Unusually short tandem repeats appear to reach chromosome ends of Rhynchosciara americana (Diptera: Sciaridae)

The characterisation of sequences at chromosome ends of Rhynchosciara americana was continued with the screening of a genomic library using as a probe a short repeat identified in a previous report (M-22, 22 bp) which was found to be specific for noncentromeric termini of this species. Simple repeats, complex tandem and apparently dispersed repeats were present in the genomic clones analysed. Repetitive sequences do not define individual chromosome tips as they were found in all noncentromeric ends. A novel and unusually short tandem repeat type for dipteran chromosome ends (named M-16) composed of 16 nucleotides and frequently associated with M-22 arrays was characterised in this work. Islands of M-16 and M-22 tandem repeats were found in all the genomic clones analysed. Individual probes representative of each repetitive element hybridised not only to all noncentromeric ends of R. americana chromosomes but also to inter-telomeric bridges. This contrasted with the other repeat types which displayed sub-telomeric localisation as seen by double detection of hybridised probe and telomeric reverse transcriptase. Some stretches composed of M-16 and M-22 tandem repeats localised in different regions of the analysed genomic clones were either identical or showed sequence similarity that was unexpectedly higher than the mean sequence similarity observed among repeats within each of their tandem arrays. The occurrence of segmental duplications, as deduced by sequence analyses involving the two repeats that appeared to reach chromosome ends, might indicate the involvement of this type of duplication process in the chromosome end maintenance in this species.

An INDEL polymorphism at the X-STR GATA172D05 flanking region

A new polymorphic INDEL was detected at the X-STR GATA172D05 flanking region, which corresponds to an 18-bp deletion, 141 bp upstream the TAGA repeat motif. This INDEL was found to be polymorphic in different population samples from Native Americans, Africans, and Europeans as well as in an admixed population from the Amazonia (Bel,m). Gene diversities varied between 37.5% in Native Americans and 49.9% in Africans. Comparison between human and chimpanzee sequences showed that the ancestral state corresponds to the presence of two copies of 18 bp, detected in both species; and the mutated allele has lost one of these two copies. The simultaneous analysis of the short tandem repeat (STR) and INDEL variation showed an association between the INDEL ancestral allele with the shorter STR alleles. High diversities were found in all population groups when combining the information provided by the INDEL and STR variation. Gene diversities varied between 76.7% in Native Americans and 80.6% in both Portugal and Bel,m.

The Genetics of Alzheimer`s Disease in Brazil: 10 Years of Analysis in a Unique Population

Alzheimer`s Disease (AD) is the most common type of dementia among the elderly, with devastating consequences for the patient, their relatives, and caregivers. More than 300 genetic polymorphisms have been involved with AD, demonstrating that this condition is polygenic and with a complex pattern of inheritance. This paper aims to report and compare the results of AD genetics studies in case-control and familial analysis performed in Brazil since our first publication, 10 years ago. They include the following genes/markers: Apolipoprotein E (APOE), 5-hidroxytryptamine transporter length polymorphic region (5-HTTLPR), brain-derived neurotrophin factor (BDNF), monoamine oxidase A (MAO-A), and two simple-sequence tandem repeat polymorphisms (DXS1047 and D10S1423). Previously unpublished data of the interleukin-1 alpha (IL-1 alpha) and interleukin-1 beta (IL-1 beta) genes are reported here briefly. Results from others Brazilian studies with AD patients are also reported at this short review. Four local families studied with various markers at the chromosome 21, 19, 14, and 1 are briefly reported for the first time. The importance of studying DNA samples from Brazil is highlighted because of the uniqueness of its population, which presents both intense ethnical miscegenation, mainly at the east coast, but also clusters with high inbreeding rates in rural areas at the countryside. We discuss the current stage of extending these studies using high-throughput methods of large-scale genotyping, such as single nucleotide polymorphism microarrays, associated with bioinformatics tools that allow the analysis of such extensive number of genetics variables, with different levels of penetrance. There is still a long way between the huge amount of data gathered so far and the actual application toward the full understanding of AD, but the final goal is to develop precise tools for diagnosis and prognosis, creating new strategies for better treatments based on genetic profile.

