A protocol for rapid isolation of flanking regions from short known sequences

We present a method for rapid isolation of flanking regions from amplified fragment length polymorphism (AFLP) fragments based on thermal asymmetric interlaced (TAIL)-PCR, in which one sequence-specific primer and one degenerate primer derived from an conserved motif found in homologies of the known sequence were used. The final result showed this to be a simple and efficient strategy, especially for short known sequences containing coding regions. Moreover this protocol was especially useful for species with little available genome information such as Hongkong Kumquat (Fortunella hindsii), since most of their genes have known homologies in other species such asArabidopsis and rice.     

Protective effects of caffeic acid phenethyl ester on skeletal muscle ischemia-reperfusion injury in rats

There is a great evidence that reactive oxygen species (ROS) play an important role in the pathophysiology of ischemia −reperfusion(I/R)injury in skeletal muscle.Caffeic acid phenethyl ester(CAPE)is a component of honeybeep ropolis.It has antioxidant, anti−inflammatory and free radical scavenger properties.The aim of this study is to determine the protective effects of CAPE against I/R injury in respect of protein oxidation, neutrophil in filtration, and the activities of xanthine oxidase(XO)and adenosine deaminase(AD)onan<invivomodel of skeletal muscle I/R injury.Rats were divided into three equal groups each consisting of sixrats:Sham operation, I/R, and I/R plus CAPE(I/R+CAPE)groups.CAPE was administered intraperitoneally 60 min before the beginning of the reperfusion.At the end of experimental procedure, blood and gastrocnemius muscle tissues were used for biochemical analyses.Tissue protein carbonyl(PC)levels and the activities of XO, myeloperoxidase(MPO) and AD in I/R group were significantly higher than that of control(p0.01, p0.05, p0.01, p0.005, respectively).Administration of CAPE significantly decreased tissue PC levels, MPO and XO activities in skeletal muscle compared to I/R group(p0.01, p0.05, p0.05, respectively).In addition, plasma creatine phosphokinase(CPK), XO and ADactivities were decreased in I/R+CAPE group compared to I/R group(p0.05, p0.05, p0.001). The results of this study revealed that free radical attacks may play an important role in the pathogenesis of skeletal muscle I/R injury. Also, the potent free radical scavenger compound, CAPE, may have protective potential in this process. Therefore, it can be speculated that CAPE or other antioxidant agents may be useful in the treatment of I/R injury as well as diffused traumatic injury of skeletal muscle.     

A new marker at DXS 115 useful for carrier detection in hemophilia A

Summary In this brief communication we report a new intergenic polymorphism at DXS115 as a marker for detection of heterozygotes in families at risk for hemophilia A. Total genomic DNA was isolated from white blood cells, double digested by KpnI and XbaI and hybridized with EcoRI/SstI fragment of the genomic probe p482.6. The incidence of the polymorphic 5.1-kb fragment was estimated as 0.069 in a German population. A technical advantage of using the XbaI/KpnI RFLP is that both the intragenic XbaI-RFLP in intron 22 of factor VIII gene and the new intergenic RFLP can be evaluated at the same time.     

Characterization of a restriction barrier and electrotransformation of the cyanobacterium Nostoc PCC 7121

We have investigated host restriction as a barrier to transformation and developed a method for gene transfer into the previously untransformable, heterotrophic cyanobacterium Nostoc PCC 7121. A restriction endonuclease, designated Nsp 7121I, has been partially purified by phosphocellulose chromatography of Nostoc cell extract. Comparisons of Nsp 7121I digests of bacteriophage lambda and plasmid DNAs with computer-generated restriction fragment profiles showed that Nsp 7121I is an isoschizomer of restriction endonucleases, such as Asu I, Nsp 7524IV, Sau 96I, and Eco 47II, that recognize the sequence GGNCC. Cleavage by Nsp 7121I within this sequence was confirmed by sequence analysis of DNA fragments cleaved at a unique Nsp 7121I site. These data further suggested that cleavage occurs after the first G (5-G/GNCC-3) in this site to generate a three base 5 overhang. Nsp 7121I degraded all plasmids used in previous transformation attempts but modification of these DNA molecules by Eco 47II methylase effectively prevented digestion by Nsp 7121I. Plasmids premethylated by passage through Escherichia coli carrying a plasmid encoded Eco 47II methylase have now been used in an electroporation procedure to transform Nostoc PCC 7121 to neomycin resistance at frequencies as high as one transformant per 10³ viable cells. Transformation, and stable replication within Nostoc of one of the transforming plasmids (pRL25), was confirmed by recovery of pRL25, in its original form, from transformants. Conjugal transfer of pRL25 from E. coli into Nostoc was also possible but at much lower efficiency than by electroporation. These findings establish the basis for genetic analysis of Nostoc PCC 7121, from which genes for photosynthetic electron transport have been cloned.     

