Conservation of key members in the course of the evolution of the insulin signaling pathway

Our understanding of the evolution of the insulin signaling pathway (ISP) is still incomplete. One intriguing unanswered question is the explanation of the emergence of the glucostatic role of insulin in mammals. To find out whether this is due to the development of new sets of signaling transduction elements in these organisms, or to the establishment of new interactions between pre-existing proteins, we rebuilt putative orthologous ISPs in 17 eukaryotic organisms. Then, we computed the conservation of orthologous ISPs at different levels, from sequence similarity of orthologous proteins to co-evolution of interacting domains. We found that the emergence of glucostatic role in mammals can neither be explained by the development of new sets of signaling elements, nor by the establishment of new interactions between pre-existing proteins. The comparison of orthologous IRS molecules indicates that only in mammals have they acquired their complete functionality as efficient recruiters of effector sub-pathways.     

Dimeric progestins from rhizomes of Ligusticum chuanxiong

Five dimeric phthalides were isolated from rhizomes of Ligusticum chuanxiong and their structures deduced based on spectral data. All compounds and their parent extracts were assessed for progesterone-like activity using a progesterone receptor driven reporter-gene bioassay. Among all the compounds, riligustilide, displayed weak progesterone-like activity (EC50 approximately 81 microM), whereas, (3Z')-(3a'R,6'R,3R,6R,7R)-3,8-dihydro-6.6',7.3a'-diligustilide (Mr: 382, EC50 approximately 90 nM), was found to be a potent and specific activator of the progesterone receptor. Levistolide A, although having a very similar plenary structure, was inactive indicating the importance of stereochemistry of chiral centers and flexibility of butylidene side chain for progestogenic activity. These bioactive phthalides and their parent extracts (EC50 approximately 8 microg/ml) may have utility for treatment of conditions requiring progesterone action.     

ProtIdent: a web server for identifying proteases and their types by fusing functional domain and sequential evolution information

Proteases are vitally important to life cycles and have become a main target in drug development. According to their action mechanisms, proteases are classified into six types: (1) aspartic, (2) cysteine, (3) glutamic, (4) metallo, (5) serine, and (6) threonine. Given the sequence of an uncharacterized protein, can we identify whether it is a protease or non-protease? If it is, what type does it belong to? To address these problems, a 2-layer predictor, called "ProtIdent", is developed by fusing the functional domain and sequential evolution information: the first layer is for identifying the query protein as protease or non-protease; if it is a protease, the process will automatically go to the second layer to further identify it among the six types. The overall success rates in both cases by rigorous cross-validation tests were higher than 92%. ProtIdent is freely accessible to the public as a web server at http://www.csbio.sjtu.edu.cn/bioinf/Protease.     

HLA class II allele frequencies in the Lebanese population

Aims

Being one of the most polymorphic genetic systems , the Human Leukocyte Antigen system is divided into class I (HLA-A, HLA-B and HLA-C) and class II (HLA-DP, -DQ and -DR). This study is the first and largest of its kind to describe the distribution of HLA-DQB1 and HLA-DRB1 alleles in Lebanon and the region.

Methods

Respectively, 560 and 563 Lebanese individuals referred for HLA typing and possible bone marrow/kidney donation were tested for HLA-DQB1 and HLA-DRB1 alleles using the polymerase chain reaction/sequence specific priming (PCR-SSP) method.

Results

Our data were compared to that of several populations with interesting common findings between the Lebanese, Jordanian, Bahraini, Saudi, Kuwaiti, Tunisian, Korean, Japanese, Thai, Irish, Bulgarian and Polish populations.

Conclusion

These data about the Lebanese population are going to aid future researchers to study the relation of HLA-DQB1 and HLA-DRB1 alleles with major and common diseases in the Lebanese population and will add to the available international literature associated with these loci. In addition it will serve as a reference for the future national bone marrow registry program in our country. We also reviewed the literature for the described association between HLA-DRB1 and -DQB1 loci and different disease entities.     