Curiously composite structures of a retrotransposon and a complex repeat associated with chromosome ends of Rhynchosciara americana (Diptera: Sciaridae)

In Drosophila, telomere retrotransposons counterbalance the loss of telomeric DNA. The exceptional mechanism of telomere recovery characterized in Drosophila has not been found in lower dipterans (Nematocera). However, a retroelement resembling a telomere transposon and termed ""RaTART"" has been described in the nematoceran Rhynchosciara americana. In this work, DNA and protein sequence analyses, DNA cloning, and chromosomal localization of probes obtained either by PCR or by screening a genomic library were carried out in order to examine additional features of this retroelement. The analyses performed raise the possibility that RaTART represents a genomic clone composed of distinct repetitive elements, one of which is likely to be responsible for its apparent enrichment at chromosome ends. RaTART sequence in addition allowed to assess a novel subtelomeric region of R. americana chromosomes that was analyzed in this work after subcloning a DNA fragment from a phage insert. It contains a complex repeat that is located in the vicinity of simple and complex tandem repeats characterized previously. Quantification data suggest that the copy number of the repeat is significantly lower than that observed for the ribosomal DNA in the salivary gland of R. americana. A short insertion of the RaTART was identified in the cloned segment, which hybridized preferentially to subtelomeres. Like RaTART, it displays truncated sequences related to distinct retrotransposons, one of which has a conceptual translation product with significant identity with an endonuclease from a lepidopteran retrotransposon. The composite structure of this DNA stretch probably reflects mobile element activity in the subtelomeric region analyzed in this work.

Possible states in the flow around two circular cylinders in tandem with separations in the vicinity of the drag inversion spacing

The possible states in the flow around two identical circular cylinders in tandem arrangements are investigated for configurations in the vicinity of the drag inversion separation. By means of numerical simulations, the hysteresis in the transition between the shedding regimes is studied and the relationship between (three-dimensional) secondary instabilities and shedding regime determination is addressed. The differences observed in the behavior of two- and three-dimensional flows are analyzed, and the regions of bistable flow are delimited. Very good agreement is found between the proposed scenario and results available in the literature. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3420111]

Long Terminal Repeat Sequence Analysis of HTLV-2 Molecular Variants Identified in Southern Brazil

In Brazil, human T-lymphotropic virus type 2 (HTLV-2) is endemic in Amerindians and epidemic in intravenous drug users (IDUs). The long terminal repeat (LTR) is the most divergent genomic region of HTLV-2, therefore useful to characterize subtypes. Nucleotide sequence and restriction fragment length polymorphism (RFLP) analysis of LTR genomic segments of fourteen HTLV-2 strains isolated from HIV-infected patients of Londrina, Southern Brazil, were carried out. Molecular analysis disclosed that all HTLV-2 strains belonged to 2a subtype, and RFLP detected the presence of the a4, a5, and a6 subgroups according to Switzer's nomenclature. RFLP correlated with nucleotide sequence, and phylogenetic analysis clustered HTLV-2 sequences of IDUs into subgroups a5 and a6. HTLV-2 sequences from individuals of sexual risk factor clustered into the a4 subgroup. These results extend the knowledge of the genetic diversity of HTLV-2 circulating in Brazil and provide insights into HTLV-2 transmission and virus movement in this geographic area.

On the wake-induced vibration of tandem circular cylinders: the vortex interaction excitation mechanism

The mechanism of wake-induced vibrations (WIV) of a pair of cylinders in a tandem arrangement is investigated by experiments. A typical WIV response is characterized by a build-up of amplitude persisting to high reduced velocities; this is different from a typical vortex-induced vibration (VIV) response, which occurs in a limited resonance range. We suggest that WIV of the downstream cylinder is excited by the unsteady vortex-structure interactions between the body and the upstream wake. Coherent vortices interfering with the downstream cylinder induce fluctuations in the fluid force that are not synchronized with the motion. A favourable phase lag between the displacement and the fluid force guarantees that a positive energy transfer from the flow to the structure sustains the oscillations. If the unsteady vortices are removed from the wake of the upstream body then WIV will not be excited. An experiment performed in a steady shear flow turned out to be central to the understanding of the origin of the fluid forces acting on the downstream cylinder.

Experimental investigation of flow-induced vibration on isolated and tandem circular cylinders fitted with strakes

