Fragmentation study of iridoid glycosides including epimers by liquid chromatography-diode array detection/electrospray ionization mass spectrometry and its application in metabolic fingerprint analysis of Gardenia jasminoides Ellis.

PubMed

Zhou, Tingting; Liu, Hua; Wen, Jun; Fan, Guorong; Chai, Yifeng; Wu, Yutian

2010-09-15

A high-performance liquid chromatography-diode array detection/electrospray ionization mass spectrometry (HPLC-DAD/ESI-MS) method was applied to the characterization of ten iridoid glycosides in Gardenia jasminoides Ellis, a traditional Chinese medicine. During the process of structural elucidation, two groups of isomers including two epimers were structurally characterized and differentiated according to their distinctive fragmentation patterns which were closely related to their isomeric differentiations. Subsequently, the major compounds were purified by multi-dimensional chromatography and semi-preparative HPLC and the structure identification was confirmed with NMR techniques. The major fragmentation pathways of iridoid glycosides in Gardenia jasminoides Ellis obtained through the MS data were schemed systematically, which provided the best sensitivity and specificity for characterization of the iridoid glycosides especially the isomers so far. Based on the fragmentation patterns of iridoid glycosides concluded, seven major iridoid glycosides were characterized in rat plasma after intravenous administration of Gardenia jasminoides Ellis. Copyright 2010 John Wiley & Sons, Ltd.

Coherent dissociation of relativistic {sup 9}C nuclei in nuclear track emulsion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krivenkov, D. O.; Artemenkov, D. A.; Bradnova, V.

2010-04-30

For the first time nuclear track emulsion is exposed to relativistic {sup 9}C nuclei. A systematic pattern of the distributions of charge combinations of fragments in the peripheral interactions of {sup 9}C nuclei in a nuclear track emulsion has been obtained. The main conclusion is that the contribution of the channel {sup 9}C->{sup 8}B+p and {sup 9}C->{sup 7}Be+2p is most important in events that do not involve the production of target-nucleus fragments or mesons (coherent dissociation). It can be concluded that in the peripheral {sup 9}C dissociation the picture hitherto obtained for {sup 8}B and {sup 7}Be with the additionmore » of one or two protons, respectively, is reproduced. Three coherent dissociation events {sup 9}C->3{sup 3}He accompanied by neither target fragments of the nucleus target nor charged mesons are identified.« less

Abstracts of papers presented at the 8th workshop of the Virology Section of the Deutsche Gesellschaft für Hygiene und Mikro-biologie, Würzburg, March 17-19, 1983.

PubMed

1983-09-01

17 adenovirus strains were found to be antigenically related to prototype Ad 15 by neutralization. No relationship to Ad 15, but to Ad 9 could be detected by hemagglutination-inhibition; we therefore named them Ad 15/H9 intermediate strains. After analysis of the genome by five different restriction enzymes, the fragment patterns obtained deviated widely from the prototype Ad 15, but only slightly from Ad 9. Differences could also be observed among the variants. After digestion by five restriction enzymes, altogether six genome types could be established among the 17 intermediate strains. To map the variations on the genome of the 15/H9 strains, two methods were employed: the double digestion of the DNA and DNA fragments together with the determination of the terminal fragments made it possible to construct a physical map. The second method depends on a particularity of adenoviruses: the DNA is covalently linked with a 55 kD protein at the 5' terminus. After digestion of the DNA, which does contain this protein, the terminal DNA fragments do not migrate into the agarose gel; after an additional digestion with pronase B, they do migrate into the gel. Thus the terminal fragments were determined by comparing the fragment patterns with and without previous pronase B treatment.

Haloacetic acid-degrading bacterial communities in drinking water systems as determined by cultivation and by terminal restriction fragment length polymorphism of PCR-amplified haloacid dehalogenase gene fragments.

PubMed

Grigorescu, A S; Hozalski, R M; Lapara, T M

2012-04-01

To characterize the HAA-degrading bacteria in drinking water systems. Haloacetic acid (HAA)-degrading bacteria were analysed in drinking water systems by cultivation and by a novel application of terminal restriction fragment length polymorphism (tRFLP). Substantial similarities were observed among the tRFLP patterns of dehI and dehII gene fragments in drinking water samples obtained from three different cities (Minneapolis, MN; St Paul, MN; Bucharest, Romania) and from one biologically active granular activated carbon filter (Hershey, PA). The dominant fragment in the tRFLP profiles of dehI genes from the drinking water samples matched the pattern from an Afipia sp. that was previously isolated from drinking water. In contrast, the dominant fragment in the tRFLP profiles of dehII genes did not match any previously characterized dehII gene fragment. PCR cloning was used to characterize this gene fragment, which had <65% nucleotide sequence identity with any previously characterized dehII gene. Afipia spp. are an appropriate model organism for studying the biodegradation of HAAs in drinking water distribution systems as encoded by dehI genes; the organism that harbours the most prominent dehII gene in drinking water has yet to be cultivated and identified. The development of a novel application of tRFLP targeting dehI and dehII genes could be broadly useful in understanding HAA-degrading bacteria in numerous environments. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Mycobacterium avium restriction fragment length polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains.

PubMed

Sequeira, Patrícia Carvalho de; Fonseca, Leila de Souza; Silva, Marlei Gomes da; Saad, Maria Helena Féres

2005-11-01

Simple double repetitive element polymerase chain reaction (MaDRE-PCR) and Pvu II-IS1245 restriction fragment length polymorphism (RFLP) typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 AIDS inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

Formation, Fragmentation, and Structures of YxOy(+) (x = 1, 2, y = 1 - 13) Clusters: Collision-Induced Dissociation Experiments and Density Functional Theory Calculations.

PubMed

Glodić, Pavle; Mihesan, Claudia; Klontzas, Emmanouel; Velegrakis, Michalis

2016-02-25

Yttrium oxide cluster cations have been experimentally and theoretically studied. We produced small, oxygen-rich yttrium oxide clusters, YxOy+ (x = 1, 2, y = 1–13), by mixing the laser-produced yttrium plasma with a molecular oxygen jet. Mass spectrometry measurements showed that the most stable clusters are those consisting of one yttrium and an odd number of oxygen atoms of the form YO(+)(2k+1) (k = 0–6). Additionally, we performed collision induced dissociation experiments, which indicated that the loss of pairs of oxygen atoms down to a YO+ core is the preferred fragmentation channel for all clusters investigated. Furthermore, we conduct DFT calculations and we obtained two types of low-energy structures: one containing an yttrium cation core and the other composed of YO+ core and O2 ligands, being in agreement with the observed fragmentation pattern. Finally, from the fragmentation studies, total collision cross sections are obtained and these are compared with geometrical cross sections of the calculated structures.

Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes.

PubMed Central

Nassar, A; Darrasse, A; Lemattre, M; Kotoujansky, A; Dervin, C; Vedel, R; Bertheau, Y

1996-01-01

Conserved regions about 420 bp long of the pelADE cluster specific to Erwinia chrysanthemi were amplified by PCR and used to differentiate 78 strains of E. chrysanthemi that were obtained from different hosts and geographical areas. No PCR products were obtained from DNA samples extracted from other pectinolytic and nonpectinolytic species and genera. The pel fragments amplified from the E. chrysanthemi strains studied were compared by performing a restriction fragment length polymorphism (RFLP) analysis. On the basis of similarity coefficients derived from the RFLP analysis, the strains were separated into 16 PCR RFLP patterns grouped in six clusters, These clusters appeared to be correlated with other infraspecific levels of E. chrysanthemi classification, such as pathovar and biovar, and occasionally with geographical origin. Moreover, the clusters correlated well with the polymorphism of pectate lyase and pectin methylesterase isoenzymes. While the pectin methylesterase profiles correlated with host monocot-dicot classification, the pectate lyase polymorphism might reflect the cell wall microdomains of the plants belonging to these classes. PMID:8779560

Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics

PubMed Central

Breed, M F; Ottewell, K M; Gardner, M G; Marklund, M H K; Dormontt, E E; Lowe, A J

2015-01-01

Most woody plants are animal-pollinated, but the global problem of habitat fragmentation is changing the pollination dynamics. Consequently, the genetic diversity and fitness of the progeny of animal-pollinated woody plants sired in fragmented landscapes tend to decline due to shifts in plant-mating patterns (for example, reduced outcrossing rate, pollen diversity). However, the magnitude of this mating-pattern shift should theoretically be a function of pollinator mobility. We first test this hypothesis by exploring the mating patterns of three ecologically divergent eucalypts sampled across a habitat fragmentation gradient in southern Australia. We demonstrate increased selfing and decreased pollen diversity with increased fragmentation for two small-insect-pollinated eucalypts, but no such relationship for the mobile-bird-pollinated eucalypt. In a meta-analysis, we then show that fragmentation generally does increase selfing rates and decrease pollen diversity, and that more mobile pollinators tended to dampen these mating-pattern shifts. Together, our findings support the premise that variation in pollinator form contributes to the diversity of mating-pattern responses to habitat fragmentation. PMID:24002239

Extracellular self-DNA as a damage-associated molecular pattern (DAMP) that triggers self-specific immunity induction in plants.

PubMed

Duran-Flores, Dalia; Heil, Martin

2017-10-16

Mammals sense self or non-self extracellular or extranuclear DNA fragments (hereinafter collectively termed eDNA) as indicators of injury or infection and respond with immunity. We hypothesised that eDNA acts as a damage-associated molecular pattern (DAMP) also in plants and that it contributes to self versus non-self discrimination. Treating plants and suspension-cultured cells of common bean (Phaseolus vulgaris) with fragmented self eDNA (obtained from other plants of the same species) induced early, immunity-related signalling responses such as H 2 O 2 generation and MAPK activation, decreased the infection by a bacterial pathogen (Pseudomonas syringae) and increased an indirect defence to herbivores (extrafloral nectar secretion). By contrast, non-self DNA (obtained from lima bean, Phaseolus lunatus, and Acacia farnesiana) had significantly lower or no detectable effects. Only fragments below a size of 700 bp were active, and treating the eDNA preparation DNAse abolished its inducing effects, whereas treatment with RNAse or proteinase had no detectable effect. These findings indicate that DNA fragments, rather than small RNAs, single nucleotides or proteins, accounted for the observed effects. We suggest that eDNA functions a DAMP in plants and that plants discriminate self from non-self at a species-specific level. The immune systems of plants and mammals share multiple central elements, but further work will be required to understand the mechanisms and the selective benefits of an immunity response that is triggered by eDNA in a species-specific manner. Copyright © 2017 Elsevier Inc. All rights reserved.

Variable Gene Dispersal Conditions and Spatial Deforestation Patterns Can Interact to Affect Tropical Tree Conservation Outcomes

PubMed Central

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H.

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with ‘Near’ distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention. PMID:26000951

Variable gene dispersal conditions and spatial deforestation patterns can interact to affect tropical tree conservation outcomes.

PubMed

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with 'Near' distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention.

Antithrombotic activities of fucosylated chondroitin sulfates and their depolymerized fragments from two sea cucumbers.

