Petrosal bones of metatherian mammals from the Late Palaeocene of Itaboraí (Brazil), and a cladistic analysis of petrosal features in metatherians

Metatherian petrosal bones were recovered from the early Late Palaeocene Itaboraí, Brazil, and are formally described. A cladistic analysis of the distribution of 56 petrosal and basicranial characters among extant and fossil metatherians was conducted, resulting in seven parsimonious trees. Relationships among metatherian ingroup taxa are congruent with current understanding of metatherian phylogeny. Metatheria is diagnosed by eight petrosal synapomorphies: stapedial artery absent in adults; reduced, intramural prootic canal; extrabullar internal carotid artery; inferior petrosal sinus between petrosal, basisphenoid, and basioccipital; cava supracochleare and epiptericum completely separated; reduction of the lateral flange; reduction of the anterior lamina; separation of the jugular foramen from the opening for the inferior petrosal sinus. The Palaeocene taxa Mayulestes , Pucadelphy s, and Andinodelphys from Tiupampa, and Petrosal Type II from Itaboraí are the sister groups of all other South American and Australian metatherians. This analysis confirms previous results showing the South American 'monito del monte' Dromiciops nested within the Australasian radiation. Within this australidelphian clade, Dromiciops is closely related to the dasyurids. The South American Caenolestes appears more closely related to the Australidelphia than to the South American didelphids. The Petrosal Types I, III, IV and V from Itaboraí are the stem taxa of the clade Australidelphia plus Caenolestes . The significant synapomorphies supporting this relationship are: enlargement of the fossa subarcuata that produces a bulbous ventral aspect of the mastoid and loss of post-temporal canal.  Journal compilation © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 85–115. No claim to original French government works.     

Purification and properties of three new phospholipase A2 isoenzymes from Micropechis ikaheka venom

Three new phospholipase A2 (PLA2) isoenzymes were purified from the Micropechis ikaheka venom by successive chromatographies. The homogeneity of them was accessed by capillary zone electrophoresis and mass spectrometry. Their N-terminal sequences showed high identity (94, 88 and 90, respectively) with MiPLA-1, a group IB PLA2 also from this venom. In addition, strong immuno-cross-reaction with anti-MiPLA-1 serum was observed. These results suggested that three newly purified PLA2 belonged to group IB. Beside enzymatic activity, they induced various pharmacological effects, including myotoxic, anticoagulant effects and insulin secretion stimulating effects. Our results indicated that enzymatic activity is essential for their myotoxic and anticoagulant effects. On the other hand, no direct correlation between their insulin secretion stimulating effect and enzymatic activity was observed, suggesting that they may stimulate insulin secretion through a non-enzymatic mechanism.     

A mixture model for estimating the local false discovery rate in DNA microarray analysis

MOTIVATION: Statistical methods based on controlling the false discovery rate (FDR) or positive false discovery rate (pFDR) are now well established in identifying differentially expressed genes in DNA microarray. Several authors have recently raised the important issue that FDR or pFDR may give misleading inference when specific genes are of interest because they average the genes under consideration with genes that show stronger evidence for differential expression. The paper proposes a flexible and robust mixture model for estimating the local FDR which quantifies how plausible each specific gene expresses differentially. RESULTS: We develop a special mixture model tailored to multiple testing by requiring the P-value distribution for the differentially expressed genes to be stochastically smaller than the P-value distribution for the non-differentially expressed genes. A smoothing mechanism is built in. The proposed model gives robust estimation of local FDR for any reasonable underlying P-value distributions. It also provides a single framework for estimating the proportion of differentially expressed genes, pFDR, negative predictive values, sensitivity and specificity. A cervical cancer study shows that the local FDR gives more specific and relevant quantification of the evidence for differential expression that can be substantially different from pFDR. AVAILABILITY: An R function implementing the proposed model is available at http://www.geocities.com/jg_liao/software     

Identification of binding sites in the nicotinic acetylcholine receptor for [3H]azietomidate, a photoactivatable general anesthetic