Proposal of Ensifer psoraleae sp. nov., Ensifer sesbaniae sp. nov., Ensifer morelense comb. nov. and Ensifer americanum comb. nov

In a survey of rhizobia associated with the native legumes in Yunnan Province, China, seven and nine strains isolated from the root nodules of Psoralea corylifolia, Sesbania cannabina and Medicago lupulina were respectively classified into the novel genomic species groups I and II in the genus Ensifer (former Sinorhizobium) based on the sequence analyses of the 16S rRNA gene. Analyses of concatenated housekeeping genes (atpD, recA and glnII) further revealed that they were distinct lineages in the genus, and group I was most similar to Ensifer terangae and Ensifer garamanticus (both with 94.2% similarity), while group II was most similar to Ensifer adhaerens (94.0%). These groups could be distinguished from closely related species by DNA–DNA relatedness, MALID-TOF MS, cellular fatty acid profiles and a series of phenotypic characters. Therefore, two novel species were proposed: Ensifer psoraleae sp. nov. (seven strains, type strain CCBAU 65732^T = LMG 26835^T = HAMBI 3286^T) and Ensifer sesbaniae sp. nov. (nine strains, type strain CCBAU 65729^T = LMG 26833^T = HAMBI 3287^T). They had a DNA G + C mol% (T_m) of 58.9 and 60.4, respectively. Both of the type strains formed effective nodules on common bean (Phaseolus vulgaris) and their hosts of origin. In addition, the previously described species Sinorhizobium morelense and Sinorhizobium americanum were renamed as Ensifer morelense comb. nov. and Ensifer americanum comb. nov. according to the accumulated data from different studies.     

Molecular insights into NF2/Merlin tumor suppressor function

The FERM domain protein Merlin, encoded by the NF2 tumor suppressor gene, regulates cell proliferation in response to adhesive signaling. The growth inhibitory function of Merlin is induced by intercellular adhesion and inactivated by joint integrin/receptor tyrosine kinase signaling. Merlin contributes to the formation of cell junctions in polarized tissues, activates anti-mitogenic signaling at tight-junctions, and inhibits oncogenic gene expression. Thus, inactivation of Merlin causes uncontrolled mitogenic signaling and tumorigenesis. Merlin’s predominant tumor suppressive functions are attributable to its control of oncogenic gene expression through regulation of Hippo signaling. Notably, Merlin translocates to the nucleus where it directly inhibits the CRL4^DCAF1 E3 ubiquitin ligase, thereby suppressing inhibition of the Lats kinases. A dichotomy in NF2 function has emerged whereby Merlin acts at the cell cortex to organize cell junctions and propagate anti-mitogenic signaling, whereas it inhibits oncogenic gene expression through the inhibition of CRL4^DCAF1 and activation of Hippo signaling. The biochemical events underlying Merlin’s normal function and tumor suppressive activity will be discussed in this Review, with emphasis on recent discoveries that have greatly influenced our understanding of Merlin biology.     

Indole alkoloids from Nauclea officinalis with weak antimalarial activity

Five indole alkaloids (naucleofficines A-E) were isolated from the stems (with bark) of Nauclea officinalis: (E)-2-(1-beta-d-glucopyranosyloxybut-2-en-2-yl)-3-(hydroxymethyl)-6,7-dihydro-indolo[2,3-a]quinolizin-4(12H)-one (1), (E)-1-propenyl-12-beta-d-glucopyranosyloxy-2,7,8-trihydro-indolo[2,3-a]pyran[3,4-g]quinolizin-4,5(13H)-dione (2), (E)-2-(1-hydroxybut-2-en-2-yl)-11-beta-d-glucopyranosyloxy-6,7-dihydro-indolo[2,3-a]quinolizin-4(12H)-one (3), (E)-1-propenyl-4-hydroxy-2,4a,7,8,13b,14,14a-hepthydro-(4alpha,4abeta,13balpha,14abeta)indolo[2,3-a]pyran[3,4-g]quinolizin-5(13H)-one (4) and 1-(1-hydroxyethyl)-10-hydroxy-7,8-dihydro-indolo[2,3-a]pirydine[3,4-g]quinolizin-5(13H)-one (10-hydroxyangustoline) (5), together with two known compounds, naucleidinal (6) and angustoline (7). All of the structures of the seven compounds above were elucidated by spectroscopic methods including use of 1D- and 2D-NMR spectroscopic analyses. Compounds 2 and 3 are rare examples of monoterpene indole alkaloids with a glucopyranosyloxy group attached to position C-12. In vitro activity screening of the above seven compounds showed weak to moderate inhibitory activity against Plasmodium falciparum.     

Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase

Cytochrome c oxidase (CcO) is the terminal enzyme of aerobic respiration. The energy released from the reduction of molecular oxygen to water is used to pump protons across the mitochondrial or bacterial membrane. The pump function introduces a mechanistic requirement of a valve that prevents protons from flowing backwards during the process. It was recently found that Glu-242, a key amino acid in transferring protons to be pumped across the membrane and to the site of oxygen reduction, fulfils the function of such a valve by preventing simultaneous contact to the pump site and to the proton-conducting D-channel (Kaila V.R.I. et al. Proc. Natl. Acad. Sci. USA 105, 2008). Here we have incorporated the valve model into the framework of the reaction mechanism. The function of the Glu valve is studied by exploring how the redox state of the surrounding metal centers, dielectric effects, and membrane potential, affects the energetics and leaks of this valve. Parallels are drawn between the dynamics of Glu-242 and the long-standing obscure difference between the metastable O_H and stable O states of the binuclear center. Our model provides a suggestion for why reduction of the former state is coupled to proton translocation while reduction of the latter is not.     

Two new 3D (3,8)-connected metal-organic frameworks based on zinc-triazole secondary building units and benzenetricarboxylate linkers

Two new zinc-triazole-carboxylate frameworks constructed from secondary building units (SBUs), [Zn₅(trz)₄(btc)₂(DMF)₂(H₂O)₂]·2H₂O·DMF (1) and [Zn₄(trz)₃(btc)₂(CH₃CN)(H₂O)]·5H₂O·(Bu₄N) (2), [Htrz = 1,2,4-triazole, H₃btc = 1,2,4-benzenetricarboxylate, Bu₄N = tetrabutylammonium], have been synthesized by solvothermal reactions and characterized by single-crystal X-ray diffraction analyses, X-ray power diffraction, elemental analyses, infrared spectra and thermogravimetric analyses. Both compounds 1 and 2 exhibit 3D (3,8)-connected tfz-d nets with {4³}₂{4⁶.6¹⁸.8⁴} topology symbol built from rod-shaped {[Zn₅(trz)₄]⁶⁺}_n SBUs (1) and {[Zn₄(trz)₃]⁵⁺}_n SBUs (2). In two compounds, rodlike units are connected by btc ligands via different modes. Additionally, solid state fluorescent emission spectra of two compounds show fluorescent properties at room temperature.     

Resolution of the EcoRII restriction endonuclease-DNA complex structure in solution using fluorescence spectroscopy

The X-ray structure for the type IIE EcoRII restriction endonuclease has been resolved [X.E. Zhou, Y. Wang, M. Reuter, M. Mucke, D.H. Kruger, E.J. Meehan and L. Chen. Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J. Mol. Biol. 335 (2004) 307-319.], but the structure of the R.EcoRII-DNA complex is still unknown. The aim of this article was to examine the structure of the pre-reactive R.EcoRII-DNA complex in solution by fluorescence spectroscopy. The structure for the R.EcoRII-DNA complex was resolved by determining the fluorescence resonance energy transfer (FRET) between two fluorescent dyes, covalently attached near the EcoRII recognition sites, that were located at opposite ends of a lengthy two-site DNA molecule. Analysis of the FRET data from the two-site DNA revealed a likely model for the arrangement of the two EcoRII recognition sites relative to each other in the R.EcoRII-DNA complex in the presence of Ca(2+) ions. According to this model, the R.EcoRII binds the two-site DNA and forms a DNA loop in which the EcoRII recognition sites are 20+/-10 A distant to each other and situated at an angle of 70+/-10 degrees.     