PubMed

Liu, Xiaoxiao; Hao, Jiejie; Shan, Xindi; Zhang, Xiao; Zhao, Xiaoliang; Li, Qinying; Wang, Xiaojiang; Cai, Chao; Li, Guoyun; Yu, Guangli

2016-11-05

Fucosylated chondroitin sulfate (FCS), a glycosaminoglycan extracted from the body wall of sea cucumber, is a promising antithrombotic agent. The chemical structures of FCSc isolated from sea cucumber Cucumaria frondosa and its depolymerized fragment (dFCSc) were characterized for the first time. Additionally, anticoagulant and antithrombotic activities were evaluated in vitro and in vivo. The results demonstrated that dFCSc exhibited better antithrombotic-hemorrhagic ratio than native FCSc on the electrical induced arterial thrombosis model in rats. Compared to FCSt obtained from Thelenota ananas, FCSc possessed different sulfation patterns but similar antithrombotic effects. Therefore, sulfation pattern of FCS might not affect anticoagulation and antithrombosis as much as molecular weight may. Our results proposed a new point of view to understand the structure-activity relationship of FCS as alternative agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin

NASA Astrophysics Data System (ADS)

Lermyte, Frederik; Łącki, Mateusz Krzysztof; Valkenborg, Dirk; Gambin, Anna; Sobott, Frank

2017-01-01

Owing to its versatility, electron transfer dissociation (ETD) has become one of the most commonly utilized fragmentation techniques in both native and non-native top-down mass spectrometry. However, several competing reactions—primarily different forms of charge reduction—occur under ETD conditions, as evidenced by the distorted isotope patterns usually observed. In this work, we analyze these isotope patterns to compare the stability of nondissociative electron transfer (ETnoD) products, specifically noncovalent c/ z fragment complexes, across a range of ubiquitin conformational states. Using ion mobility, we find that more extended states are more prone to fragment release. We obtain evidence that for a given charge state, populations of ubiquitin ions formed either directly by electrospray ionization or through collapse of more extended states upon charge reduction, span a similar range of collision cross-sections. Products of gas-phase collapse are, however, less stabilized towards unfolding than the native conformation, indicating that the ions retain a memory of previous conformational states. Furthermore, this collapse of charge-reduced ions is promoted if the ions are `preheated' using collisional activation, with possible implications for the kinetics of gas-phase compaction.

Forest fragmentation in Massachusetts, USA: a town-level assessment using Morphological Spatial Pattern Analysis and affinity propagation

Treesearch

J. Rogan; T.M. Wright; J. Cardille; H. Pearsall; Y. Ogneva-Himmelberger; Rachel Riemann; Kurt Riitters; K. Partington

2016-01-01

Forest fragmentation has been studied extensively with respect to biodiversity loss, disruption of ecosystem services, and edge effects although the relationship between forest fragmentation and human activities is still not well understood. We classified the pattern of forests in Massachusetts using fragmentation indicators to address...

Analysis of sesterterpenoids from Aspergillus terreus using ESI-QTOF and ESI-IT.

PubMed

Wu, Zhi-Jun; Fang, Dong-Mei; Han, Dan; Li, Guo-You; Chen, Xiao-Zhen; Qi, Hua-Yi; Zhang, Guo-Lin

2010-01-01

Biosynthesis of terretonin was studied due to the interesting skeleton of this series of sesterterpenoids. Very recently, López-Gresa reported two new sesterterpenoids (terretonins E and F) which are inhibitors of the mammalian mitochondrial respiratory chain. Mass spectrometry (MS), especially tandem mass spectrometry, has been one of the most important physicochemical methods for the identification of trace natural products due to it rapidity, sensitivity and low levels of sample consumption. The potential application prospect and unique skeleton prompted us to study structural characterisation using MS. To obtain sufficient information for rapid structural elucidation of this class of compounds using MS. The elemental composition of the product ions was confirmed by low-energy ESI-CID-QTOF-MS/MS analyses. The fragmentation pathways were postulated on the basis of ESI-QTOF-MS/MS/MS and ESI-IT-MS(n) spectra. Common features and major differences between ESI-QTOF-MS/MS and IT-MS(n) spectra were compared. For ESI-QTOF-MS/MS/MS experiments, capillary exit voltage was raised to induce in-source dissociation. Ammonium acetate or acetic acid were added into solutions to improve the intensity of [M + H]+. The collision energy was optimised to achieve sufficient fragmentation. Some fragmentation pathways were unambiguously proposed by the variety of abundance of fragment ions at different collision energies even without MS(n) spectra. Fragmentation pathways of five representative sesterterpenoids were elucidated using ESI-QTOF-MS/MS/MS and ESI-IT-MS(n) in both positive- and negative-ion mode. The key group of characterising fragmentation profiles was ring B, and these fragmentation patterns are helpful to identify different types of sestertepenoids. Complementary information obtained from fragmentation experiments of [M + H]+ (or [M + NH4]+ and [M-H](-) precursor ions is especially valuable for rapid identification of this kind of sesterterpenoid.

[Preliminary analysis of retinal gene expression profile of diabetic rat].

PubMed

Mei, Yan; Zhou, Hong-ying; Xiang, Tao; Lu, You-guang; Li, Ai-dong; Tang, En-jie; Yang, Hui-jun

2005-10-01

Establishing the retinal gene expression profiles of non-diabetic rat and diabetic rat and comparing the profiles in order to analyze the possible genes related with diabetic retinopathy. The whole retinal transcriptional fragments of non-diabetic rat and 8-week diabetic rat were obtained by restriction fragments differential display-PCR (RFDD-PCR). Bioinformatic analysis of retinal gene expression was performed using soft wares, including Fragment Analysis. After comparison of the expression profiles, the related gene fragments of diabetic retinopathy were initially selected as the target gene of further approach. A total of 3639 significant fragments were obtained. By means of more than 3-fold contrast of fluorescent intensity as the differential expression standard, the authors got 840 differential fragments, accounting for 23.08% of the expressed numbers and including 5 visual related genes, 13 excitatory neruotransmitter genes and 3 inhibitory neurotransmitter genes. At the 8th week, the expression of Rhodopsin kinase, beta-arrestin, Phosducinìrod photoreceptor cGMP-gated channel and Rpe65 as well as iGlu R1-4 were down-regulated. mGluRs and GABA-Rs were all up-regulated, whereas the expression of GlyR was unchanged. These results prompt again that the changes in retinal nervous layer of rat have occurred at an early stage of diabetes. The genes expression pattern of visual related genes and excitatory and inhibitory neurotransmitters in rat diabetic retina have been involved in neuro-dysfunctions of diabetic retina.

Modelling fragmentations of aminoacids after resonant electron attachment: quantum evidence of possible direct -OH detachment

NASA Astrophysics Data System (ADS)

Panosetti, C.; Baccarelli, I.; Sebastianelli, F.; Gianturco, F. A.

2010-10-01

We investigate some aspects of the radiation damage mechanisms in biomolecules, focusing on the modelling of resonant fragmentation caused by the attachment of low-energy electrons (LEEs) initially ejected by biological tissues when exposed to ionizing radiation. Scattering equations are formulated within a symmetry-adapted, single-center expansion of both continuum and bound electrons, and the interaction forces are obtained from a combination of ab initio calculations and a nonempirical model of exchange and correlation effects developped in our group. We present total elastic scattering cross-sections and resonance features obtained for the equilibrium geometries of glycine, alanine, proline and valine. Our results at those geometries of the target molecules are briefly shown to qualitatively explain some of the fragmentation patterns obtained in experiments. We further carry out a one-dimensional (1D) modeling for the dynamics of intramolecular energy transfers mediated by the vibrational activation of selected bonds: our calculations indicate that resonant electron attachment to glycine can trigger direct, dissociative evolution of the complex into (Gly-OH)- and -OH losses, while they also find that the same process does not occur via a direct, 1D dissociative path in the larger aminoacids of the present study.

Biosensor-based small molecule fragment screening with biolayer interferometry

NASA Astrophysics Data System (ADS)

Wartchow, Charles A.; Podlaski, Frank; Li, Shirley; Rowan, Karen; Zhang, Xiaolei; Mark, David; Huang, Kuo-Sen

2011-07-01

Biosensor-based fragment screening is a valuable tool in the drug discovery process. This method is advantageous over many biochemical methods because primary hits can be distinguished from non-specific or non-ideal interactions by examining binding profiles and responses, resulting in reduced false-positive rates. Biolayer interferometry (BLI), a technique that measures changes in an interference pattern generated from visible light reflected from an optical layer and a biolayer containing proteins of interest, is a relatively new method for monitoring small molecule interactions. The BLI format is based on a disposable sensor that is immersed in 96-well or 384-well plates. BLI has been validated for small molecule detection and fragment screening with model systems and well-characterized targets where affinity constants and binding profiles are generally similar to those obtained with surface plasmon resonsance (SPR). Screens with challenging targets involved in protein-protein interactions including BCL-2, JNK1, and eIF4E were performed with a fragment library of 6,500 compounds, and hit rates were compared for these targets. For eIF4E, a protein containing a PPI site and a nucleotide binding site, results from a BLI fragment screen were compared to results obtained in biochemical HTS screens. Overlapping hits were observed for the PPI site, and hits unique to the BLI screen were identified. Hit assessments with SPR and BLI are described.

Map misclassifications can cause large errors in landscape pattern indices: examples from habitat fragmentation.

Treesearch

William T. Langford; Sarah E. Gergel; Thomas G. Dietterich; Warren Cohen

2006-01-01

Although habitat fragmentation is one of the greatest threats to biodiversity worldwide, virtually no attention has been paid to the quantification of error in fragmentation statistics. Landscape pattern indices (LPIs), such as mean patch size and number of patches, are routinely used to quantify fragmentation and are often calculated using remote sensing imagery that...

Application of heteroduplex analysis for detecting variation within the growth hormone 2 gene in Salmo trutta L. (brown trout).

PubMed

Gross, R; Nilsson, J

1995-03-01

A new method to detect variation at a single copy nuclear gene in brown trout, Salmo trutta L., is provided. The technique entails (i) selective gene amplification by the polymerase chain reaction (PCR), (ii) digestion of amplification products by restriction endonucleases to obtain fragments of suitable size, (iii) hybridization with heterologous DNA followed by denaturation and reannealing to obtain heteroduplex molecules, and (iv) screening for variation in polyacrylamide gels. Variation was studied within a growth hormone 2 gene 1489 bp segment and polymorphism was detected in two HinfI-digested fragments. Formation of different heteroduplex patterns in experimental mixtures of digested amplification products from brown trout and Atlantic salmon, Salmo salar L., allowed us to determine the genotype of the brown trout. Polymorphism was observed in four out of six studied populations.

Sequence-specific "gene signatures" can be obtained by PCR with single specific primers at low stringency.

PubMed Central

Pena, S D; Barreto, G; Vago, A R; De Marco, L; Reinach, F C; Dias Neto, E; Simpson, A J

1994-01-01

Low-stringency single specific primer PCR (LSSP-PCR) is an extremely simple PCR-based technique that detects single or multiple mutations in gene-sized DNA fragments. A purified DNA fragment is subjected to PCR using high concentrations of a single specific oligonucleotide primer, large amounts of Taq polymerase, and a very low annealing temperature. Under these conditions the primer hybridizes specifically to its complementary region and nonspecifically to multiple sites within the fragment, in a sequence-dependent manner, producing a heterogeneous set of reaction products resolvable by electrophoresis. The complex banding pattern obtained is significantly altered by even a single-base change and thus constitutes a unique "gene signature." Therefore LSSP-PCR will have almost unlimited application in all fields of genetics and molecular medicine where rapid and sensitive detection of mutations and sequence variations is important. The usefulness of LSSP-PCR is illustrated by applications in the study of mutants of smooth muscle myosin light chain, analysis of a family with X-linked nephrogenic diabetes insipidus, and identity testing using human mitochondrial DNA. Images PMID:8127912

Dynamic of negative ions in potassium-D-ribose collisions.

PubMed

Almeida, D; Ferreira da Silva, F; García, G; Limão-Vieira, P

2013-09-21

We present negative ion formation from collisions of neutral potassium atoms with D-ribose (C5H10O5), the sugar unit in the DNA/RNA molecule. From the negative ion time-of-flight (TOF) mass spectra, OH(-) is the main fragment detected in the collision range 50-100 eV accounting on average for 50% of the total anion yield. Prominence is also given to the rich fragmentation pattern observed with special attention to O(-) (16 m/z) formation. These results are in sharp contrast to dissociative electron attachment experiments. The TOF mass spectra assignments show that these channels are also observed, albeit with a much lower relative intensity. Branching ratios of the most abundant fragment anions as a function of the collision energy are obtained, allowing to establish a rationale on the collision dynamics.