Attenuation of human influenza a viruses

The attenuation of two human influenza A viruses has been carried out, using the selection of inhibitor-resistant strains and multiple passages at low temperatures. A virus related to A2/Tokyo/3/67 was obtained in an inhibitor-resistant form. When this was compared with the inhibitor-sensitive strain in a volunteer trial it was relatively non-pathogenic. The second virus, A2/Hongkong/1/68, was subjected to much longer treatment, but nevertheless remained slightly sensitive to serum inhibitor. When given to volunteers it was less pathogenic than before but attenuation was incomplete. A2/Hongkong/1/68 was also modified by passage at low temperatures. Many of these passages are apparently necessary for full attenuation.All attenuated viruses were infective and antigenic.     

Catabolite repression of the colonization factor antigen I (CFA/I) operon ofEscherichia coli

Experiments were performed to study whether the synthesis of the fimbrial colonization factor antigen I (CFA/I) of enterotoxigenicEscherichia coli is affected by glucose. The CFA/I-producing strain H-10407 (O78:H11:CFA/I) was grown in CFA medium containing various concentrations of glucose. Addition of 1% glucose into the medium resulted in a pronounced decrease in CFA/I production by H-10407 as assessed by ELISA, hemagglutination, and electron microscopy. The repressive effect of glucose was reversed by the addition of 10 mM cAMP to the medium. Examination of the promoter sequence of thecfaA gene of the CFA/I operon revealed a consensus binding site for the catabolite activator protein-cAMP complex. With a reporter plasmid containing a fusion of thecfaA promoter, a portion of thecfaA gene, and thelacZ gene, it was shown that the activity of this promoter was influenced by glucose. In a wild-typeE. coli strain, addition of 0.5% glucose to the growth medium diminished the promoter activity more than 70%. ThecfaA promoter also exhibited a lower level of activity incya (adenyl cyclase) andcrp (cAMP receptor protein) mutants than in the wild-type strain. The addition of 10 mM cAMP resulted in a marked increase in the expression from thecfaA promoter in thecya but not in thecrp mutant. These results suggest that the suppressive effect of glucose in the CFA/I system is mediated via the mechanism of catabolite repression through thecfaA promoter of the CFA/I operon.     

Gender Symbolism and Power Relations: A Reassessment of the Amb Kor Cult of Mt. Hagen

This paper explores expressions of gender symbolism in a fertility cult of Mount Hagen. This cult – the amb kor – has been analysed by Andrew Strathern in terms of its symbolic construction as a set of statements about male/female relations, his emphasis being on the operation of reversal, pairing and opposition within the cult. My contention is that such a structural analysis is insufficient. Through a discussion of historical process in Hagen I attempt to locate amb kor in a more materialist framework, viewing is as a discourse on the state of power relations in Hagen. In this respect, I see amb kor as being equally a set of statements about male/male relations as male/female.     

A Distributed Multi-Storage Resource Architecture and I/O Performance Prediction for Scientific Computing

I/O intensive applications have posed great challenges to computational scientists. A major problem of these applications is that users have to sacrifice performance requirements in order to satisfy storage capacity requirements in a conventional computing environment. Further performance improvement is impeded by the physical nature of these storage media even when state-of-the-art I/O optimizations are employed.In this paper, we present a distributed multi-storage resource architecture, which can satisfy both performance and capacity requirements by employing multiple storage resources. Compared to a traditional single storage resource architecture, our architecture provides a more flexible and reliable computing environment. This architecture can bring new opportunities for high performance computing as well as inherit state-of-the-art I/O optimization approaches that have already been developed. It provides application users with high-performance storage access even when they do not have the availability of a single large local storage archive at their disposal. We also develop an Application Programming Interface (API) that provides transparent management and access to various storage resources in our computing environment. Since I/O usually dominates the performance in I/O intensive applications, we establish an I/O performance prediction mechanism which consists of a performance database and a prediction algorithm to help users better evaluate and schedule their applications. A tool is also developed to help users automatically generate performance data stored in databases. The experiments show that our multi-storage resource architecture is a promising platform for high performance distributed computing.     

Bifunctional thiosialosides inhibit influenza virus

We have synthesized a panel of bivalent S-sialoside analogues, with modifications at the 4 position, as inhibitors of influenza virus. These first generation compounds show IC₅₀ values ranging from low micromolar to high nanomolar in enzyme inhibition and plaque reduction assays with two intact viruses, Influenza H1N1 (A/California/07/2009) and H3N2 (A/Hongkong/8/68).     