To identify binding domains in a ligand-gated ion channel for etomidate, an intravenous general anesthetic, we photolabeled nicotinic acetylcholine receptor (nAChR)-rich membranes from Torpedo electric organ with a photoactivatable analog, [(3)H]azietomidate. Based upon the inhibition of binding of the noncompetitive antagonist [(3)H]phencyclidine, azietomidate and etomidate bind with 10-fold higher affinity to nAChRs in the desensitized state (IC(50) = 70 microm) than in the closed channel state. In addition, both drugs between 0.1 and 1 mm produced a concentration-dependent enhancement of [(3)H]ACh equilibrium binding affinity, but they inhibited binding at higher concentrations. UV irradiation resulted in preferential [(3)H]azietomidate photoincorporation into the nAChR alpha and delta subunits. Photolabeled amino acids in both subunits were identified in the ion channel domain and in the ACh binding sites by Edman degradation. Within the nAChR ion channel in the desensitized state, there was labeling of alphaGlu-262 and deltaGln-276 at the extracellular end and deltaSer-258 and deltaSer-262 toward the cytoplasmic end. Within the acetylcholine binding sites, [(3)H]azietomidate photolabeled alphaTyr-93, alphaTyr-190, and alphaTyr-198 in the site at the alpha-gamma interface and deltaAsp-59 (but not the homologous position, gammaGlu-57). Increasing [(3)H]azietomidate concentration from 1.8 to 150 microm increased the efficiency of incorporation into amino acids within the ion channel by 10-fold and in the ACh sites by 100-fold, consistent with higher affinity binding within the ion channel. The state dependence and subunit selectivity of [(3)H]azietomidate photolabeling are discussed in terms of the structures of the nAChR transmembrane and extracellular domains.     

Iterative ACORN as a high throughput tool in structural genomics

High throughput macromolecular structure determination is very essential in structural genomics as the available number of sequence information far exceeds the number of available 3D structures. ACORN, a freely available resource in the CCP4 suite of programs is a comprehensive and efficient program for phasing in the determination of protein structures, when atomic resolution data are available. ACORN with the automatic model-building program ARP/wARP and refinement program REFMAC is a suitable combination for the high throughput structural genomics. ACORN can also be run with secondary structural elements like helices and sheets as inputs with high resolution data. In situations, where ACORN phasing is not sufficient for building the protein model, the fragments (incomplete model/dummy atoms) can again be used as a starting input. Iterative ACORN is proved to work efficiently in the subsequent model building stages in congerin (PDB-ID: lis3) and catalase (PDB-ID: 1gwe) for which models are available.     

Phenotypic and genotypic characterization of B.t.LDC-391 strain that produce cytocidal proteins against human cancer cells

An indigenous Bacillus thuringiensis strain B.t.LDC-391 producing cytocidal proteins against human colon cancer cell line, HCT-116, was subjected to phenotypic and genotypic characterization to evaluate its relatedness to B.anthracis. The morphological features of this strain were meta-analyzed with data of other parasporin and insecticidal protein producing Bacillus thuringiensis strains. The conventional biochemical analysis and antibiotic sensitivity test proved it as an ampicillin resistant which is a salient feature, absent in B.anthracis Ames. PCR analysis showed the absence of cyt and parasporin related genes in the genome of B.t.LDC-391. But the strain was positive for cap gene. The sequencing and bio-informatic analysis of cap gene and 16S rDNA of B.t.LDC-391 placed it closer to B.thuringiensis and revealed significant divergence from that of any B.anthracis strain. However our strain lacked β- hemolysis on human erythrocytes which is a common feature of B.anthracis strains and parasporin producers.     

三种绿叶挥发性物质对云南切梢小蠹寄主定位行为的干扰作用

为了研究环境中非寄主阔叶植物释放出的绿叶挥发性物质（GLVs）对针叶树蛀干害虫云南切梢小蠹Tomicus yunnanesis的影响, 选取了(E)-2-己烯醛、 (E)-2-己烯醇和(Z)-3-己烯醇3种释放量较大的绿叶挥发性物质, 通过室内松梢取食试验测试了单组分及两两混合后对云南切梢小蠹寄主定位行为的干扰作用。结果表明： 源于阔叶植物的3种绿叶挥发性物质及其混合物能够不同程度干扰云南切梢小蠹的寄主定位行为。当虫放入广口瓶12 h后, 3个单组分绿叶挥发性物质处理组［A： (E)-2-己烯醛, P＜0.01; B： (E)-2-己烯醇, P＜0.01; C： (Z)-3-己烯醇, P＜0.01］及2个混合组分［D： (E)-2-己烯醛+(E)-2-己烯醇, P＜0.01）; E： (E)-2-己烯醛+(Z)-3-己烯醇, P＜0.01］中滞留在松梢外部的虫数与对照组相比都有显著性差异, 绿叶挥发性物质的存在显著降低了云南切梢小蠹侵害云南松松梢的概率。但是, 24 h后只有D组（P＜0.01）和E组（P＜0.01）滞留在松梢外部的虫数与对照组相比具有显著性差异, 在48 h后只有D组（P＜0.01）与对照相比仍具有显著性差异。本研究为利用非寄主植物的次生代谢产物防治云南切梢小蠹进行了有益的探索。