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bathany, Katell; Owens, Neil W.; Guichard, Gilles; Schmitter, Jean-Marie

2013-03-01

This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N'H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.

Identification of substances migrating from plastic baby bottles using a combination of low-resolution and high-resolution mass spectrometric analysers coupled to gas and liquid chromatography.

PubMed

Onghena, Matthias; Van Hoeck, Els; Van Loco, Joris; Ibáñez, María; Cherta, Laura; Portolés, Tania; Pitarch, Elena; Hernandéz, Félix; Lemière, Filip; Covaci, Adrian

2015-11-01

This work presents a strategy for elucidation of unknown migrants from plastic food contact materials (baby bottles) using a combination of analytical techniques in an untargeted approach. First, gas chromatography (GC) coupled to mass spectrometry (MS) in electron ionisation mode was used to identify migrants through spectral library matching. When no acceptable match was obtained, a second analysis by GC-(electron ionisation) high resolution mass spectrometry time of flight (TOF) was applied to obtain accurate mass fragmentation spectra and isotopic patterns. Databases were then searched to find a possible elemental composition for the unknown compounds. Finally, a GC hybrid quadrupole-TOF-MS with an atmospheric pressure chemical ionisation source was used to obtain the molecular ion or the protonated molecule. Accurate mass data also provided additional information on the fragmentation behaviour as two acquisition functions with different collision energies were available (MS(E) approach). In the low-energy function, limited fragmentation took place, whereas for the high-energy function, fragmentation was enhanced. For less volatile unknowns, ultra-high pressure liquid chromatography-quadrupole-TOF-MS was additionally applied. Using a home-made database containing common migrating compounds and plastic additives, tentative identification was made for several positive findings based on accurate mass of the (de)protonated molecule, product ion fragments and characteristic isotopic ions. Six illustrative examples are shown to demonstrate the modus operandi and the difficulties encountered during identification. The combination of these techniques was proven to be a powerful tool for the elucidation of unknown migrating compounds from plastic baby bottles. Copyright © 2015 John Wiley & Sons, Ltd.

Genotypic characterization of psittacid herpesvirus isolates from Brazil.

PubMed

Luppi, Marcela Miranda; Luiz, Ana Paula Moreira Franco; Coelho, Fabiana Magalhães; Ecco, Roselene; da Fonseca, Flávio Guimarães; Resende, Mauricio

2016-01-01

Thirty-six isolates of psittacid herpesvirus (PsHV), obtained from 12 different species of psittacids in Brazil, were genotypically characterized by restriction fragment length polymorphism (RFLP) analysis and PCR amplification. RFLP analysis with the PstI enzyme revealed four distinct restriction patterns (A1, X, W and Y), of which only A1 (corresponding to PsHV-1) had previously been described. To study PCR amplification patterns, six pairs of primers were used. Using this method, six variants were identified, of which, variants 10, 8, and 9 (in this order) were most prevalent, followed by variants 1, 4, and 5. It was not possible to correlate the PCR and RFLP patterns. Twenty-nine of the 36 isolates were shown to contain a 419bp fragment of the UL16 gene, displaying high similarity to the PsHV-1 sequences available in GenBank. Comparison of the results with the literature data suggests that the 36 Brazilian isolates from this study belong to genotype 1 and serotype 1. Copyright © 2015 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Gas-phase fragmentation of peptides by MALDI in-source decay with limited amide hydrogen (1H/2H) scrambling.

PubMed

Bache, Nicolai; Rand, Kasper D; Roepstorff, Peter; Jørgensen, Thomas J D

2008-08-15

To achieve a fundamental understanding of the function of proteins and protein complexes at the molecular level, it is crucial to obtain a detailed knowledge about their dynamic and structural properties. The kinetics of backbone amide hydrogen exchange is intimately linked to the structural dynamics of the protein, and in recent years, the monitoring of the isotopic exchange of these hydrogens by mass spectrometry has become a recognized method. At present, the resolution of this method is, however, limited and single-residue resolution is typically only obtained for a few residues in a protein. It would therefore be desirable if gas-phase fragmentation could be used to localize incorporated deuterons as this would ultimately lead to single-residue resolution. A central obstacle for this approach is, however, the occurrence of intramolecular migration of amide hydrogens upon activation of the gaseous protein (i.e., hydrogen scrambling). Here we investigate the occurrence of scrambling in selectively labeled peptides upon fragmentation by matrix-assisted laser desorption/ionization in-source decay (MALDI ISD). We have utilized peptides with a unique regioselective deuterium incorporation that allows us to accurately determine the extent of scrambling upon fragmentation. Our results show that the level of scrambling upon MALDI ISD is so low that the solution deuteration pattern is readily apparent in the gas-phase fragment ions. These results suggest that MALDI ISD may prove useful for hydrogen exchange studies of purified peptides and small proteins.

Monte Carlo simulation as a tool to predict blasting fragmentation based on the Kuz Ram model

NASA Astrophysics Data System (ADS)

Morin, Mario A.; Ficarazzo, Francesco

2006-04-01

Rock fragmentation is considered the most important aspect of production blasting because of its direct effects on the costs of drilling and blasting and on the economics of the subsequent operations of loading, hauling and crushing. Over the past three decades, significant progress has been made in the development of new technologies for blasting applications. These technologies include increasingly sophisticated computer models for blast design and blast performance prediction. Rock fragmentation depends on many variables such as rock mass properties, site geology, in situ fracturing and blasting parameters and as such has no complete theoretical solution for its prediction. However, empirical models for the estimation of size distribution of rock fragments have been developed. In this study, a blast fragmentation Monte Carlo-based simulator, based on the Kuz-Ram fragmentation model, has been developed to predict the entire fragmentation size distribution, taking into account intact and joints rock properties, the type and properties of explosives and the drilling pattern. Results produced by this simulator were quite favorable when compared with real fragmentation data obtained from a blast quarry. It is anticipated that the use of Monte Carlo simulation will increase our understanding of the effects of rock mass and explosive properties on the rock fragmentation by blasting, as well as increase our confidence in these empirical models. This understanding will translate into improvements in blasting operations, its corresponding costs and the overall economics of open pit mines and rock quarries.

Activity budget and ranging patterns of Colobus vellerosus in forest fragments in central Ghana.

PubMed

Wong, Sarah N P; Sicotte, Pascale

2007-01-01

The forest fragments surrounding the 192-ha Boabeng-Fiema Monkey Sanctuary (BFMS) in central Ghana contain small populations of Colobus vellerosus. Data were collected on activity budget, ranging patterns and habitat use of 3 groups living in these small fragments in August-November 2003, and compared to 3 BFMS groups. Fragment groups spent less time moving and more time resting than BFMS groups. Home ranges of fragment groups tended to be smaller than those of BFMS groups. Fragment and BFMS groups used similarly sized trees. Comparisons of activity budget and ranging between fragments and the BFMS suggest that fragment habitat quality was sufficient to sustain current numbers. These behavioral trends are consistent with a concurrent study that we conducted investigating ecological quality in the same fragments. Copyright 2007 S. Karger AG, Basel.

Mass Ordering of Spectra from Fragmentation of Saturated Gluon States in High-Multiplicity Proton-Proton Collisions

DOE PAGES

Schenke, Björn; Schlichting, Sören; Tribedy, Prithwish; ...

2016-10-14

The mass ordering of mean transverse momentummore » $$\\langle$$p T$$\\rangle$$ and of the Fourier harmonic coefficient v 2 (p T) of azimuthally anisotropic particle distributions in high energy hadron collisions is often interpreted as evidence for the hydrodynamic flow of the matter produced. We investigate an alternative initial state interpretation of this pattern in high-multiplicity proton-proton collisions at the LHC. The QCD Yang-Mills equations describing the dynamics of saturated gluons are solved numerically with initial conditions obtained from the color-glass-condensate-based impact-parameter-dependent glasma model. The gluons are subsequently fragmented into various hadron species employing the well established Lund string fragmentation algorithm of the pythia event generator. Lastly, we find that this initial state approach reproduces characteristic features of bulk spectra, in particular, the particle mass dependence of $$\\langle$$p T$$\\rangle$$ and v 2 (p T).« less

A STUDY OF MEIOSIS IN THE PROGENY OF X-IRRADIATED LUZULA PURPUREA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nordenskiold, H.

1963-01-01

In Luzula the chromosomes have diffuse or nonlocalized centromeres; thus, if the chromosomes are broken or rearranged by x-ray treatment, the changed chromosome patterns may survive through the mitotic cell divisions, on account of the centromeric action along the whole chromosomes. Hence, such plants with diffuse centromeres are able to survive and reach adult stages in spite of the fact that their chromosomes have been rearranged or broken by x-ray treatment of the seedlings. A study was made of plants selected from the progeny of material treated as seedlings with 1000 or 2500 r. Plants treated with stronger doses (5000more » to 10000 r) were almost or completely sterile. The chromosome patterns of the root tips of X/sub 2/ plants were investigated in order to find plants with desirable chrom-osome patterns for the meiotic investigation. The x-irradiated plants themselves showed intricate metaphasic configurations during meiosis. The separation of the multi-associations at first anaphase is cytologically equational, and in most cases without bridges. Migration of chromatids during second anaphase is also regular without lagging chromosomes, but chromosome sets of 4 tetrad cells usually become unbalanced, causing reduced fertility. The mitotic chromosome patterns of X/sub 2/ plants showed three categories of patterns: 2n = 6; most of these plants have all chromosomes the same size, but some of them possess one long and one short chromosome indicating a reciprocal translocation between two chromosomes; 2n = 7, with one of the original chromosomes fragmented into two pieces; and 2n = 8, with two of the original chromosomes fragmented into two pieces each. A study was made of meiosis in X/ sub 2/ plants with a cytologically observable rearrangement in the root tips, determined as a reciprocal progeny plants were obtained. Meiosis of X/sub 2/ plants heterozygous for one chromosome fragmented into two pieces, i.e., possessing 2n = 7 with five normal-sized and two small half-sized chromosomes, was also studied. The expected course of meiosis was realized, giving rise to four balanced chromosome sets of the tetrads, two of them containing three normal- sized chromosomes and the remaining two having two normal-sized and two half- sized ones. These studied plants were all fertile. Examination of somatic chromosome patterns of the progenies originating from the X/sub 2/ plants heterozygous for one fragmented chromosome revealed the three expected chromosome patterns, i.e., 2n =6, 2n =7, 2n =8. X/sub 2/ plants with 2n =8 were homozygous for the fragmented chromosome, and had a completely regular meiosis with two large and two small bivalents during first metaphase and a regular pairing and separation during the second division. Consequently they gave rise to a fertile strain with a constart chromosome pattern. The origin of the aneuploidy and endonuclear polyploidy of material with diffuse centromeres was discussed in relation to the survival of the fragmented chromosomes in L. purpurea. The survival of broken chromosomes through consecutive generations thus gives an explanation of the occurrence of aneuploid chromosome numbers in material with diffuse centromeres. However, no interpretation of the phenomenon causing the survival of the fragments was provided by this study, since sufficient knowledge about the nature of the diffuse or nonlocalized centromeres is unavailable. (BBB)« less

Partial Purification and Characterization of Restriction Endonuclease from Neisseria meningitidis.

