that in land plants, SA is biosynthesized from chorismate through the isochorismate(IC)     

Channelrhodopsins provide a breakthrough insight into strategies for curing blindness

Photoreceptor cells are the only retinal neurons that can absorb photons. Their degeneration due to some diseases or injuries leads to blindness. Retinal prostheses electrically stimulating surviving retinal cells and evoking a pseudo light sensation have been investigated over the past decade for restoring vision. Currently, a gene therapy approach is under development. Channelrhodopsin-2 derived from the green alga Chlamydomonas reinhardtii, is a microbial-type rhodopsin. Its specific characteristic is that it functions as a light-driven cation-selective channel. It has been reported that the channelrhodopsin-2 transforms inner light-insensitive retinal neurons to light-sensitive neurons. Herein, we introduce new strategies for restoring vision by using channelrhodopsins and discuss the properties of adeno-associated virus vectors widely used in gene therapy.     

FRET studies with factor X mutants provide insight into the topography of the membrane-bound factor X/Xa

FRET (fluorescence resonance energy transfer) studies have shown that the vitamin K-dependent coagulation proteases bind to membrane surfaces perpendicularly, positioning their active sites above the membrane surfaces. To investigate whether EGF (epidermal growth factor) domains of these proteases play a spacer function in this model of the membrane interaction, we used FRET to measure the distance between the donor fluorescein dye in the active sites of Fl-FPR (fluorescein-D-Phe-Pro-Arg-chloromethane)-inhibited fXa (activated Factor Xa) and its N-terminal EGF deletion mutant (fXa-desEGF1), and the acceptor OR (octadecylrhodamine) dye incorporated into phospholipid vesicles composed of 80% phosphatidylcholine and 20% phosphatidylserine. The average distance of closest approach (L) between fluorescein in the active site and OR at the vesicle surface was determined to be 56+/-1 A (1 A=0.1 nm) and 63+/-1 A for fXa-desEGF1 compared with 72+/-2 A and 75+/-1 A for fXa, in the absence and presence of fVa (activated Factor V) respectively, assuming kappa2=2/3. In comparison, an L value of 95+/-6 A was obtained for a S195C mutant of fXa in the absence of fVa in which fluorescein was attached directly to Cys(195) of fXa. These results suggest that (i) EGF1 plays a spacer function in holding the active site of fXa above the membrane surface, (ii) the average distance between fluorescein attached to Fl-FPR in the active site of fXa and OR at the vesicle surface may not reflect the actual distance of the active-site residue relative to the membrane surface, and (iii) fVa alters the orientation and/or the height of residue 195 above the membrane surface.     

Pressure dissociation studies provide insight into oligomerization competence of temperature-sensitive folding mutants of P22 tailspike

Several temperature-sensitive folding (tsf) mutants of the tailspike protein from bacteriophage P22 have been found to fold with lower efficiency than the wild-type sequence, even at lowered temperatures. Previous refolding studies initiated from the unfolded monomer have indicated that the tsf mutations decrease the rate of structured monomer formation. We demonstrate that pressure treatment of the tailspike aggregates provides a useful tool to explore the effects of tsf mutants on the assembly pathway of the P22 tailspike trimer. The effects of pressure on two different tsf mutants, G244R and E196K, were explored. Pressure treatment of both G244R and E196K aggregates produced a folded trimer. E196K forms almost no native trimer in in vitro refolding experiments, yet it forms a trimer following pressure in a manner similar to the native tailspike protein. In contrast, trimer formation from pressure-treated G244R aggregates was not rapid, despite the presence of a G244R dimer after pressure treatment. The center-of-mass shifts of the fluorescence spectra under pressure are nearly identical for both tsf aggregates, indicating that pressure generates similar intermediates. Taken together, these results suggest that E196K has a primary defect in formation of the beta-helix during monomer collapse, while G244R is primarily an assembly defect.     