The effect of varying the geometric parameters of helical strakes on vortex-induced vibration (VIV) is investigated in this paper. The degree of oscillation attenuation or even suppression is analysed for isolated circular cylinder cases. How a cylinder fitted with strakes behaves when immersed in the wake of another cylinder in tandem arrangement is also investigated and these results are compared to those with a single straked cylinder. The experimental tests are conducted at a circulating water channel facility and the cylindrical models are mounted on a low-damping air bearing elastic base with one degree-of-freedom, restricted to oscillate in the transverse direction to the channel flow. Three strake pitches (p) and heights (h) are tested: p = 5, 10, 15d, and h = 0.1, 0.2, 0.25d. The mass ratio is 1.8 for all models. The Reynolds number range is from 1000 to 10000, and the reduced velocity varies up to 21. The cases with h = 0.1d strakes reduce the amplitude response when compared to the isolated plain cylinder, however the oscillation still persists. On the other hand, the cases with h = 0.2, 0.25d strakes almost completely suppress VIV. Spanwise vorticity fields, obtained through stereoscopic digital particle image velocimetry (SDPIV), show an alternating vortex wake for the p = 10d and h = 0.1d straked cylinder. The p = 10d and h = 0.2d cylinder wake has separated shear layers with constant width and no roll-up close to the body. The strakes do not increase the magnitude of the out-of-plane velocity compared to the isolated plain cylinder. However, they deflect the flow in the out-of-plane direction in a controlled way, which can prevent the vortex shedding correlation along the span. In order to investigate the wake interference effect on the strake efficiency, an experimental arrangement with two cylinders in tandem is employed. The centre-to-centre distance for the tandem arrangement varies from 2 to 6. When the downstream p = 10d and h = 0.2d cylinder is immersed in the wake of an upstream fixed plain cylinder, it loses its effectiveness compared with the isolated case. Although the oscillations have significant amplitude, they are limited, which is a different behaviour from that of a tandem configuration with two plain cylinders. For this particular case, the amplitude response monotonically increases for all gaps, except one, a trait usually found in galloping-like oscillations. SDPIV results for the tandem arrangements show alternating vortex shedding and oscillatory wake. (C) 2010 Elsevier Ltd. All rights reserved.

Secondary instabilities in the flow around two circular cylinders in tandem

Direct stability analysis and numerical simulations have been employed to identify and characterize secondary instabilities in the wake of the flow around two identical circular cylinders in tandem arrangements. The centre-to-centre separation was varied from 1.2 to 10 cylinder diameters. Four distinct regimes were identified and salient cases chosen to represent the different scenarios observed, and for each configuration detailed results are presented and compared to those obtained for a flow around an isolated cylinder. It was observed that the early stages of the wake transition changes significantly if the separation is smaller than the drag inversion spacing. The onset of the three-dimensional instabilities were calculated and the unstable modes are fully described. In addition, we assessed the nonlinear character of the bifurcations and physical mechanisms are proposed to explain the instabilities. The dependence of the critical Reynolds number on the centre-to-centre separation is also discussed.

Adaptation for tandem cold mill models

The ideal conditions for the operation of tandem cold mills are connected to a set of references generated by models and used by dynamic regulators. Aiming at the optimization of the friction and yield stress coefficients an adaptation algorithm is proposed in this paper. Experimental results obtained from an industrial cold rolling mill are presented. (C) 2008 Elsevier B.V. All rights reserved.

Methods for detection of anatoxin-a(s) by liquid chromatography coupled to electrospray ionization-tandem mass spectrometry

Anatoxin-a(s) is a potent irreversible inhibitor of the enzyme acetylcholinesterase with a unique N-hydroxyguanidine methylphosphate ester chemical structure. Determination of this toxin in environmental samples is hampered by the lack of specific methods for its detection. Using the toxic strain of Anabaena lemmermani PH-160 B as positive control, the fragmentation characteristics of anatoxin-a(s) under collision-induced dissociation conditions have been investigated and new LC-MS/MS methods proposed. Recommended ion transitions for correct detection of this toxin are 253 > 58, 253 > 159, 235 > 98 and 235 > 96. Chromatographic separation is better achieved under HILIC conditions employing a ZIC-HILIC column. This method was used to confirm for the first time the production of anatoxin-a(s) by strains of Anabaena oumiana ITEP-025 and ITEP-026. Considering no standard solutions are commercially available, our results will be of significant use for the correct identification of this toxin by LC-MS/MS. (C) 2009 Elsevier Ltd. All rights reserved.

Negative ion `chip-based` nanospray tandem mass spectrometry for the analysis of flavonoids in glandular trichomes of Lychnophora ericoides Mart. (Asteraceae)

This paper reports a method for the analysis of secondary metabolites stored in glandular trichomes, employing negative ion `chip-based` nanospray tandem mass spectrometry. The analyses of glandular trichomes from Lychnophora ericoides, a plant endemic to the Brazilian `cerrado` and used in traditional medicine as an anti-inflammatory and analgesic agent, led to the identification of five flavonoids (chrysin, pinocembrin, pinostrobin, pinobanksin and 3-O-acetylpinobanksin) by direct infusion of the extracts of glandular trichomes into the nanospray ionisation source. All the flavonoids have no oxidation at ring B, which resulted in a modification of the fragmentation pathways compared with that of the oxidised 3,4-dihydroflavonoids already described in the literature. The absence of the anti-inflammatory and antioxidant di-C-glucosylflavone vicenin-2, or any other flavonoid glycosides, in the glandular trichomes was also demonstrated. The use of the,`chip-based` nanospray QqTOF apparatus is a new fast and useful tool for the identification of secondary metabolites stored in the glandular trichomes, which can be useful for chemotaxonomic studies based on metabolites from glandular trichomes. Copyright (C) 2008 John Wiley & Sons, Ltd.