DTIC Science & Technology

1983-12-01

by centrifugation at 15,000 x g for 10 min. Preparation of Cell-Free Extract The cell pellet was suspended in 10 mL of Tris-HCI buffer pH 7.6 (Tris, 20...free extract (CFE) was obtained by centrifugation at 100,000 x g for I h. To the CFE, glycerol was added to a final concentration of 10% and stored at... extract obtained from N. meningilidis when incubated with A DNA and analyzed by agarose gel electrophoresis did not give a clean fragmentation pattern

Physical and genetic map of Streptococcus thermophilus A054.

PubMed Central

Roussel, Y; Pebay, M; Guedon, G; Simonet, J M; Decaris, B

1994-01-01

The three restriction endonucleases SfiI, BssHII, and SmaI were found to generate fragments with suitable size distributions for mapping the genome of Streptococcus thermophilus A054. A total of 5, 8, and 24 fragments were produced with SfiI, BssHII, and SmaI, respectively. An average genome size of 1,824 kb was determined by summing the total fragment sizes obtained by digestions with these three enzymes. Partial and multiple digestions of genomic DNA in conjunction with Southern hybridization were used to map SfiI, BssHII, and SmaI fragments. All restriction fragments were arranged in a unique circular chromosome. Southern hybridization analysis with specific probes allowed 23 genetic markers to be located on the restriction map. Among them, six rrn loci were precisely located. The area of the chromosome containing the ribosomal operons was further detailed by mapping some of the ApaI and SgrAI sites. Comparison of macrorestriction patterns from three clones derived from strain A054 revealed two variable regions in the chromosome. One was associated with the tandem rrnD and rrnE loci, and the other was mapped in the region of the lactose operon. Images PMID:8002562

Strong and nonlinear effects of fragmentation on ecosystem service provision at multiple scales

NASA Astrophysics Data System (ADS)

Mitchell, Matthew G. E.; Bennett, Elena M.; Gonzalez, Andrew

2015-09-01

Human actions, such as converting natural land cover to agricultural or urban land, result in the loss and fragmentation of natural habitat, with important consequences for the provision of ecosystem services. Such habitat loss is especially important for services that are supplied by fragments of natural land cover and that depend on flows of organisms, matter, or people across the landscape to produce benefits, such as pollination, pest regulation, recreation and cultural services. However, our quantitative knowledge about precisely how different patterns of landscape fragmentation might affect the provision of these types of services is limited. We used a simple, spatially explicit model to evaluate the potential impact of natural land cover loss and fragmentation on the provision of hypothetical ecosystem services. Based on current literature, we assumed that fragments of natural land cover provide ecosystem services to the area surrounding them in a distance-dependent manner such that ecosystem service flow depended on proximity to fragments. We modeled seven different patterns of natural land cover loss across landscapes that varied in the overall level of landscape fragmentation. Our model predicts that natural land cover loss will have strong and unimodal effects on ecosystem service provision, with clear thresholds indicating rapid loss of service provision beyond critical levels of natural land cover loss. It also predicts the presence of a tradeoff between maximizing ecosystem service provision and conserving natural land cover, and a mismatch between ecosystem service provision at landscape versus finer spatial scales. Importantly, the pattern of landscape fragmentation mitigated or intensified these tradeoffs and mismatches. Our model suggests that managing patterns of natural land cover loss and fragmentation could help influence the provision of multiple ecosystem services and manage tradeoffs and synergies between services across different human-dominated landscapes.

Spectroscopy analysis of phenolic and sugar patterns in a food grade chestnut tannin.

PubMed

Ricci, A; Lagel, M-C; Parpinello, G P; Pizzi, A; Kilmartin, P A; Versari, A

2016-07-15

Tannin of chestnut (Castanea sativa Mill.) wood, commonly used in winemaking was characterised with a spectroscopy qualitative approach that revealed its phenolic composition: several vibrational diagnostic bands assigned using the Attenuated Total Reflectance-Infrared Spectroscopy, and fragmentation patterns obtained using the Laser-Desorption-Ionization Time-of-Flight technique evidenced polygalloylglucose, e.g. castalagin/vescalagin-like structures as the most representative molecules, together with sugar moieties. The implication of these findings on winemaking application and the potential influence of the chemical structure on the sensory properties of wine are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.

PubMed

Asara, John M; Schweitzer, Mary H; Freimark, Lisa M; Phillips, Matthew; Cantley, Lewis C

2007-04-13

Fossilized bones from extinct taxa harbor the potential for obtaining protein or DNA sequences that could reveal evolutionary links to extant species. We used mass spectrometry to obtain protein sequences from bones of a 160,000- to 600,000-year-old extinct mastodon (Mammut americanum) and a 68-million-year-old dinosaur (Tyrannosaurus rex). The presence of T. rex sequences indicates that their peptide bonds were remarkably stable. Mass spectrometry can thus be used to determine unique sequences from ancient organisms from peptide fragmentation patterns, a valuable tool to study the evolution and adaptation of ancient taxa from which genomic sequences are unlikely to be obtained.

Effects of fragmentation on the spatial ecology of the California Kingsnake (Lampropeltis californiae)

USGS Publications Warehouse

Anguiano, Michael P.; Diffendorfer, James E.

2015-01-01

We investigated the spatial ecology of the California Kingsnake (Lampropeltis californiae) in unfragmented and fragmented habitat with varying patch sizes and degrees of exposure to urban edges. We radiotracked 34 Kingsnakes for up to 3 yr across four site types: interior areas of unfragmented ecological reserves, the urbanized edge of these reserves, large habitat fragments, and small habitat fragments. There was no relationship between California Kingsnake movements and the degree of exposure to urban edges and fragmentation. Home range size and movement patterns of Kingsnakes on edges and fragments resembled those in unfragmented sites. Average home-range size on each site type was smaller than the smallest fragment in which snakes were tracked. The persistence of California Kingsnakes in fragmented landscapes may be related directly to their small spatial movement patterns, home-range overlap, and ability to use urban edge habitat.

Quantifying landscape pattern and assessing the land cover changes in Piatra Craiului National Park and Bucegi Natural Park, Romania, using satellite imagery and landscape metrics.

PubMed

Vorovencii, Iosif

2015-11-01

Protected areas of Romania have enjoyed particular importance after 1989, but, at the same time, they were subject to different anthropogenic and natural pressures which resulted in the occurrence of land cover changes. These changes have generally led to landscape degradation inside and at the borders of the protected areas. In this article, 12 landscape metrics were used in order to quantify landscape pattern and assess land cover changes in two protected areas, Piatra Craiului National Park (PCNP) and Bucegi Natural Park (BNP). The landscape metrics were obtained from land cover maps derived from Landsat Thematic Mapper (TM) and Landsat Enhanced Thematic Mapper Plus (ETM+) images from 1987, 1993, 2000, 2009 and 2010. Three land cover classes were analysed in PCNP and five land cover map classes in BNP. The results show a landscape fragmentation trend for both parks, affecting different types of land covers. Between 1987 and 2010, in PCNP fragmentation was, in principle, the result not only of anthropogenic activities such as forest cuttings and illegal logging but also of natural causes. In BNP, between 1987 and 2009, the fragmentation affected the pasture which resulted in the occurrence of bare land and rocky areas because of the erosion on the Bucegi Plateau.

Computation of pattern invariance in brain-like structures.

PubMed

Ullman, S; Soloviev, S

1999-10-01

A fundamental capacity of the perceptual systems and the brain in general is to deal with the novel and the unexpected. In vision, we can effortlessly recognize a familiar object under novel viewing conditions, or recognize a new object as a member of a familiar class, such as a house, a face, or a car. This ability to generalize and deal efficiently with novel stimuli has long been considered a challenging example of brain-like computation that proved extremely difficult to replicate in artificial systems. In this paper we present an approach to generalization and invariant recognition. We focus our discussion on the problem of invariance to position in the visual field, but also sketch how similar principles could apply to other domains.The approach is based on the use of a large repertoire of partial generalizations that are built upon past experience. In the case of shift invariance, visual patterns are described as the conjunction of multiple overlapping image fragments. The invariance to the more primitive fragments is built into the system by past experience. Shift invariance of complex shapes is obtained from the invariance of their constituent fragments. We study by simulations aspects of this shift invariance method and then consider its extensions to invariant perception and classification by brain-like structures.

Synthesis and Mass Spectra of Butenyltin Compounds

DTIC Science & Technology

1989-03-01

activities or operations. One instance of this concern has focused on the Navy’s use of tributyltin compounds as antifoulants on ships’ hulls. Such...butene, and 1-chloro- 2-butene were obtained from Pfaltz & Bauer (Waterbury, CT). Resublimed magne- sium chips, tetrabutyltin and tributyltin bromide...preferential elimination of R minus R to form RSn ’from R3Sn + The fragmentation patterns of tributyltin bromide and tributenyltin bromides are dominated

Comprehensive Study On The Metastable Negative Ion Fragmentation Of Individual Dna Components And Larger Oligonucleotides

NASA Astrophysics Data System (ADS)

Ingolfsson, O.; Flosadottir, H. D.; Omarsson, B.; Ilko, B.

2010-07-01

Here we present a systematic study on the unimolecular decay pathways of the deprotonated building blocks of DNA and RNA to address the following questions: 1. Are the negative ion fragmentation patterns observed in the metastable decay of individual DNA components still evident when these are combined to larger oligonucleotides? 2. What is the significance of the charge location in determining the fragmentation pathways in the metastable decay process? 3. Are those metastable decay channels relevant in dissociative electron attachment to DNA components? To address these questions we have studied the fragmentation patterns of the deprotonated ribose and ribose 5'-monophosphate, the fragmentation patterns of the individual bases, all nucleosides and all 2'-deoxynucleosides as well as the individual nucleotides and several combinations of hexameric oligonucleotides. Furthermore, to understand the significance of the charge location in determining the fragmentation path in the metastable decay process of these deprotonated ions we have also studied modified uridine and guanosine. These have been modified to block different deprotonation sites and thus to control the initial step in the in the fragmentation process i.e. the site of deprotonation. In addition to our experimental approach we have also simulated the metastable fragmentation of the deprotonated uridine and 2'-deoxyguanosine to clarify the mechanisms and fragmentation patterns observed. Where data is available, the results are compared to dissociative electron attachment to DNA components and discussed in context to the underlying mechanism. Experiments on modified nucleosides where selected deprotonation sites have been blocked are used to verify the predicted reaction paths and imulations on uridine and 2'-deoxyguanosine are compared to the experimental results and used to shed light on the mechanisms involved.

Induced in-source fragmentation pattern of certain novel (1Z,2E)-N-(aryl)propanehydrazonoyl chlorides by electrospray mass spectrometry (ESI-MS/MS)

PubMed Central

2013-01-01

Background Collision induced dissociation (CID) in the triple quadrupole mass spectrometer system (QQQ) typically yields more abundant fragment ions than those produced with resonance excitation in the presence of helium gas in the ion trap mass spectrometer system (IT). Detailed product ion spectra can be obtained from one stage MS2 scan using the QQQ. In contrast, generating the same number of fragment ions in the ion trap requires multiple stages of fragmentation (MSn) using CID via in-trap resonance excitation with the associated time penalties and drop in sensitivity. Results The use of in-source fragmentation with electrospray ionization (ESI) followed by product ion scan (MS2) in a triple quadrupole mass spectrometer system, was demonstrated. This process enhances the qualitative power of tandem mass spectrometry to simulate the MS3 of ion trap for a comprehensive study of fragmentation mechanisms. A five pharmacologically significant (1Z, 2E)-N-arylpropanehydrazonoyl chlorides (3a-e) were chosen as model compounds for this study. In this work, detailed fragmentation pathways were elucidated by further dissociation of each fragment ion in the ion spectrum, essentially, by incorporating fragmentor voltage induced dissociation (in-source fragmentation) and isolation of fragments in a quadrupole cell Q1. Subsequently, CID occurs in cell, Q2, and fragment ions are analyzed in Q3 operated in product ion mode this process can be referred to as pseudo-MS3 scan mode. Conclusions This approach allowed unambiguous assignment of all fragment ions using tandem mass spectrometer and provided adequate sensitivity and selectivity. It is beneficial for structure determination of unknown trace components. The data presented in this paper provide useful information on the effect of different substituents on the ionization/fragmentation processes and can be used in the characterization of this important class of compounds. PMID:23351484

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish.