Insights into Lou Gehrig's disease from the structure and instability of the A4V mutant of human Cu,Zn superoxide dismutase

We have engineered enhanced DNA-binding function into the a1 homeodomain by making changes in a loop distant from the DNA-binding surface. Comparison of the free and bound a1 structures suggested a mechanism linking van der Waals stacking changes in this loop to the ordering of a final turn in the DNA-binding helix of a1. Inspection of the protein sequence revealed striking differences in amino acid identity at positions 24 and 25 compared to related homeodomain proteins. These positions lie in the loop connecting helix-1 and helix-2, which is involved in heterodimerization with the alpha 2 protein. A series of single and double amino acid substitutions (a1-Q24R, a1-S25Y, a1-S25F and a1-Q24R/S25Y) were engineered, expressed and purified for biochemical and biophysical study. Calorimetric measurements and HSQC NMR spectra confirm that the engineered variants are folded and are equally or more stable than the wild-type a1 homeodomain. NMR analysis of a1-Q24R/S25Y demonstrates that the DNA recognition helix (helix-3) is extended by at least one turn as a result of the changes in the loop connecting helix-1 and helix-2. As shown by EMSA, the engineered variants bind DNA with enhanced affinity (16-fold) in the absence of the alpha 2 cofactor and the variant alpha 2/a1 heterodimers bind cognate DNA with specificity and affinity reflective of the enhanced a1 binding affinity. Importantly, in vivo assays demonstrate that the a1-Q24R/S25Y protein binds with fivefold greater affinity than wild-type a1 and is able to partially suppress defects in repression by alpha 2 mutants. As a result of these studies, we show how subtle differences in residues at a surface distant from the functional site code for a conformational switch that allows the a1 homeodomain to become active in DNA binding in association with its cofactor alpha 2.     

Internal charge transfer in cytochrome c oxidase at a limited proton supply: Proton pumping ceases at high pH

Background

In the membrane-bound enzyme cytochrome c oxidase, electron transfer from cytochrome c to O₂ is linked to proton uptake from solution to form H₂O, resulting in a charge separation across the membrane. In addition, the reaction drives pumping of protons across the membrane.

Methods

In this study we have measured voltage changes as a function of pH during reaction of the four-electron reduced cytochrome c oxidase from Rhodobacter sphaeroides with O₂. These electrogenic events were measured across membranes containing purified enzyme reconstituted into lipid vesicles.

Results

The results show that the pH dependence of voltage changes (primarily associated with proton transfer) during O₂ reduction does not match that of the previously studied absorbance changes (primarily associated with electron transfer). Furthermore, the voltage changes decrease with increasing pH.

Conclusions

The data indicate that cytochrome c oxidase does not pump protons at high pH (10.5) (or protons are taken from the “wrong” side of the membrane) and that at this pH the net proton-uptake stoichiometry is ∼ 1/2 of that at pH 8. Furthermore, the results provide a basis for interpretation of results from studies of mutant forms of the enzyme.

General significance

These results provide new insights into the function of cytochrome c oxidase.     

Wing morphometrics as a possible tool for the diagnosis of the Ceratitis fasciventris,C. anonae,C. rosa complex (Diptera,Tephritidae)

Previous attempts to resolve the Ceratitis FAR complex (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa, Diptera, Tephritidae) showed contrasting results and revealed the occurrence of five microsatellite genotypic clusters (A, F1, F2, R1, R2). In this paper we explore the potential of wing morphometrics for the diagnosis of FAR morphospecies and genotypic clusters. We considered a set of 227 specimens previously morphologically identified and genotyped at 16 microsatellite loci. Seventeen wing landmarks and 6 wing band areas were used for morphometric analyses. Permutational multivariate analysis of variance detected significant differences both across morphospecies and genotypic clusters (for both males and females). Unconstrained and constrained ordinations did not properly resolve groups corresponding to morphospecies or genotypic clusters. However, posterior group membership probabilities (PGMPs) of the Discriminant Analysis of Principal Components (DAPC) allowed the consistent identification of a relevant proportion of specimens (but with performances differing across morphospecies and genotypic clusters). This study suggests that wing morphometrics and PGMPs might represent a possible tool for the diagnosis of species within the FAR complex. Here, we propose a tentative diagnostic method and provide a first reference library of morphometric measures that might be used for the identification of additional and unidentified FAR specimens.     

