Sequencing complete mitochondrial and plastid genomes

Organelle genomics has become an increasingly important research field, with applications in molecular modeling, phylogeny, taxonomy, population genetics and biodiversity. Typically, research projects involve the determination and comparative analysis of complete mitochondrial and plastid genome sequences, either from closely related species or from a taxonomically broad range of organisms. Here, we describe two alternative organelle genome sequencing protocols. The "random genome sequencing" protocol is suited for the large majority of organelle genomes irrespective of their size. It involves DNA fragmentation by shearing (nebulization) and blunt-end cloning of the resulting fragments into pUC or BlueScript-type vectors. This protocol excels in randomness of clone libraries as well as in time and cost-effectiveness. The "long-PCR-based genome sequencing" protocol is specifically adapted for DNAs of low purity and quantity, and is particularly effective for small organelle genomes. Library construction by either protocol can be completed within 1 week.     

The specificity of SNARE pairing in biological membranes is mediated by both proof-reading and spatial segregation

Soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins mediate organelle fusion in the secretory pathway. Different fusion steps are catalyzed by specific sets of SNARE proteins. Here we have used the SNAREs mediating the fusion of early endosomes and exocytosis, respectively, to investigate how pairing specificity is achieved. Although both sets of SNAREs promiscuously assemble in vitro, there is no functional crosstalk. We now show that they not only colocalize to overlapping microdomains in the membrane of early endosomes of neuroendocrine cells, but also form cis-complexes promiscuously, with the proportion of the different complexes being primarily dependent on mass action. Addition of soluble SNARE molecules onto native membranes revealed preference for cognate SNAREs. Furthermore, we found that SNAREs are laterally segregated at endosome contact sites, with the exocytotic synaptobrevin being depleted. We conclude that specificity in endosome fusion is mediated by the following two synergistically operating mechanisms: (i) preference for the cognate SNARE in 'trans' interactions and (ii) lateral segregation of SNAREs, leading to relative enrichment of the cognate ones at the prospective fusion sites.     

CRIM1 complexes with ß-catenin and cadherins, stabilizes cell-cell junctions and is critical for neural morphogenesis

In multicellular organisms, morphogenesis is a highly coordinated process that requires dynamically regulated adhesion between cells. An excellent example of cellular morphogenesis is the formation of the neural tube from the flattened epithelium of the neural plate. Cysteine-rich motor neuron protein 1 (CRIM1) is a single-pass (type 1) transmembrane protein that is expressed in neural structures beginning at the neural plate stage. In the frog Xenopus laevis, loss of function studies using CRIM1 antisense morpholino oligonucleotides resulted in a failure of neural development. The CRIM1 knockdown phenotype was, in some cases, mild and resulted in perturbed neural fold morphogenesis. In severely affected embryos there was a dramatic failure of cell adhesion in the neural plate and complete absence of neural structures subsequently. Investigation of the mechanism of CRIM1 function revealed that it can form complexes with ?-catenin and cadherins, albeit indirectly, via the cytosolic domain. Consistent with this, CRIM1 knockdown resulted in diminished levels of cadherins and ?-catenin in junctional complexes in the neural plate. We conclude that CRIM1 is critical for cell-cell adhesion during neural development because it is required for the function of cadherin-dependent junctions.     

Trendtests with adaptive scoring

The concept of adaptive two‐stage designs is applied to the problem of testing the equality of several normal means against an ordered (monotone) alternative. The likelihood‐ratio‐test proposed by Bartholomew is known to have favorable power properties when testing against a monotonic trend. Tests based on contrasts provide a flexible way to incorporate available information regarding the pattern of the unknown true means through appropriate specification of the scores. The basic idea of the presented concept is the combination of Bartholomew 's test (first stage) with an “adaptive score test” (second stage) which utilizes the information resulting from isotonic regression estimation at the first stage. In a Monte Carlo simulation study the adaptive scoring procedure is compared to the non‐adaptive two‐stage procedure using the Bartholomew test at both stages. We found that adaptive scoring may improve the power of the two stage design, in particular if the sample size at the first stage is considerably larger than at the second stage.     

Are human beings part of the rest of nature?

Unified explanations seek to situate the traits of human beings in a causal framework that also explains the trait values found in nonhuman species. Disunified explanations claim that the traits of human beings are due to causal processes not at work in the rest of nature. This paper outlines a methodology for testing hypotheses of these two types. Implications are drawn concerning evolutionary psychology, adaptationism, and anti-adaptationism. This revised version was published online in July 2006 with corrections to the Cover Date.     