PubMed

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-08-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change - an important component of biological conservation and ecosystem management.

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish

PubMed Central

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-01-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change – an important component of biological conservation and ecosystem management. PMID:26240605

The impact of habitat fragmentation on tsetse abundance on the plateau of eastern Zambia.

PubMed

Ducheyne, E; Mweempwa, C; De Pus, C; Vernieuwe, H; De Deken, R; Hendrickx, G; Van den Bossche, P

2009-09-01

Tsetse-transmitted human or livestock trypanosomiasis is one of the major constraints to rural development in sub-Saharan Africa. The epidemiology of the disease is determined largely by tsetse fly density. A major factor, contributing to tsetse population density is the availability of suitable habitat. In large parts of Africa, encroachment of people and their livestock resulted in a destruction and fragmentation of such suitable habitat. To determine the effect of habitat change on tsetse density a study was initiated in a tsetse-infested zone of eastern Zambia. The study area represents a gradient of habitat change, starting from a zone with high levels of habitat destruction and ending in an area where livestock and people are almost absent. To determine the distribution and density of the fly, tsetse surveys were conducted throughout the study area in the dry and in the rainy season. Landsat ETM+ imagery covering the study area were classified into four land cover classes (munga, miombo, agriculture and settlements) and two auxiliary spectral classes (clouds and shadow) using a Gaussian Maximum Likelihood Classifier. The classes were regrouped into natural vegetation and agricultural zone. The binary images were overlaid with hexagons to obtain the spatial spectrum of spatial pattern. Hexagonal coverage was selected because of its compact and regular form. To identify scale-specific spatial patterns and associated entomological phenomena, the size of the hexagonal coverage was varied (250 and 500 m). Per coverage, total class area, mean patch size, number of patches and patch size standard deviation were used as fragmentation indices. Based on the fragmentation index values, the study zone was classified using a Partitioning Around Mediods (PAM) method. The number of classes was determined using the Wilks' lambda coefficient. To determine the impact of habitat fragmentation on tsetse abundance, the correlation between the fragmentation indices and the index of apparent density of the flies was determined and habitat changes most affecting tsetse abundance was identified. From this it followed that there is a clear relationship between habitat fragmentation and the abundance of tsetse flies. Heavily fragmented areas have lower numbers of tsetse flies, but when the fragmentation of natural vegetation decreases, the number of tsetse flies increases following a sigmoidal-like curve.

Deforestation and fragmentation of natural forests in the upper Changhua watershed, Hainan, China: implications for biodiversity conservation.

PubMed

Zhai, De-Li; Cannon, Charles H; Dai, Zhi-Cong; Zhang, Cui-Ping; Xu, Jian-Chu

2015-01-01

Hainan, the largest tropical island in China, belongs to the Indo-Burma biodiversity hotspot. The Changhua watershed is a center of endemism for plants and birds and the cradle of Hainan's main rivers. However, this area has experienced recent and ongoing deforestation and habitat fragmentation. To quantify habitat loss and fragmentation of natural forests, as well as the land-cover changes in the Changhua watershed, we analyzed Landsat images obtained in 1988, 1995, and 2005. Land-cover dynamics analysis showed that natural forests increased in area (97,909 to 104,023 ha) from 1988 to 1995 but decreased rapidly to 76,306 ha over the next decade. Rubber plantations increased steadily throughout the study period while pulp plantations rapidly expanded after 1995. Similar patterns of land cover change were observed in protected areas, indicating a lack of enforcement. Natural forests conversion to rubber and pulp plantations has a general negative effect on biodiversity, primarily through habitat fragmentation. The fragmentation analysis showed that natural forests area was reduced and patch number increased, while patch size and connectivity decreased. These land-cover changes threatened local biodiversity, especially island endemic species. Both natural forests losses and fragmentation should be stopped by strict enforcement to prevent further damage. Preserving the remaining natural forests and enforcing the status of protected areas should be a management priority to maximize the watershed's biodiversity conservation value.

The investigation of substituent effects on the fragmentation pathways of pentacoordinated phenoxyspirophosphoranes by ESI-MSn.

PubMed

Cui, Xiaoyan; Sun, Can; Zhao, Pei; Wang, Yanyan; Guo, Yanchun; Zhao, Yufen; Cao, Shuxia

2018-04-01

The fragmentation pathways of pentacoordinated phenoxyspirophosphoranes were investigated in the positive mode by electrospray ionization multistage mass spectrometry. The results demonstrate that the sodium adducts of the title compounds undergo two competitive fragmentation pathways, and the fragmentation patterns are heavily dependent on the various substituent patterns at the phenolic group. An electron-withdrawing substituent at the ortho-position always results in the removal of a corresponding phenol analogue, while cleavage by spiroring opening becomes the predominant fragmentation pathway if an electron-donating substituent is at the phenolic group. The substituent effects on the competitive fragmentation pathways were further elucidated by theoretical calculations, single crystal structure analysis, and high-resolution mass spectrometry. The results contribute to the understanding of the gas-phase fragmentation reactions and the structure identification of spirophosphorane analogues by electrospray ionization multistage mass spectrometry. Copyright © 2018 John Wiley & Sons, Ltd.

Molecular analysis of RAPD DNA based markers: their potential use for the detection of genetic variability in jojoba (Simmondsia chinensis L Schneider).

PubMed

Amarger, V; Mercier, L

1995-01-01

We have applied the recently developed technique of random amplified polymorphic DNA (RAPD) for the discrimination between two jojoba clones at the genomic level. Among a set of 30 primers tested, a simple reproducible pattern with three distinct fragments for clone D and two distinct fragments for clone E was obtained with primer OPB08. Since RAPD products are the results of arbitrarily priming events and because a given primer can amplify a number of non-homologous sequences, we wondered whether or not RAPD bands, even those of similar size, were derived from different loci in the two clones. To answer this question, two complementary approaches were used: i) cloning and sequencing of the amplification products from clone E; and ii) complementary Southern analysis of RAPD gels using cloned or amplified fragments (directly recovered from agarose gels) as RFLP probes. The data reported here show that the RAPD reaction generates multiple amplified fragments. Some fragments, although resolved as a single band on agarose gels, contain different DNA species of the same size. Furthermore, it appears that the cloned RAPD products of known sequence that do not target repetitive DNA can be used as hybridization probes in RFLP to detect a polymorphism among individuals.

Comparative analysis by polymerase chain reaction amplified minicircles of kinetoplast DNA of a stable strain of Trypanosoma cruzi from São Felipe, Bahia, its clones and subclones: possibility of predominance of a principal clone in this area.

PubMed

Campos, R F; Gonçalves, M S; dos Reis, E A; dos Reis, M G; Andrade, S G

1999-01-01

Molecular characterization of one stable strain of Trypanosoma cruzi, the 21 SF, representative of the pattern of strains isolated from the endemic area of São Felipe, State of Bahia, Brazil, maintained for 15 years in laboratory by serial passages in mice and classified as biodeme Type II and zymodeme 2 has been investigated. The kinetoplast DNA (kDNA) of parental strain, 5 clones and 14 subclones were analyzed. Schizodeme was established by comparative study of the fragments obtained from digestion of the 330-bp fragments amplified by polymerase chain reaction (PCR) from the variable regions of the minicircles, and digested by restriction endonucleases Rsa I and Hinf I. Our results show a high percentual of similarity between the restriction fragment length polymorphism (RFLP) for the parental strain and its clones and among these individual clones and their subclones at a level of 80 to 100%. This homology indicates a predominance of the same "principal clone" in the 21SF strain and confirms the homogeneity previously observed at biological and isozymic analysis. These results suggest the possibility that the T. cruzi strains with similar biological and isoenzymic patterns, circulating in this endemic area, are representative of one dominant clone. The presence of "principal clones" could be responsible for a predominant tropism of the parasites for specific organs and tissues and this could contribute to the pattern of clinico-pathological manifestations of Chagas's disease in one geographical area.

A Computational/Experimental Platform for Investigating Three-Dimensional Puzzle Solving of Comminuted Articular Fractures

PubMed Central

Thomas, Thaddeus P.; Anderson, Donald D.; Willis, Andrew R.; Liu, Pengcheng; Frank, Matthew C.; Marsh, J. Lawrence; Brown, Thomas D.

2011-01-01

Reconstructing highly comminuted articular fractures poses a difficult surgical challenge, akin to solving a complicated three-dimensional (3D) puzzle. Pre-operative planning using CT is critically important, given the desirability of less invasive surgical approaches. The goal of this work is to advance 3D puzzle solving methods toward use as a pre-operative tool for reconstructing these complex fractures. Methodology for generating typical fragmentation/dispersal patterns was developed. Five identical replicas of human distal tibia anatomy, were machined from blocks of high-density polyetherurethane foam (bone fragmentation surrogate), and were fractured using an instrumented drop tower. Pre- and post-fracture geometries were obtained using laser scans and CT. A semi-automatic virtual reconstruction computer program aligned fragment native (non-fracture) surfaces to a pre-fracture template. The tibias were precisely reconstructed with alignment accuracies ranging from 0.03-0.4mm. This novel technology has potential to significantly enhance surgical techniques for reconstructing comminuted intra-articular fractures, as illustrated for a representative clinical case. PMID:20924863

An evaluation of a new approach to the regeneration of Helichrysum italicum (Roth) G. Don, and the molecular characterization of the variation among sets of differently derived regenerants.

PubMed

Perrini, Rosaria; Alba, Vittorio; Ruta, Claudia; Morone-Fortunato, Irene; Blanco, Antonio; Montemurro, Cinzia

2009-01-01

A protocol for the induction of regeneration from leaves of Helichrysum italicum was established. Calli were found to form on the basal medium only when it was supplemented with thidiazuron (TDZ) alone or in combination with naphthalene acetic acid (NAA), with a percentage ranking of at least 80%. The hormone-free medium showed the highest percentage of shoot regeneration (62%) even though no callus formed. AFLP markers were employed to verify tissue culture-induced variation in the regenerated plantlets obtained by direct shoot regeneration or the indirect shoot regeneration process (callus formation). Seven out of the eleven AFLP primer pairs yielded polymorphic patterns. The average number of fragments per primer pair was 64.1. Singletons were represented by 12 (2.7%) fragments. Student's T-test was performed both on the average number of shared fragments and on the nucleotide diversity, and no significant statistical difference was observed between the two regeneration treatments.

Dissecting the dynamic conformations of the metamorphic protein lymphotactin.