Calcium and cGMP target distinct phytochrome-responsive elements

Previous work using microinjection into single cells of the tomato aurea mutant demonstrated that phytochrome A-dependent activation of rbcS and chs genes was mediated by calcium and cGMP, respectively. This work sought to identify promoter cis-elements that respond to these two small molecules. Box II and Unit I, derived from rbcS-3A and chs promoters, respectively, were previously shown to function as light-responsive cis-elements. Eleven copies of Box II and four copies of Unit I were linked 5′ to the ?90 and ?46 35 S promoters, respectively, and, both constructs were fused to the β-glucuronidase (GUS) reporter gene. GUS activities were obtained upon co-injection of either Box II/-90GUS or Unit I/-46GUS with oat phytochrome A (phyA) and GTPγS, an activator of heterotrimeric G proteins. The activation of Box II/-90GUS by phyA was insensitive to the cGMP antagonist, Rp-cGMPS, although anthocyanin accumulation, but not chloroplast development, was totally blocked in the injected cells. Consistent with this result, calcium, but not cGMP, induced Box II/-90GUS activity. In contrast to Box II/-90GUS, phyA-dependent activation of Unit I/-46GUS activity was blocked by Rp-cGMPS. Moreover, cGMP, not calcium, induced Unit I/-46GUS activity. Control experiments showed that ?90 GUS and ?46 GUS were inactive in the presence of calcium and cGMP, respectively. These results provide evidence that Box II and Unit I are targets of the calcium and cGMP pathways, respectively. Interestingly, calcium activation of Box II/-90GUS was repressed by a high concentration of cGMP and cGMP induction of Unit I/-46GUS was blocked by a high concentration of calcium/CaM. Thus, these two small cis-elements can also serve as targets of the reciprocal control mechanisms that operate to regulate the activities of the two phyA signaling branches.     

An RFLP marker in tomato linked to the Fusarium oxysporum resistance gene I2

Summary The locus, I2, which in tomato confers resistance against Fusarium oxysporum f. sp. lycopersici race 2, was introgressed into Lycopersicon esculentum from the wild species L. pimpinellifolium (P.I. 126915). We searched for restriction fragment length polymorphisms (RFLPs) between nearly isogenic lines (NILs) in clones that map to the region introgressed from the wild species. Since I2 maps to chromosome 11, we used DNA clones from this chromosome as hybridization probes to Southern blots containing bound DNA of the NILs digested with 23 restriction enzymes. Of the 14 chromosome 11 clones, 9 exhibited polymorphism. These clones were further hybridized to verification filters that contained DNA from resistant and susceptible L. esculentum varieties digested with the enzymes that gave the polymorphism. One clone, TG105, was found to be associated with I2; 19 susceptible lines showed a different RFLP with this probe than 16 resistant lines, including the original L. pimpinellifolium accession used as a source for the resistance gene. These results together with our mapping analysis indicate that TG105 is closely linked to the resistance gene.     

Spectroscopic characterization of cytochrome P450 Compound I

The cytochrome P450 protein-bound porphyrin complex with the iron-coordinated active oxygen atom as Fe(IV)O is called Compound I (Cpd I). Cpd I is the intermediate species proposed to hydroxylate directly the inert carbon–hydrogen bonds of P450 substrates. In the natural reaction cycle of cytochrome P450 Cpd I has not yet been detected, presumably because it is very short-lived. A great variety of experimental approaches has been applied to produce Cpd I artificially aiming to characterize its electronic structure with spectroscopic techniques. In spite of these attempts, none of the spectroscopic studies of the last decades proved capable of univocally identifying the electronic state of P450 Cpd I. Very recently, however, Rittle and Green [9] have shown that Cpd I of CYP119, the thermophillic P450 from Sulfolobus acidocaldarius, is univocally a Fe(IV)O–porphyrin radical with the ferryl iron spin (S = 1) antiferromagnetically coupled to the porphyrin radical spin (S′ = 1/2) yielding a S_tot = 1/2 ground state very similar to Cpd I of chloroperoxidase from Caldariomyces fumago. In this mini-review the efforts to characterize Cpd I of cytochrome P450 by spectroscopic methods are summarized.     

Transcellobiosylation Reactions Catalyzed by Different Exoglucanase Components of a Trichoderma viride Cellulase in Aqueous Organic Solvent

The contribution of three exoglucanases from a commercial Trichoderma viride cellulase to transcellobiosylation, and the tolerance of these enzymes to acetonitrile co-solvent were studied. The enzymatic reactions were performed with p-nitrophenyl-β-d-cellobioside as the starting substrate. Among these enzymes, the least anionic exoglucanase (Exo I) showed the highest transcellobiosylation activity and acetonitrile tolerance. Exo I retained considerable activity even in 30% MeCN/water and produced p-nitrophenyl-β-d-cellotetraoside at about 1.5% conversion from the initial substrate in 30% MeCN/water. The residual activity of Exo I after incubation in MeCN/water mixture was almost identical to that of the crude cellulase and a considerable amount of the transcellobiosylation properties of the crude cellulase seemed to be attributable to this Exo I component.     