Limonoids from the seeds of a Godavari mangrove, Xylocarpus moluccensis

Ten limonoids, named godavarins A-J (1-7, 9-11), were isolated from seeds of an Indian mangrove (Xylocarpus moluccensis) collected in the mangrove wetlands of Godavari estuary, Andhra Pradesh. Eight known limonoids, viz. xyloccensins L (8), P (12), Q (13), mexicanolide (14), 6-deoxy-3-detigloyl-swietenine acetate (15), fissinolide (16), methyl 3β-acetoxy-1-oxomeliaca-8(30),14-dienoate (17), and methyl 3β-acetoxy-1-oxomeliaca-8(9),14-dienoate (18), were also obtained. The structures of these compounds were established on the basis of spectroscopic data or comparison with data in the literature (known compounds). The stereostructure of godavarin D was confirmed by means of single-crystal X-ray analysis. Godavarins A-C are the first mexicanolide derivatives with a C₇-C₂₈ ester-linked δ-lactone ring, while godavarins D-G are further additions to the small group of limonoids with a C₁-C₂₉ oxygen bridge. Godavarin H is a phragmalin with five acetoxy groups. Two limonoids, mexicanolide and fissinolide, were found to exhibit marked antifeedant activity against the third-instar larvae of Brontispa longissima (Gestro) at a concentration of 0.5 mg/mL. The most potent compound was mexicanolide. It also showed moderate insecticidal activity.     

Results of the global conservation assessment of the freshwater crabs (Brachyura,Pseudothelphusidae and Trichodactylidae): The Neotropical region,with an update on diversity

The freshwater crabs of the Neotropics comprise 311 species in two families (Pseudothelphusidae and Trichodactylidae) and one or both of these families are found in all of the countries in the Neotropical region (except for Chile and some of the Caribbean islands). Colombia (102 species, 81% endemic) and Mexico (67 species, 95% endemic) are the biodiversity hotspots of freshwater crab species richness and country-level endemism for this region. The results of the IUCN Red List conservation assessments show that 34% of pseudothelphusids and 10% of trichodactylids have an elevated risk of extinction, 29% of pseudothelphusids and 75% of trichodactylids are not at-risk (Least Concern), and although none are actually extinct, 56% of pseudothelphusids and 17% of trichodactylids are too poorly known to assess (Data Deficient). Colombia (14 species), Venezuela (7 species), Mexico (6 species), and Ecuador (5 species) are the countries with the highest number of threatened species of Neotropical freshwater crabs. The majority of threatened species are restricted-range semiterrestrial endemics living in habitats subjected to deforestation, alteration of drainage patterns, and pollution. This underlines the need to prioritize and develop conservation measures before species decline to levels from which they cannot recover. These results represent a baseline that can be used to design strategies to save threatened Neotropical species of freshwater crabs.     

An integrative approach to unravel the Ceratitis FAR (Diptera,Tephritidae) cryptic species complex: a review

This paper reviews all information gathered from different disciplines and studies to resolve the species status within the Ceratitis FAR (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa) complex, a group of polyphagous fruit fly pest species (Diptera, Tephritidae) from Africa. It includes information on larval and adult morphology, wing morphometrics, cuticular hydrocarbons, pheromones, microsatellites, developmental physiology and geographic distribution. The general consensus is that the FAR complex comprises Ceratitis anonae, two species within Ceratitis rosa (so-called R1 and R2) and two putatitve species under Ceratitis fasciventris. The information regarding the latter is, however, too limited to draw final conclusions on specific status. Evidence for this recognition is discussed with reference to publications providing further details.     