PubMed

Harvey, Sophie R; Porrini, Massimiliano; Konijnenberg, Albert; Clarke, David J; Tyler, Robert C; Langridge-Smith, Patrick R R; MacPhee, Cait E; Volkman, Brian F; Barran, Perdita E

2014-10-30

A mass spectrometer provides an ideal laboratory to probe the structure and stability of isolated protein ions. Interrogation of each discrete mass/charge-separated species enables the determination of the intrinsic stability of a protein fold, gaining snapshots of unfolding pathways. In solution, the metamorphic protein lymphotactin (Ltn) exists in equilibrium between two distinct conformations, a monomeric (Ltn10) and a dimeric (Ltn40) fold. Here, we use electron capture dissociation (ECD) and drift tube ion mobility-mass spectrometry (DT IM-MS) to analyze both forms and use molecular dynamics (MD) to consider how the solution fold alters in a solvent-free environment. DT IM-MS reveals significant conformational flexibility for the monomer, while the dimer appears more conformationally restricted. These findings are supported by MD calculations, which reveal how salt bridges stabilize the conformers in vacuo. Following ECD experiments, a distinctive fragmentation pattern is obtained for both the monomer and dimer. Monomer fragmentation becomes more pronounced with increasing charge state especially in the disordered regions and C-terminal α-helix in the solution fold. Lower levels of fragmentation are seen in the β-sheet regions and in regions that contain salt bridges, identified by MD simulations. The lowest charge state of the dimer for which we obtain ECD data ([D+9H](9+)) exhibits extensive fragmentation with no relationship to the solution fold and has a smaller collision cross section (CCS) than charge states 10-13+, suggesting a "collapsed" encounter complex. Other charge states of the dimer, as for the monomer, are resistant to fragmentation in regions of β-sheets in the solution fold. This study provides evidence for preservation and loss of global fold and secondary structural elements, providing a tantalizing glimpse into the power of the emerging field of native top-down mass spectrometry.

Mechanics of fragmentation of crocodile skin and other thin films.

PubMed

Qin, Zhao; Pugno, Nicola M; Buehler, Markus J

2014-05-27

Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile's head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young's modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin.

Mechanics of fragmentation of crocodile skin and other thin films

PubMed Central

Qin, Zhao; Pugno, Nicola M.; Buehler, Markus J.

2014-01-01

Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile's head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young's modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin. PMID:24862190

Mechanics of fragmentation of crocodile skin and other thin films

NASA Astrophysics Data System (ADS)

Qin, Zhao; Pugno, Nicola M.; Buehler, Markus J.

2014-05-01

Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile's head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young's modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin.

Comparing forest fragmentation and its drivers in China and the USA with Globcover v2.2

USGS Publications Warehouse

Chen, Mingshi; Mao, Lijun; Zhou, Chunguo; Vogelmann, James E.; Zhu, Zhiliang

2010-01-01

Forest loss and fragmentation are of major concern to the international community, in large part because they impact so many important environmental processes. The main objective of this study was to assess the differences in forest fragmentation patterns and drivers between China and the conterminous United States (USA). Using the latest 300-m resolution global land cover product, Globcover v2.2, a comparative analysis of forest fragmentation patterns and drivers was made. The fragmentation patterns were characterized by using a forest fragmentation model built on the sliding window analysis technique in association with landscape indices. Results showed that China’s forests were substantially more fragmented than those of the USA. This was evidenced by a large difference in the amount of interior forest area share, with China having 48% interior forest versus the 66% for the USA. China’s forest fragmentation was primarily attributed to anthropogenic disturbances, driven particularly by agricultural expansion from an increasing and large population, as well as poor forest management practices. In contrast, USA forests were principally fragmented by natural land cover types. However, USA urban sprawl contributed more to forest fragmentation than in China. This is closely tied to the USA’s economy, lifestyle and institutional processes. Fragmentation maps were generated from this study, which provide valuable insights and implications regarding habitat planning for rare and endangered species. Such maps enable development of strategic plans for sustainable forest management by identifying areas with high amounts of human-induced fragmentation, which improve risk assessments and enable better targeting for protection and remediation efforts. Because forest fragmentation is a long-term, complex process that is highly related to political, institutional, economic and philosophical arenas, both nations need to take effective and comprehensive measures to mitigate the negative effects of forest loss and fragmentation on the existing forest ecosystems.

Comparing forest fragmentation and its drivers in China and the USA with Globcover v2.2.

PubMed

Li, Mingshi; Mao, Lijun; Zhou, Chunguo; Vogelmann, James E; Zhu, Zhiliang

2010-12-01

Forest loss and fragmentation are of major concern to the international community, in large part because they impact so many important environmental processes. The main objective of this study was to assess the differences in forest fragmentation patterns and drivers between China and the conterminous United States (USA). Using the latest 300-m resolution global land cover product, Globcover v2.2, a comparative analysis of forest fragmentation patterns and drivers was made. The fragmentation patterns were characterized by using a forest fragmentation model built on the sliding window analysis technique in association with landscape indices. Results showed that China's forests were substantially more fragmented than those of the USA. This was evidenced by a large difference in the amount of interior forest area share, with China having 48% interior forest versus the 66% for the USA. China's forest fragmentation was primarily attributed to anthropogenic disturbances, driven particularly by agricultural expansion from an increasing and large population, as well as poor forest management practices. In contrast, USA forests were principally fragmented by natural land cover types. However, USA urban sprawl contributed more to forest fragmentation than in China. This is closely tied to the USA's economy, lifestyle and institutional processes. Fragmentation maps were generated from this study, which provide valuable insights and implications regarding habitat planning for rare and endangered species. Such maps enable development of strategic plans for sustainable forest management by identifying areas with high amounts of human-induced fragmentation, which improve risk assessments and enable better targeting for protection and remediation efforts. Because forest fragmentation is a long-term, complex process that is highly related to political, institutional, economic and philosophical arenas, both nations need to take effective and comprehensive measures to mitigate the negative effects of forest loss and fragmentation on the existing forest ecosystems. Copyright © 2010 Elsevier Ltd. All rights reserved.

Linkage and Anomeric Differentiation in Trisaccharides by Sequential Fragmentation and Variable-Wavelength Infrared Photodissociation

NASA Astrophysics Data System (ADS)

Tan, Yanglan; Polfer, Nicolas C.

2015-02-01

Carbohydrates and their derivatives play important roles in biological systems, but their isomeric heterogeneity also presents a considerable challenge for analytical techniques. Here, a stepwise approach using infrared multiple-photon dissociation (IRMPD) via a tunable CO2 laser (9.2-10.7 μm) was employed to characterize isomeric variants of glucose-based trisaccharides. After the deprotonated trisaccharides were trapped and fragmented to disaccharide C2 fragments in a Fourier transform ion cyclotron resonance (FTICR) cell, a further variable-wavelength infrared irradiation of the C2 ion produced wavelength-dependent dissociation patterns that are represented as heat maps. The photodissociation patterns of these C2 fragments are shown to be strikingly similar to the photodissociation patterns of disaccharides with identical glycosidic bonds. Conversely, the photodissociation patterns of different glycosidic linkages exhibit considerable differences. On the basis of these results, the linkage position and anomericity of glycosidic bonds of disaccharide units in trisaccharides can be systematically differentiated and identified, providing a promising approach to characterize the structures of isomeric oligosaccharides.

Fragmentation modes and the evolution of life cycles.

PubMed

Pichugin, Yuriy; Peña, Jorge; Rainey, Paul B; Traulsen, Arne

2017-11-01

Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles.

Fragmentation modes and the evolution of life cycles

PubMed Central

Rainey, Paul B.

2017-01-01

Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles. PMID:29166656

Landscape trends in Mid-Atlantic and Southeastern United States ecoregions

USGS Publications Warehouse

Griffith, J.A.; Stehman, S.V.; Loveland, Thomas R.

2003-01-01

Landscape pattern and composition metrics are potential indicators for broad-scale monitoring of change and for relating change to human and ecological processes. We used a probability sample of 20-km × 20-km sampling blocks to characterize landscape composition and pattern in five US ecoregions: the Middle Atlantic Coastal Plain, Southeastern Plains, Northern Piedmont, Piedmont, and Blue Ridge Mountains. Land use/land cover (LULC) data for five dates between 1972 and 2000 were obtained for each sample block. Analyses focused on quantifying trends in selected landscape pattern metrics by ecoregion and comparing trends in land cover proportions and pattern metrics among ecoregions. Repeated measures analysis of the landscape pattern documented a statistically significant trend in all five ecoregions towards a more fine-grained landscape from the early 1970s through 2000. The ecologically important forest cover class also became more fine-grained with time (i.e., more numerous and smaller forest patches). Trends in LULC, forest edge, and forest percent like adjacencies differed among ecoregions. These results suggest that ecoregions provide a geographically coherent way to regionalize the story of national land use and land cover change in the United States. This study provides new information on LULC change in the southeast United States. Previous studies of the region from the 1930s to the 1980s showed a decrease in landscape fragmentation and an increase in percent forest, while this study showed an increase in forest fragmentation and a loss of forest cover.

Assessment of forest fragmentation in southern New England using remote sensing and geographic information systems technology

USGS Publications Warehouse

Vogelmann, James E.

1995-01-01

Spatial patterns and rates of forest fragmentation were assessed using digital remote sensing data for a region in southern New England that included 157 townships in southern New Hampshire and northeastern Massachusetts. The study area has undergone marked population increases over the last several decades. Following classification of 1973 and 1988 Landsat Multispectral Scanner data into forest and nonforest classes, data were incorporated into a geographic information system. The natural logarithms of forest area to perimeter ratios, referred to as the forest continuity index, were used to assess patterns and trends of forest fragmentation across the region Forest continuity index values were extracted from each township for both data sets and compared with population data. Forest continuity index values were found to decrease with increasing population density until about 200 persons per square kilometer, after which the relationship stabilized. With slight population increases at low densities forest continuity index values declined sharply, implying abrupt increases in forest fragmentation. Results from the study indicated good negative correlations (r2 values of 0.81 and 0.77) between the Multispectral Scanner-derived forest continuity index and natural logs of township population density. Socioeconomic indicators such as affluence and commuting patterns did not appear to correlate well with forest fragmentation estimates. Decreases in forest continuity index values occurred throughout much of the study region between 1973 and 1988, suggesting that forest fragmentation is occurring over large regions within the eastern United States. It is technologically feasible to assess patterns and rates of forest fragmentation across much larger areas than analyzed in this study; such analyses would provide useful overviews enabling objective assessment of the magnitude of forest fragmentation.

Light meromyosin paracrystal formation.

PubMed

Chowrashi, P K; Pepe, F A

1977-07-01

STUDIES OF PARACRYSTAL FORMATION BY COLUMN PURIFIED LIGHT MEROMYOSIN (LMM) PREPARED IN A VARIETY OF WAYS LED TO THE FOLLOWING CONCLUSIONS: (a) different portions of the myosin rod may be coded for different stagger relationships. This was concluded from observations that paracrystals with different axial repeat periodicities could be obtained either with LMM framents of different lengths prepared with the same enzyme, or with LMM fragments of identical lengths but prepared with different enzymes. (b) Paracrystals with a 14-nm axial repeat periodicity are most likely formed by the aggregation of sheets with a 44-nm axial repeat within the sheets which are staggered by 14 nm. All of the axial repeat patterns expected from one sheet or aggregates of more than one sheet, on this basis, were observed in the same electron micrograph. (c) C-protein binding probably occurs preferentially to LMM molecules related in some specific way. This was concluded from the observation that the same axial repeat pattern was obtained in paracrystals formed from different LMM preparations in the presence of C-protein, regardless of differences in the axial repeat obtained in the absence of C-protein. (d) Nucleic acid is responsible for the 43-nm axial repeat patterns observed in paracrystals formed by the ethanol-resistant fraction of LMM. In the absence of nuclei acid, paracrystals with a 14nm axial repeat are obtained. (e) The 43-nm axial repeat pattern observed with the ethanol-resistant fraction of LMM is different for LMM preparations obtained by trypsin and papain digestions.

Influence of volcanic activity on the population genetic structure of Hawaiian Tetragnatha spiders: Fragmentation, rapid population growth and the potential for accelerated evolution

USGS Publications Warehouse

Vandergast, A.G.; Gillespie, R.G.; Roderick, G.K.