Cloning and characterization of class I Mhc genes of the zebrafish,Brachydanio rerio

The zebrafish (Brachydanio rerio) offers many advantages for immunological and immunogenetic research and has the potential for becoming one of the most important nonmammalian vertebrate research models. With this in mind, we initiated a systematic study of the zebrafish major histocompatibility complex (Mhc) genes. In this report, we describe the cloning and characteristics of the zebrafish class I A genes coding for the chains of the heterodimer and thus complete the identification of all four classes and subclasses of the Mhc in this species. We describe the full class I cDNA sequence as well as the exon-intron organization of the class I A genes, including intron sequences. We identify three families of class I A genes which we designate Bree-UAA,-UBA, and -UCA. The three families originated about the time of the divergence of cyprinid and salmonid fishes. All three families are members of an ancient lineage that diverged from another, older lineage also represented in cyprinid fishes before the radiation of teleost orders. The fish class I A genes therefore evolve differently from mammalian class I A genes, in which the establishment of lineages and families mostly postdates the divergence of orders.The nucleotide sequence data reported in this Papershave been submitted to the EMBL/GenBank nucleotide sequence databases and have been assigned the accession numbers Z46776–Z46779     

Property as sovereignty in micro: the state/property nexus and the Cyprus Problem

This article shows that landed property can be an exercise of state sovereignty in micro. I argue that property tightly relates to statehood and that the concept of ‘community’ offers us a lens with which to investigate that relation. Property's ‘communal’ character in Cyprus often transcends individual rights to ownership. A house belongs not to an individual, but to persons in their capacity as members of either the Greek-Cypriot or Turkish-Cypriot constitutional communities of the Republic. Focusing on the moral and political claims that ensue from this premise, I show how refugee Cypriots encounter and rearticulate the state in a variety of institutions as they lay claims to property (periousia) – their own or others’. Consequently, I argue that thinking through ‘community’ contributes to understandings of the linkage between property and statecraft (what I call the state/property nexus). In turn, this allows us to better comprehend statehood in post-conflict domains.     

Loss and restoration of viability of E. coli due to combinations of mutations affecting DNA polymerase I and repair activities

Summary We have found that the cells possessing the polA6 mutation affecting DNA polymerase I are unable to accept another mutation (uvr502) leading to UV-sensitivity. The introduction of the polA12 mutation determining the synthesis of a temperature sensitive DNA polymerase I into the uvr502 mutant results in the temperature sensitivity of colony forming ability of the double mutant. These data show that the uvr502 derivatives lacking DNA polymerase I are inviable. Reversions to temperature resistance in the population of the double mutant uvr502 polA12 may occur because of reverse mutations at one of the mutated sites or because of mutations suppressing DNA polymerase I deficiency but not UV- or MMS-sensitivity of revertants. DNA and protein synthesis in uvr502 polA12 cells continues after a shift to 45°C with rates almost indistinguishable from those in single mutants or wild type cells. No differences in DNA degradation were observed during incubation of single and double mutants at 45°C. The single strand molecular weight distribution of parent DNA from the double mutant as well as that from wild type cells is not affected by the shift to 45°C and 3 hours incubation at this temperature. We suggest that DNA polymerase I and/or the product altered by the uvr502 mutation are required for some step(s) of discontinuous DNA replication nonessential for the formation of acid insoluble DNA. The DNA polymerase I and the uvr gene product seem to be able to substitute for each other in accomplishing this process.     

The right end of MudI(Ap,lac)

Stable derivatives of the bacteriophage MudI(Ap,lac) were used to generate operon fusions in S. typhimurium which exhibit a sectoring phenotype with respect to lacZ expression. The Lac^- to Lac⁺ conversion was shown to be the result of small deletions involving the right end of the MudI element. DNA sequence analysis of several different fusions revealed that this end of MudI(Ap,lac) contains an assymetric inverted repeat of the attR site found in the wild-type Mu phage. A model is presented which explains how such a structure was formed in the construction of MudI(Ap,lac). In addition, this model explains the observed deletion formation and the Lac^- to Lac⁺ conversion in the sectoring fusions.This paper is dedicated to our padrinos, John and Marge Ingraham, whose love of truth has served us as constant inspiration