The origin and early evolution of metatherian mammals: the Cretaceous record

Metatherians, which comprise marsupials and their closest fossil relatives, were one of the most dominant clades of mammals during the Cretaceous and are the most diverse clade of living mammals after Placentalia. Our understanding of this group has increased greatly over the past 20 years, with the discovery of new specimens and the application of new analytical tools. Here we provide a review of the phylogenetic relationships of metatherians with respect to other mammals, discuss the taxonomic definition and diagnosis of Metatheria, outline the Cretaceous history of major metatherian clades, describe the paleobiology, biogeography, and macroevolution of Cretaceous metatherians, and provide a physical and climatic background of Cretaceous metatherian faunas. Metatherians are a clade of boreosphendian mammals that must have originated by the Late Jurassic, but the first unequivocal metatherian fossil is from the Early Cretaceous of Asia. Metatherians have the distinctive tightly interlocking occlusal molar pattern of tribosphenic mammals, but differ from Eutheria in their dental formula and tooth replacement pattern, which may be related to the metatherian reproductive process which includes an extended period of lactation followed by birth of extremely altricial young. Metatherians were widespread over Laurasia during the Cretaceous, with members present in Asia, Europe, and North America by the early Late Cretaceous. In particular, they were taxonomically and morphologically diverse and relatively abundant in the Late Cretaceous of western North America, where they have been used to examine patterns of biogeography, macroevolution, diversification, and extinction through the Late Cretaceous and across the Cretaceous-Paleogene (K-Pg) boundary. Metatherian diversification patterns suggest that they were not strongly affected by a Cretaceous Terrestrial Revolution, but they clearly underwent a severe extinction across the K-Pg boundary.     

Design of a potent, soluble glucokinase activator with increased pharmacokinetic half-life

The continued optimization of a series of glucokinase activators is described, including attempts to understand the interplay between molecular structure and the composite parameter of unbound clearance. These studies resulted in the discovery of a new scaffold for glucokinase activators and further exploration of this scaffold led to the identification of GKA60. GKA60 maintains an excellent balance of potency and physical properties whilst possessing a significantly different, but complimentary, pre-clinical pharmacokinetic profile compared with the previously disclosed compound GKA50.     

Heterogeneous catalytic reduction of anthropogenic pollutant, 4-nitrophenol by silver-bionanocomposite using Cylindrocladium floridanum

In the present investigation, the silver-bionanocomposite with fcc structured Ag-nanocrystals was synthesized using the fungus, Cylindrocladium floridanum through a novel, environmentally benign biological process. Silver-bionanocomposite was systematically characterized by UV-Vis spectroscopy, XRD, SEM, EDX, and TEM techniques. TEM analysis of mycelia confirmed the presence of silver nanoparticles (AgNPs) on the outer surface of the cell wall and inner of cytoplasmic membrane of the fungus, when cultured in aqueous solution of AgNO3 at 30 °C for a period of 7 days in static condition. Additionally, it was observed that bionanocomposite with AgNPs functions as an efficient heterogeneous catalyst in the degradation of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP), in the presence of reducing agent, sodium borohydride which was reflected by UV-Vis spectra of the catalytic reaction kinetics. This is the first report of the silver-bionanocomposite using fungus, Cy. floridanum, heterogeneously catalyzing the reduction of a toxic pollutant, 4-NP to 4-AP.     

Genotyping of celiac disease-related-risk haplotypes using a closed-tube polymerase chain reaction analysis of dried blood and saliva disk samples.

Expansion of molecular diagnostics more widely into clinical routines requires simplified methods allowing automation. We developed a homogeneous, multilabel polymerase chain reaction (PCR) method based on time-resolved fluorometry, and studied the use of dried disk samples in PCR. Celiac disease-related HLA-DQA1*05, HLA-DQB1*02, and HLA-DQB1*0302 genotyping was used to verify the method with blood and saliva samples dried on S&S 903 and IsoCode sample collection papers. Three sample preparation procedures, including manufacturer’s manual elution, an automated elution, and direct use of disk samples, were compared using dried disk samples. The three procedures gave successful amplification and correct genotyping results. Owing to the simplicity of the direct use of disk samples in PCR, this method was chosen for the subsequent homogeneous analysis of blood (n = 194) and saliva (n = 30) disk samples on S&S 903 paper. The results revealed that, in addition to DNA samples (n = 29), both blood and saliva disk samples were successfully amplified and genotyped using the homogeneous PCR assays for HLA-DQA1 and HLA-DQB1. The homogeneous PCR assays developed provide a useful tool to genotype celiac disease-related HLA-DQA1*05, HLA-DQB1*02, and HLA-DQB1*0302 alleles. Furthermore, the method provides a direct way to perform a closed-tube PCR analysis of dried blood and saliva disk samples enabling simple automation.