Circular dichroism studies of extracellular domains of human nicotinic acetylcholine receptors provide an insight into their structure

The extracellular domains (ECDs) of human nicotinic acetylcholine receptors (nAChRs) are of major pharmacological interest as drug targets in the autoimmune disease myasthenia gravis and in various neurological disorders. We have previously expressed and purified the human muscle alpha1-, beta1-, gamma- and epsilon-nAChR-ECDs, as well as the wild type and a mutant of neuronal alpha7-ECD, in yeast Pichia pastoris. The far-UV circular dichroism (CD) studies of these ECDs, presented here, revealed a major prevalence of beta-sheet ( approximately 40%) and a small proportion of alpha-helical ( approximately 5%) structure for all ECDs, in good agreement with the secondary structure composition of the Torpedo muscle-type nAChR-ECDs and in less, but considerable, agreement with that of the homologous invertebrate acetylcholine-binding proteins (AChBPs). The near-UV CD studies of these nAChR-ECDs indicated well-defined tertiary structures, as was previously suggested by biochemical and immunochemical studies. Furthermore, the binding of cholinergic ligands to the mutant of alpha7-ECD resulted in no changes in its secondary structure, but revealed significant local conformational changes. Our present studies probe the structure of human nAChR-ECDs for the first time and further suggest that our expressed proteins fold to a near-native conformation, thus being suitable for further structural studies.     

pH dependence studies provide insight into the structure and mechanism of thimet oligopeptidase (EC 3.4.24.15)

Thimet oligopeptidase (EC 3.4.24.15; TOP) is a Zn(II) endopeptidase implicated in physiological regulation of processes involving neuropeptides. The present study clarifies the active site structure and mechanism of catalysis of TOP. The enzyme exhibited a bell-shaped pH dependence of activity having an acidic limb due to a protonation event with a pK(a) of 5.7 and a basic limb with pK(a) of 8.8. The acidic limb can be attributed to protonation of a residue affecting k(cat) while the alkaline limb may be due to conformational change. Mutation of Tyr612 to Phe resulted in more than 400-fold decrease in activity. This result, supported by modeling studies, implicates Tyr612 in transition state stabilization analogous to the role of His231 of thermolysin.     

DNA barcode libraries provide insight into continental patterns of avian diversification

Background

The causes for the higher biodiversity in the Neotropics as compared to the Nearctic and the factors promoting species diversification in each region have been much debated. The refuge hypothesis posits that high tropical diversity reflects high speciation rates during the Pleistocene, but this conclusion has been challenged. The present study investigates this matter by examining continental patterns of avian diversification through the analysis of large-scale DNA barcode libraries.

Methodology and Principal Findings

Standardized COI datasets from the avifaunas of Argentina, the Nearctic, and the Palearctic were analyzed. Average genetic distances between closest congeners and sister species were higher in Argentina than in North America reflecting a much higher percentage of recently diverged species in the latter region. In the Palearctic genetic distances between closely related species appeared to be more similar to those of the southern Neotropics. Average intraspecific variation was similar in Argentina and North America, while the Palearctic fauna had a higher value due to a higher percentage of variable species. Geographic patterning of intraspecific structure was more complex in the southern Neotropics than in the Nearctic, while the Palearctic showed an intermediate level of complexity.

Conclusions and Significance

DNA barcodes can reveal continental patterns of diversification. Our analysis suggests that avian species are older in Argentina than in the Nearctic, supporting the idea that the greater diversity of the Neotropical avifauna is not caused by higher recent speciation rates. Species in the Palearctic also appear to be older than those in the Nearctic. These results, combined with the patterns of geographic structuring found in each region, suggest a major impact of Pleistocene glaciations in the Nearctic, a lesser effect in the Palearctic and a mild effect in the southern Neotropics.     

Strandings provide insight into social group structure of Atlantic white-sided dolphins

Atlantic white-sided dolphins (Lagenorhynchus acutus) are highly social odontocetes with a poorly understood tendency to mass strand. With limited capacity to study social ecology in the open ocean, mass strandings provide an opportunity to improve our understanding of group structure. Our study of 32 mass stranding events that occurred on Cape Cod, Massachusetts, between 1999 and 2009 identifies aspects of social ecology that vary across the year. A greater number of mass stranding events occurred outside of the breeding season and there was evidence of age-structuring during the breeding season. We find generally low average intragroup pairwise relatedness assessed across eight microsatellite loci in a subset of 16 mass stranding events. Mass stranded groups do not show higher than expected relatedness when compared to a baseline estimate derived from single-stranded individuals. Overall, our integration of genetic estimates of relatedness with data on sex and maturity-class from stranded specimens suggests that Atlantic white-sided dolphins fall near the more fluid end of the continuum from short-term, highly fluid social associations to long-term, stable groups represented among the odontocetes. Despite their tendency to mass strand, stable, kin-based associations are not a defining feature of social group structure in this species.     