2004-01-01

Volcanic activity on the island of Hawaii results in a cyclical pattern of habitat destruction and fragmentation by lava, followed by habitat regeneration on newly formed substrates. While this pattern has been hypothesized to promote the diversification of Hawaiian lineages, there have been few attempts to link geological processes to measurable changes in population structure. We investigated the genetic structure of three species of Hawaiian spiders in forests fragmented by a 150-year-old lava flow on Mauna Loa Volcano, island of Hawaii: Tetragnatha quasimodo (forest and lava flow generalist), T. anuenue and T. brevignatha (forest specialists). To estimate fragmentation effects on population subdivision in each species, we examined variation in mitochondrial and nuclear genomes (DNA sequences and allozymes, respectively). Population subdivision was higher for forest specialists than for the generalist in fragments separated by lava. Patterns of mtDNA sequence evolution also revealed that forest specialists have undergone rapid expansion, while the generalist has experienced more gradual population growth. Results confirm that patterns of neutral genetic variation reflect patterns of volcanic activity in some Tetragnatha species. Our study further suggests that population subdivision and expansion can occur across small spatial and temporal scales, which may facilitate the rapid spread of new character states, leading to speciation as hypothesized by H. L. Carson 30 years ago.

Simple Process-Based Simulators for Generating Spatial Patterns of Habitat Loss and Fragmentation: A Review and Introduction to the G-RaFFe Model

PubMed Central

Pe'er, Guy; Zurita, Gustavo A.; Schober, Lucia; Bellocq, Maria I.; Strer, Maximilian; Müller, Michael; Pütz, Sandro

2013-01-01

Landscape simulators are widely applied in landscape ecology for generating landscape patterns. These models can be divided into two categories: pattern-based models that generate spatial patterns irrespective of the processes that shape them, and process-based models that attempt to generate patterns based on the processes that shape them. The latter often tend toward complexity in an attempt to obtain high predictive precision, but are rarely used for generic or theoretical purposes. Here we show that a simple process-based simulator can generate a variety of spatial patterns including realistic ones, typifying landscapes fragmented by anthropogenic activities. The model “G-RaFFe” generates roads and fields to reproduce the processes in which forests are converted into arable lands. For a selected level of habitat cover, three factors dominate its outcomes: the number of roads (accessibility), maximum field size (accounting for land ownership patterns), and maximum field disconnection (which enables field to be detached from roads). We compared the performance of G-RaFFe to three other models: Simmap (neutral model), Qrule (fractal-based) and Dinamica EGO (with 4 model versions differing in complexity). A PCA-based analysis indicated G-RaFFe and Dinamica version 4 (most complex) to perform best in matching realistic spatial patterns, but an alternative analysis which considers model variability identified G-RaFFe and Qrule as performing best. We also found model performance to be affected by habitat cover and the actual land-uses, the latter reflecting on land ownership patterns. We suggest that simple process-based generators such as G-RaFFe can be used to generate spatial patterns as templates for theoretical analyses, as well as for gaining better understanding of the relation between spatial processes and patterns. We suggest caution in applying neutral or fractal-based approaches, since spatial patterns that typify anthropogenic landscapes are often non-fractal in nature. PMID:23724108

Simple process-based simulators for generating spatial patterns of habitat loss and fragmentation: a review and introduction to the G-RaFFe model.

PubMed

Pe'er, Guy; Zurita, Gustavo A; Schober, Lucia; Bellocq, Maria I; Strer, Maximilian; Müller, Michael; Pütz, Sandro

2013-01-01

Landscape simulators are widely applied in landscape ecology for generating landscape patterns. These models can be divided into two categories: pattern-based models that generate spatial patterns irrespective of the processes that shape them, and process-based models that attempt to generate patterns based on the processes that shape them. The latter often tend toward complexity in an attempt to obtain high predictive precision, but are rarely used for generic or theoretical purposes. Here we show that a simple process-based simulator can generate a variety of spatial patterns including realistic ones, typifying landscapes fragmented by anthropogenic activities. The model "G-RaFFe" generates roads and fields to reproduce the processes in which forests are converted into arable lands. For a selected level of habitat cover, three factors dominate its outcomes: the number of roads (accessibility), maximum field size (accounting for land ownership patterns), and maximum field disconnection (which enables field to be detached from roads). We compared the performance of G-RaFFe to three other models: Simmap (neutral model), Qrule (fractal-based) and Dinamica EGO (with 4 model versions differing in complexity). A PCA-based analysis indicated G-RaFFe and Dinamica version 4 (most complex) to perform best in matching realistic spatial patterns, but an alternative analysis which considers model variability identified G-RaFFe and Qrule as performing best. We also found model performance to be affected by habitat cover and the actual land-uses, the latter reflecting on land ownership patterns. We suggest that simple process-based generators such as G-RaFFe can be used to generate spatial patterns as templates for theoretical analyses, as well as for gaining better understanding of the relation between spatial processes and patterns. We suggest caution in applying neutral or fractal-based approaches, since spatial patterns that typify anthropogenic landscapes are often non-fractal in nature.

Typing of Human Mycobacterium avium Isolates in Italy by IS1245-Based Restriction Fragment Length Polymorphism Analysis

PubMed Central

Lari, Nicoletta; Cavallini, Michela; Rindi, Laura; Iona, Elisabetta; Fattorini, Lanfranco; Garzelli, Carlo

1998-01-01

All but 2 of 63 Mycobacterium avium isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS1245 restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS1245 patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS1245 RFLP pattern. PMID:9817900

Characterization of carotenoids and carotenoid esters in red pepper pods (Capsicum annuum L.) by high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry.

PubMed

Schweiggert, Ute; Kammerer, Dietmar R; Carle, Reinhold; Schieber, Andreas

2005-01-01

Carotenoids and carotenoid esters were extracted from red pepper pods (Capsicum annuum L.) without saponification. Among the 42 compounds detected, 4 non-esterified, 11 mono- and 17 diesters were characterized based on their retention times, UV/Vis spectra and their fragmentation patterns in collision-induced dissociation experiments in atmospheric pressure chemical ionization mass spectrometry (APCI-MS). Positive and negative ion mode measurements were used for the characterization of major and minor carotenoids and their esters. Capsanthin esterified with lauric, palmitic and myristic acids represented the predominant compounds in the red pepper extracts. Additionally, three beta-cryptoxanthin and one zeaxanthin monoester were tentatively identified in red pepper pods for the first time. Furthermore, the specific fragmentation patterns of capsanthin-laurate-myristate and capsanthin-myristate-palmitate were used for the distinction of both regioisomers. The results obtained from LC-DAD-APCI-MSn experiments demonstrated that the carotenoid profile of red pepper pods is considerably more complex than considered hitherto. Copyright (c) 2005 John Wiley & Sons, Ltd.

ESI-MS, ESI-MS/MS fingerprint and LC-ESI-MS analysis of proathocyanidins from Bursera simaruba Sarg bark.

PubMed

Maldini, Mariateresa; Montoro, Paola; Piacente, Sonia; Pizza, Cosimo

2009-12-01

Direct flow injection/electrospray ionization/ion trap tandem mass spectrometry was used to investigate the presence of proanthocyanidins (PAs) in the methanolic extract of B. simaruba bark. Additionally, an LC-ESI-MS qualitative study was performed by using a monolithic stationary phase. The fragmentation pattern obtained evidenced the presence in B. simaruba bark of PAs belonging to the series of polymers of epicatechin, along with their glycosilated derivatives.

DNA fingerprinting and analysis of population structure in the chestnut blight fungus, Cryphonectria parasitica.

PubMed

Milgroom, M G; Lipari, S E; Powell, W A

1992-06-01

We analyzed DNA fingerprints in the chestnut blight fungus, Cryphonectria parasitica, for stability, inheritance, linkage and variability in a natural population. DNA fingerprints resulting from hybridization with a dispersed moderately repetitive DNA sequence of C. parasitica in plasmid pMS5.1 hybridized to 6-17 restriction fragments per individual isolate. In a laboratory cross and from progeny from a single perithecium collected from a field population, the presence/absence of 11 fragments in the laboratory cross and 12 fragments in the field progeny set segregated in 1:1 ratios. Two fragments in each progeny set cosegregated; no other linkage was detected among the segregating fragments. Mutations, identified by missing bands, were detected for only one fragment in which 4 of 43 progeny lacked a band present in both parents; no novel fragments were detected in any progeny. All other fragments appeared to be stably inherited. Hybridization patterns did not change during vegetative growth or sporulation. However, fingerprint patterns of single conidial isolates of strains EP155 and EP67 were found to be heterogenous due to mutations that occurred during culturing in the laboratory since these strains were first isolated in 1976-1977. In a population sample of 39 C. parasitica isolates, we found 33 different fingerprint patterns with pMS5.1. Most isolates differed from all other isolates by the presence or absence of several fragments. Six fingerprint patterns each occurred twice. Isolates with identical fingerprints occurred in cankers on the same chestnut stems three times; isolates within the other three pairs were isolated from cankers more than 5 m apart. The null hypothesis of random mating in this population could not be rejected if the six putative clones were removed from the analysis. Thus, a rough estimate of the clonal fraction of this population is 6 in 39 isolates (15.4%).

Coulomb Fission in Multiply-Charged Ammonia Clusters: Accurate Measurements of the Rayleigh Instability Limit from Fragmentation Patterns.

PubMed

Harris, Christopher; Stace, Anthony J

2018-03-15

A series of experiments have been undertaken on the fragmentation of multiply charged ammonia clusters, (NH 3 ) n z+ , where z ≤ 8 and n ≤ 850, to establish Rayleigh instability limits, whereby clusters at certain critical sizes become unstable due to Coulomb repulsion between the resident charges. Experimental results on size-selected clusters are found to be in excellent agreement with theoretical predictions of Rayleigh instability limits at all values of the charge. Electrostatic theory has been used to help identify fragmentation patterns on the assumption that the clusters separate into two dielectric spheres, and the predicted Coulomb repulsion energies used to establish pathways and the sizes of cluster fragments. The results show that fragmentation is very asymmetric in terms of both the numbers of molecules involved and the amount of charge each fragment accommodates. For clusters carrying a charge ≤+4, the results show that fragmentation proceeds via the loss of small, singly charged clusters. When clusters carry a charge of +5 or more, the experimental observations suggest a marked switch in behavior. Although the laboratory measurements equate to fragmentation via the loss of a large dication cluster, electrostatic theory supports an interpretation that involves the sequential loss of two smaller, singly charged clusters possibly accompanied by the extensive evaporation of neutral molecules. It is suggested that this change in fragmentation pattern is driven by the channelling of Coulomb repulsion energy into intermolecular modes within these larger clusters. Overall, the results appear to support the ion evaporation model that is frequently used to interpret electrospray experiments.

Evaluating differences in forest fragmentation and restoration between western natural forests and southeastern plantation forests in the United States.