Increased luminal pH in the epididymis of infertile c-ros knockout mice and the expression of sodium-hydrogen exchangers and vacuolar proton pump H+-ATPase

Transgenic mice targeted for the c-ros gene, which are fertile when heterozygous (HET), but infertile when homozygous (knockout, KO) and associated with failure in pubertal differentiation of the epididymal initial segment, provide a model for studying the role of the epididymal luminal environment in sperm development. Luminal fluid from the cauda epididymidis was measured by both ion-selective microelectrodes and pH strips to be 0.3 pH units higher in the KO than HET. Of the genes responsible for luminal acidification, expression of mRNA of vacuolar H(+)-ATPase was found in all epididymal regions, but with no difference between KO and HET. Immunohistochemistry showed its presence in epithelial apical cells and clear cells. The Na(+)-hydrogen exchanger NHE2 was expressed at mRNA and protein levels in the caput but only marginally detectable if at all in the distal epididymis. This was compensated for by NHE3 which was expressed strongest in the cauda region, in agreement with immunohistochemical staining. Quantification of Western blot data revealed slight, but significant, decreases of NHE2 in the caput and of NHE3 in the cauda in the KO mice. The increase in luminal fluid pH in the KO mice could also be contributed to by other epithelial regulating factors including the Na(+)-dependent glutamate transporter EAAC1 formerly reported to be down regulated in the KO.     

Action of Pasteurella multocida toxin depends on the helical domain of Galphaq

Pasteurella multocida produces a 146-kDa protein toxin (PMT), which activates multiple cellular signal transduction pathways, resulting in the activation of phospholipase Cbeta, RhoA, Jun kinase, and extracellular signal-regulated kinase. Using Galpha(q)/Galpha(11) -deficient cells, it was shown that the PMT-induced pleiotropic effects are mediated by Galpha(q) but not by the highly related Galpha(11) protein (Zywietz, A., Gohla, A., Schmelz, M., Schultz, G., and Offermanns, S. (2001) J. Biol. Chem. 276, 3840-3845). Here we studied the molecular basis of the unique specificity of PMT to distinguish between Galpha(q) and/or Galpha(11). Infection of Galpha(q) -deficient cells with retrovirus-encoding Galpha(q) caused reconstitution of PMT-induced activation of phospholipase Cbeta, whereas Galpha(11) -encoding virus did not reconstitute PMT activity. Chimeras between Galpha(q) and/or Galpha(11) revealed that a peptide region of Galpha(q), covering amino acid residues 105-113, is essential for the action of PMT to activate phospholipase Cbeta. Exchange of glutamine 105 or asparagine 109 of Galpha(11), which are located in the all-helical domain of the Galpha subunit, with the equally positioned histidines of Galpha(q), renders Galpha(11) capable of transmission PMT-induced phospholipase Cbeta activation. The data indicate that the all-helical domain of Galpha(q) is essential for the action of PMT and suggest an essential functional role of this domain in signal transduction via G(q) proteins.     

Ultrasonic absorption studies of poly-benzyl-L-aspartate in mixed solvents, in relation to the helix-cell transition

Ultrasonic absorption measurements were carried out on solutions of polybenzyl-L -aspartate (PBLA) in chloroform–dichloroacetic acid (DCA) and in 1,2-dichloroethane (DCE)–DCA, in the range 3.9–155 MHZ . The helix–coil transition of PBLA produces an increase of absorption which is larger in CHCl₃–DCA than in DCE–DCA solutions. The influence of the solvent on the excess ultrasonic absorption suggests that solvation processes may be involved in these changes of absorption. The plots of the absorption vs. the volume fraction of DCA do not show any absorption maximum. This indicates that the ultrasonic absorption is not sensitive to the helix–coil equilibrium of PBLA in the frequency range investigated. A maximum value of 10⁹ S ^?1 has been obtained for the rate constant of growth of a helix region.     

唐菖蒲球茎芽的离体培养及快速繁殖

将带1-2个芽眼的唐菖蒲球茎切块接种到附加1.0mg/LBA的MS基本培养基上可诱导休眠芽萌动、无菌芽转移至附加3.0mg/LBA的培养基上可分化产生丛生芽。丛生芽的继代增殖宜采用附加1.5mg/LBA的培养基生根培养,以MS+NAA 0.1-0.5mg/L或MS+IBA 1.5mg/L效果最佳。试管苗移栽存活率可达50%左右。