Xenopus tropicalis egg extracts provide insight into scaling of the mitotic spindle

The African clawed frog Xenopus laevis has been instrumental to investigations of both development and cell biology, but the utility of this model organism for genetic and proteomic studies is limited by its long generation time and unsequenced pseudotetraploid genome. Xenopus tropicalis, which is a small, faster-breeding relative of X. laevis, has recently been adopted for research in developmental genetics and functional genomics, and has been chosen for genome sequencing. We show that X. tropicalis egg extracts reconstitute the fundamental cell cycle events of nuclear formation and bipolar spindle assembly around exogenously added sperm nuclei. Interestingly, X. tropicalis spindles were approximately 30% shorter than X. laevis spindles, and mixing experiments revealed a dynamic, dose-dependent regulation of spindle size by cytoplasmic factors. Measurements of microtubule dynamics revealed that microtubules polymerized slower in X. tropicalis extracts compared to X. laevis, but that this difference is unlikely to account for differences in spindle size. Thus, in addition to expanding the range of developmental and cell biological experiments, the use of X. tropicalis provides novel insight into the complex mechanisms that govern spindle morphogenesis.     

Agonists for 13 trace amine-associated receptors provide insight into the molecular basis of odor selectivity

Trace amine-associated receptors (TAARs) are vertebrate olfactory receptors. However, ligand recognition properties of TAARs remain poorly understood, as most are "orphan receptors" without known agonists. Here, we identify the first ligands for many rodent TAARs and classify these receptors into two subfamilies based on the phylogeny and binding preference for primary or tertiary amines. Some mouse and rat orthologs have similar response profiles, although independent Taar7 gene expansions led to highly related receptors with altered ligand specificities. Using chimeric TAAR7 receptors, we identified an odor contact site in transmembrane helix III that functions as a selectivity filter. Homology models based on the β(2) adrenergic receptor structure indicate spatial proximity of this site to the ligand. Gain-of-function mutations at this site created olfactory receptors with radically altered odor recognition properties. These studies provide new TAAR ligands, valuable tools for studying receptor function, and general insights into the molecular pharmacology of G protein-coupled receptors.     

The collagens of hydra provide insight into the evolution of metazoan extracellular matrices

A collagen-based extracellular matrix is one defining feature of all Metazoa. The thick sheet-like extracellular matrix (mesoglia) of the diploblast, hydra, has characteristics of both a basement membrane and an interstitial matrix. Several genes associated with mesoglea have been cloned including a basement membrane and fibrillar collagen and an A and B chain of laminin. Here we report the characterization of a further three fibrillar collagen genes (Hcol2, Hcol3, and Hcol5) and the partial sequence of a collagen gene with a unique structural organization consisting of multiple von Willebrand factor A domains interspersed with interrupted collagenous triple helices (Hcol6) from Hydra vulgaris. Hcol2 and -5 have major collagenous domains of classical length ( approximately 1020 amino acid residues), whereas the equivalent domain in Hcol3 is shorter (969 residues). The N-propeptide of Hcol2 contains a whey acid protein four-cysteine repeat (WAP) domain, and the equivalent domain of Hcol3 contains two WAP and two von Willebrand factor A domains. Phylogenetic analyses reveal that the hydra fibrillar collagen genes form a distinct clade that appears related to the protostome/deuterostome A clade of fibrillar collagens. Data base searches reveal Hcol2, -5, and -6 are highly conserved in Hydra magnipapillata, which also provided preliminary evidence for the expression of a B-clade fibrillar collagen. All four of the H. vulgaris collagens are expressed specifically by the ectoderm. The expression pattern for Hcol2 is similar to that previously reported for Hcol1 (Deutzmann, R., Fowler, S., Zhang, X., Boone, K., Dexter, S., Boot-Handford, R. P., Rachel, R., and Sarras, M. P., Jr. (2000) Development 127, 4669-4680) but distinct from the pattern shared by Hcol3 and Hcol5. The characterization of multiple collagen genes in relatively simple diploblastic organisms provides new insights into the molecular evolution of collagens and the origins of the collagen-based extracellular matrix found throughout the multicellular animal kingdom.     