Enantioselective analysis of zopiclone and its metabolites in plasma by liquid chromatography/tandem mass spectrometry

A high-performance liquid chromatographic method with triple-quadrupole mass spectrometry detection (LC-MS-MS) was developed and validated for the first time for the simultaneous quantification of zopiclone and its metabolites in rat plasma samples. The analytes were isolated from rat plasma by liquid-liquid extraction and separated using a chiral stationary phase based on an amylose derivative, Chiralpak ADR-H column, and ethanol-methanol-acetonitrile (50:45:5, v/v/v) plus 0.025% diethylamine as the mobile phase, at a flow-rate of 1.0 mL min(-1). Moclobemide was used as the internal standard. The developed method was linear over the concentration range of 7.5-500 ng mL(-1). The mean absolute recoveries were 74.6 and 75.7; 61.6 and 56.9; 72.5, and 70.7 for zopiclone enantiomers, for N-desmethyl zopiclone enantiomers and for zopiclone-N-oxide enantiomers, respectively, and 75.9 for the internal standard. Precision and accuracy were within acceptable levels of confidence (<15%). The method application in a pilot study of zopiclone kinetic disposition in rats showed that the levels of (+)-(S)-zopiclone were always higher than those of (-)-R-zopiclone. Higher concentrations were also observed for (+)-(S)-N-desmethyl zopiclone and (+)-(S)-N-oxide zopiclone, confirming the stereoselective disposition of zopiclone.

Determination of beta-artemether and its main metabolite dihydroartemisinin in plasma employing liquid-phase microextraction prior to liquid chromatographic-tandem mass spectrometric analysis

A method for the determination of artemether (ART) and its main metabolite dihydroartemisinin (DHA) in plasma employing liquid-phase microextraction (LPME) for sample preparation prior to liquid chromatography-tandem mass spectrometry (LC-MS-MS) was developed. The analytes were extracted from 1 nil, of plasma utilizing a two-phase LPME procedure with artemisinin as internal standard. Using the optimized LPME conditions, mean absolute recovery rates of 25 and 32% for DHA and ART, respectively, were achieved using toluene-n-octanol (1:1, viv) as organic phase with an extraction time of 30 min. After extraction, the analytes were resolved within 5 min using a mobile phase consisting of methanol-ammonium acetate (10 mmol L(-1) pH 5.0, 80:20. v/v) on a laboratory-made column based on poly(methyltetradecylsiloxane) attached to a zirconized-silica support. MS-MS detection was employed using an electrospray interface in the positive ion mode. The method developed was linear over the range of 5-1000 ng mL(-1) for both analytes. Precision and accuracy were within acceptable levels of confidence (<15%). The assay was applied to the determination of these analytes in plasma from rats treated with ART. The two-phase LPME procedure is affordable and the solvent consumption was very low compared to the traditional methods of sample preparation. (C) 2010 Elsevier B.V. All rights reserved.

Re-examination of the anion derivatives of isoflavones by radical fragmentation in negative electrospray ionization tandem mass spectrometry: experimental and computational studies

This paper reports theoretical and experimental studies of gas-phase fragmentation reactions of four naturally occurring isoflavones. The samples were analyzed in negative ion mode by direct infusion in ESI-QqQ, ESI-QqTOF and ESI-Orbitrap systems. The MS/MS and MS(n) spectra are in agreement with the fragmentation proposals and high-resolution analyses have confirmed the formulae for each ion observed. As expected, compounds with methoxyl aromatic substitution have showed a radical elimination of center dot CH(3) as the main fragmentation pathway. A second radical loss (center dot H) occurs as previously observed for compounds which exhibit a previous homolytic center dot CH(3) cleavage (radical anion) and involves radical resonance to stabilize the anion formed. However, in this study we suggest another mechanism for the formation of the main ions, on the basis of the enthalpies for each species. Compounds without methoxy substituent dissociate at the highest energies and exhibit the deprotonated molecule as the most intense ion. Finally, energy-resolved experiments were carried out to give more details about the gas-phase dissociation reaction of the isoflavones and the results are in agreement with the theoretical approaches. Copyright (C) 2011 John Wiley & Sons, Ltd.