Multiple conformations of the FliG C-terminal domain provide insight into flagellar motor switching

Bacterial flagellar switching between counterclockwise and clockwise directions is mediated by the coupling of the chemotactic system and the motor switch complex. The conformational changes of FliG are closely associated with this switching mechanism. We present two crystal structures of FliG(MC) from Helicobacter pylori, each showing distinct domain orientations from previously solved structures. A 180° rotation of the charged ridge-containing C-terminal subdomain FliG(Cα1-6) that is prompted by the rotational freedom of Met245 psi and Phe246 phi at the MFXF motif was revealed. Studies on the swarming and swimming behavior of Escherichia coli mutants further identified the importance of the ???MFXF??? motif and a highly conserved residue, Asn216, in motor switching. Additionally, multiple conformations of FliG(Cα1-6) were demonstrated by intramolecular cysteine crosslinking. The conformational flexibility of FliGc leads us to propose a model that accounts for the symmetrical torque generation process and for the dynamics of the motor.     

A case-cohort design for assessing covariate effects in longitudinal studies

The case-cohort design for longitudinal data consists of a subcohort sampled at the beginning of the study that is followed repeatedly over time, and a case sample that is ascertained through the course of the study. Although some members in the subcohort may experience events over the study period, we refer to it as the "control-cohort." The case sample is a random sample of subjects not in the control-cohort, who have experienced at least one event during the study period. Different correlations among repeated observations on the same individual are accommodated by a two-level random-effects model. This design allows consistent estimation of all parameters estimable in a cohort design and is a cost-effective way to study the effects of covariates on repeated observations of relatively rare binary outcomes when exposure assessment is expensive. It is an extension of the case-cohort design (Prentice, 1986, Biometrika73, 1-11) and the bidirectional case-crossover design (Navidi, 1998, Biometrics54, 596-605). A simulation study compares the efficiency of the longitudinal case-cohort design to a full cohort analysis, and we find that in certain situations up to 90% efficiency can be obtained with half the sample size required for a full cohort analysis. A bootstrap method is presented that permits testing for intra-subject homogeneity in the presence of unidentifiable nuisance parameters in the two-level random-effects model. As an illustration we apply the design to data from an ongoing study of childhood asthma.     

Antisense oligodeoxynucleotides provide insight into mechanism of translation initiation of two Sendai virus mRNAs

Translation of Sendai virus nucleocapsid protein (NP) and phosphoprotein (P/C) mRNAs in rabbit reticulocyte lysates in the presence of antisense oligodeoxynucleotides (15-20-mers) showed that oligonucleotides having complementarity within the 5' noncoding region of the mRNAs blocked translation, oligonucleotides having complementarity within 20 nucleotides upstream from the initiator codon blocked translation only partially, and oligonucleotides complementary to the coding region of mRNA had no effect on translation. The results suggest the possibility that the 80 S initiation complex may form about 20 bases upstream from the initiator codon. Alternatively, the 40 S preinitiation complex may recognize an initiator codon at least 20 nucleotides upstream from the codon, activating a helix-destabilizing process.     

Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time

Nested association mapping (NAM) offers power to dissect complex, quantitative traits. This study made use of a recently developed sorghum backcross (BC)-NAM population to dissect the genetic architecture of flowering time in sorghum; to compare the QTL identified with other genomic regions identified in previous sorghum and maize flowering time studies and to highlight the implications of our findings for plant breeding. A subset of the sorghum BC-NAM population consisting of over 1,300 individuals from 24 families was evaluated for flowering time across multiple environments. Two QTL analysis methodologies were used to identify 40 QTLs with predominately small, additive effects on flowering time; 24 of these co-located with previously identified QTL for flowering time in sorghum and 16 were novel in sorghum. Significant synteny was also detected with the QTL for flowering time detected in a comparable NAM resource recently developed for maize (Zea mays) by Buckler et al. (Science 325:714–718, 2009). The use of the sorghum BC-NAM population allowed us to catalogue allelic variants at a maximal number of QTL and understand their contribution to the flowering time phenotype and distribution across diverse germplasm. The successful demonstration of the power of the sorghum BC-NAM population is exemplified not only by correspondence of QTL previously identified in sorghum, but also by correspondence of QTL in different taxa, specifically maize in this case. The unification across taxa of the candidate genes influencing complex traits, such as flowering time can further facilitate the detailed dissection of the genetic control and causal genes.     

Pitx genes in Tunicates provide new molecular insight into the evolutionary origin of pituitary

We have initiated a project aimed at documenting molecular and cellular changes underlying the emergence of the hypothalamo-hypophyseal axis in Chordates. Considering the phylogenetic position of Tunicates and the 'pan-hypophyseal' expression pattern of Pitx genes in Vertebrate pituitary, we searched for a Pitx-related homeobox gene in the ascidian Ciona intestinalis, and identified Ci-Pitx (ona intestinalis uitary homeobo gene). We also isolated Cs-Pitx and Bs-Pitx, the Ci-Pitx respective counterparts of Ciona savignyi and Botryllus schlosseri, two other Tunicate species. Ci-Pitx mRNA encodes a putative protein exhibiting the diagnostic K50-Paired-class homeodomain and a conserved C-terminal Aristaless domain. Embryonic expression pattern of Ci-Pitx revealed a conserved expression domain in the anterior neural ridge and subsequently in the pharyngeal primordium, defined in Vertebrates as the stomodeal ectomere, which encompasses the presumptive pituitary territory. This shows that expression at early steps of pituitary development is a feature of Pitx-related genes that was already present in the last common ancestor of Chordates.     

Three high-resolution crystal structures of cadmium-substituted carboxypeptidase A provide insight into the enzymatic function

Three high-resolution crystal structures of Cd(II)-substituted carboxypeptidase A (CPA) have been determined by X-ray diffraction from crystals prepared in three different buffer systems to assess the effect of pH and ionic strength on the Cd(II) coordination geometry. All crystallize in the space group P2(1) with identical cell dimensions. Cd-CPA(7.5): Cd(II)-substituted CPA prepared at pH 7.5 with [Cl(-)]=2 mM determined to 1.70 A resolution ( R=17.4% and R(free)=19.8%); Cd-CPA(5.5): Cd(II)-substituted CPA prepared at pH 5.5 with [Cl(-)]=2 mM to 2.00 A resolution ( R=16.1% and R(free)=18.6%); Cd-CPA(7.5)-Cl: Cd(II)-substituted CPA prepared at pH 7.5 with [Cl(-)]=250 mM to 1.76 A resolution ( R=16.7% and R(free)=17.8%). No noticeable structural changes were observed between the three structures. Two water molecules coordinate to Cd(II), in contrast to the single water molecule coordinating to Zn(II) in the Zn-CPA structure. No binding sites for anions could be identified, even in the structure with a high concentration of chloride ions. It is suggested that the anion inhibition is due to weak outer-sphere association of Cl(-) ions at several binding sites, shielding the strong positive charge distribution at the surface of the protein near the active site. Based on structural data and a sequence alignment of 18 non-redundant carboxypeptidases, a more elaborate version of the earlier reaction model is proposed that also addresses the transport of water to and from the active site. Conserved residues whose function was not addressed previously delineate the proposed pathways used in the transport of water during catalysis.     

Osteoarthritis subpopulations and implications for clinical trial design

Treatment guidelines for osteoarthritis have stressed the need for research on clinical predictors of response to different treatments. However, identifying such clinical predictors of response is less easy than it seems, and there is not a given classification of osteoarthritis subpopulations. This review article highlights the key methodical issues when analyzing and designing clinical studies to detect important subgroups with respect to treatment effect. In addition, we discuss the main osteoarthritis subpopulations and give examples of how specific treatment effects in these subpopulations have been assessed.