PubMed

Ren, Xinyu; Lv, Yingying; Li, Mingshi

2017-03-01

Changes in forest ecosystem structure and functions are considered some of the research issues in landscape ecology. In this study, advancing Forman's theory, we considered five spatially explicit processes associated with fragmentation, including perforation, dissection, subdivision, shrinkage, and attrition, and two processes associated with restoration, i.e., increment and expansion processes. Following this theory, a forest fragmentation and restoration process model that can detect the spatially explicit processes and ecological consequences of forest landscape change was developed and tested in the current analysis. Using the National Land Cover Databases (2001, 2006 and 2011), the forest fragmentation and restoration process model was applied to US western natural forests and southeastern plantation forests to quantify and classify forest patch losses into one of the four fragmentation processes (the dissection process was merged into the subdivision process) and to classify the newly gained forest patches based on the two restoration processes. At the same time, the spatio-temporal differences in fragmentation and restoration patterns and trends between natural forests and plantations were further compared. Then, through overlaying the forest fragmentation/restoration processes maps with targeting year land cover data and land ownership vectors, the results from forest fragmentation and the contributors to forest restoration in federal and nonfederal lands were identified. Results showed that, in natural forests, the forest change patches concentrated around the urban/forest, cultivated/forest, and shrubland/forest interfaces, while the patterns of plantation change patches were scattered sparsely and irregularly. The shrinkage process was the most common type in forest fragmentation, and the average size was the smallest. Expansion, the most common restoration process, was observed in both natural forests and plantations and often occurred around the previous expansion or covered the previous subdivision or shrinkage processes. The overall temporal fragmentation pattern of natural forests had a "perforation-subdivision/shrinkage-attrition" pathway, which corresponded to Forman's landscape fragmentation rule, while the plantation forests did not follow the rule strictly. The main land cover types resulted from forest fragmentation in natural forests and plantation forests were shrubland and herbaceous, mainly through subdivision and shrinkages process. The processes and effects of restoration of plantation forests were more diverse and efficient, compared to the natural forest, which were simpler with a lower regrowth rate. The fragmentation mostly occurred in nonfederal lands. In natural forests, forest fragmentation pattern differed in different land tenures, yet plantations remained the same in federal and nonfederal lands. Copyright © 2016 Elsevier Ltd. All rights reserved.

Behavioral response of the coachwhip (Masticophis flagellum) to habitat fragment size and isolation in an urban landscape

USGS Publications Warehouse

Mitrovich, Milan J.; Diffendorfer, Jay E.; Fisher, Robert N.

2009-01-01

Habitat fragmentation is a significant threat to biodiversity worldwide. Habitat loss and the isolation of habitat fragments disrupt biological communities, accelerate the extinction of populations, and often lead to the alteration of behavioral patterns typical of individuals in large, contiguous natural areas. We used radio-telemetry to study the space-use behavior of the Coachwhip, a larger-bodied, wide-ranging snake species threatened by habitat fragmentation, in fragmented and contiguous areas of coastal southern California. We tracked 24 individuals at three sites over two years. Movement patterns of Coachwhips changed in habitat fragments. As area available to the snakes was reduced, individuals faced increased crowding, had smaller home-range sizes, tolerated greater home-range overlap, and showed more concentrated movement activity and convoluted movement pathways. The behavioral response shown by Coachwhips suggests, on a regional level, area-effects alone cannot explain observed extinctions on habitat fragments but, instead, suggests changes in habitat configuration are more likely to explain the decline of this species. Ultimately, if "edge-exposure" is a common cause of decline, then isolated fragments, appropriately buffered to reduce emigration and edge effects, may support viable populations of fragmentation-sensitive species.

[The investigation of genomes of some species of the genus Gentiana in nature and in vitro cell culture].

PubMed

Mel'nyk, V M; Spiridonova, K V; Andrieiev, I O; Strashniuk, N M; Kunakh, V A

2002-01-01

The comparative study of the genomes of intact plants-representatives of some species of the genus Gentiana L. as well as cultured cells of G. lutea and G. punctata was performed using restriction analysis. Species specificity of restriction fragment patterns for studied representatives of this genus was revealed. The differences between electrophoretic patterns of digested DNA purified from rhizome and leaves of G. lutea and G. punctata were found. The changes in genomes of G. lutea and G. punctata cells cultured in vitro compared with the genomes of intact plants were detected. The data obtained evidence that some of them may be of nonrandom character.

Associations between forest fragmentation patterns and geneticstructure in Pfrimer’s Parakeet (Pyrrhura pfrimeri), an endangered endemic to central Brazil’s dry forests

USGS Publications Warehouse

Haig, Susan M.; Miller, Leonard F.; Bianchi, Carlos; Mullins, Thomas D.

2012-01-01

When habitat becomes fragmented, populations of species may become increasingly isolated. In the absence of habitat corridors, genetic structure may develop and populations risk reductions in genetic diversity from increased genetic drift and inbreeding. Deforestation of the Cerrado biome of Brazil, particularly of the dry forests within the Parana˜ River Basin, has incrementally occurred since the 1970s and increased forest fragmentation within the region. We performed landscape genetic analyses of Pfrimer’s parakeet (Pyrrhura pfrimeri), a globally endangered endemic to the region, to determine if forest fragmentation patterns were associated with genetic structuring in this species. We used previously generated satellite imagery that identified the locations of Parana˜ River Basin forest fragments in 1977, 1993/94, and 2008. Behavioral data quantifying the affinity of Pfrimer’s parakeet for forest habitat was used to parameterize empirically derived landscape conductance surfaces. Though genetic structure was observed among Pfrimer’s parakeet populations, no association between genetic and geographic distance was detected. Likewise, least cost path lengths, circuit theorybased resistance distances, and a new measure of least cost path length complexity could not be conclusively associated with genetic structure patterns. Instead, a new quantity that encapsulated connection redundancy from the 1977 forest fragmentation data provided the clearest associations with pairwise genetic differentiation patterns (Jost’s D: r = 0.72, P = 0.006; FST: r = 0.741, P = 0.001). Our analyses suggest a 35-year or more lag between deforestation and its effect on genetic structure. Because 66 % of the Parana˜ River Basin has been deforested since 1977, we expect that genetic structure will increase substantially among Pfrimer’s Parakeet populations in the future, especially if fragmentation continues at its current pace.

Global-scale patterns of forest fragmentation

Treesearch

Kurt H. Riitters; James D. Wickham; R. O' Neill; B. Jones; E. Smith

2000-01-01

We report an analysis of forest fragmentation based on 1-km resolution land-cover maps for the globe. Measurements in analysis windows from 81 km 2 (9 x 9 pixels, "small" scale) to 59,049 km 2 (243 x 243 pixels, "large" scale) were used to characterize the fragmentation around each forested pixel. We identified six categories of fragmentation (...

Characterization of Metarhizium viride Mycosis in Veiled Chameleons (Chamaeleo calyptratus), Panther Chameleons (Furcifer pardalis), and Inland Bearded Dragons (Pogona vitticeps).

PubMed

Schmidt, Volker; Klasen, Linus; Schneider, Juliane; Hübel, Jens; Pees, Michael

2017-03-01

Metarhizium viride has been associated with fatal systemic mycoses in chameleons, but subsequent data on mycoses caused by this fungus in reptiles are lacking. The aim of this investigation was therefore to obtain information on the presence of M. viride in reptiles kept as pets in captivity and its association with clinical signs and pathological findings as well as improvement of diagnostic procedures. Beside 18S ribosomal DNA (rDNA) (small subunit [SSU]) and internal transcribed spacer region 1 (ITS-1), a fragment of the large subunit (LSU) of 28S rDNA, including domain 1 (D1) and D2, was sequenced for the identification of the fungus and phylogenetic analysis. Cultural isolation and histopathological examinations as well as the pattern of antifungal drug resistance, determined by using agar diffusion testing, were additionally used for comparison of the isolates. In total, 20 isolates from eight inland bearded dragons ( Pogona vitticeps ), six veiled chameleons ( Chamaeleo calyptratus ), and six panther chameleons ( Furcifer pardalis ) were examined. Most of the lizards suffered from fungal glossitis, stomatitis, and pharyngitis or died due to visceral mycosis. Treatment with different antifungal drugs according to resistance patterns in all three different lizard species was unsuccessful. Sequence analysis resulted in four different genotypes of M. viride based on differences in the LSU fragment, whereas the SSU and ITS-1 were identical in all isolates. Sequence analysis of the SSU fragment revealed the first presentation of a valid large fragment of the SSU of M. viride According to statistical analysis, genotypes did not correlate with differences in pathogenicity, antifungal susceptibility, or species specificity. Copyright © 2017 American Society for Microbiology.

Characterization of Metarhizium viride Mycosis in Veiled Chameleons (Chamaeleo calyptratus), Panther Chameleons (Furcifer pardalis), and Inland Bearded Dragons (Pogona vitticeps)

PubMed Central

Klasen, Linus; Schneider, Juliane; Hübel, Jens; Pees, Michael

2016-01-01

ABSTRACT Metarhizium viride has been associated with fatal systemic mycoses in chameleons, but subsequent data on mycoses caused by this fungus in reptiles are lacking. The aim of this investigation was therefore to obtain information on the presence of M. viride in reptiles kept as pets in captivity and its association with clinical signs and pathological findings as well as improvement of diagnostic procedures. Beside 18S ribosomal DNA (rDNA) (small subunit [SSU]) and internal transcribed spacer region 1 (ITS-1), a fragment of the large subunit (LSU) of 28S rDNA, including domain 1 (D1) and D2, was sequenced for the identification of the fungus and phylogenetic analysis. Cultural isolation and histopathological examinations as well as the pattern of antifungal drug resistance, determined by using agar diffusion testing, were additionally used for comparison of the isolates. In total, 20 isolates from eight inland bearded dragons (Pogona vitticeps), six veiled chameleons (Chamaeleo calyptratus), and six panther chameleons (Furcifer pardalis) were examined. Most of the lizards suffered from fungal glossitis, stomatitis, and pharyngitis or died due to visceral mycosis. Treatment with different antifungal drugs according to resistance patterns in all three different lizard species was unsuccessful. Sequence analysis resulted in four different genotypes of M. viride based on differences in the LSU fragment, whereas the SSU and ITS-1 were identical in all isolates. Sequence analysis of the SSU fragment revealed the first presentation of a valid large fragment of the SSU of M. viride. According to statistical analysis, genotypes did not correlate with differences in pathogenicity, antifungal susceptibility, or species specificity. PMID:28003420

Characterizing fragmentation of the collective forests in southern China from multitemporal Landsat imagery: A case study from Kecheng district of Zhejiang province

USGS Publications Warehouse

Li, M.; Zhu, Z.; Vogelmann, James E.; Xu, D.; Wen, W.; Liu, A.

2011-01-01

Tropical and subtropical forests provide important ecosystem goods and services including carbon sequestration and biodiversity conservation. These forests are facing increasing socioeconomic pressures and are rapidly being degraded and fragmented. This analysis focuses on the rate of change and patterns of fragmentation in a collective forest area in Zhejiang province, China, during the time period 1988–2005. The research consisted of two parts. The first was the development of general land cover maps and the identification of land cover changes by interpreting Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper Plus (ETM+) time series imagery. The second part involved the computation and analysis of forest fragmentation metrics. For this portion of the study, fragmentation statistics were analyzed, and images were developed to depict forest fragmentation patterns and trends. Results revealed that there was a net loss of 7.8% in forest coverage, dropping from 66.8% in 1988 to 59.0% in 2005, primarily caused by agricultural expansion and poor forest management practices. An acceleration of forest fragmentation was also witnessed during the time intervals, which was evidenced by a decreasing trend in interior forest (57.2% in 1988, 55.0% in 1996 and 54.8% in 2005 respectively) coupled with the scales of the selected geospatial metrics. Continued forest loss and fragmentation are closely correlated with the existing political, educational, institutional and economic processes of contemporary China. To unlock the developmental potentials of the collective forests and to effectively mitigate the rate of forest loss and fragmentation, reforms of forest tenure and ecological immigration practices are recognized as a prospective alternative. The produced fragmentation maps further illustrates the importance of assessing landscape change history, especially the spatiotemporal patterns of forest fragments, when developing landscape level plans for biodiversity conservation, land use management and ecologically sustainable forestry.

A novel isoflavone profiling method based on UPLC-PDA-ESI-MS.

PubMed

Zhang, Shuang; Zheng, Zong-Ping; Zeng, Mao-Mao; He, Zhi-Yong; Tao, Guan-Jun; Qin, Fang; Chen, Jie

2017-03-15

A novel non-targeted isoflavone profiling method was developed using the diagnostic fragment-ion-based extension strategy, based on ultra-high performance liquid chromatography coupled with photo-diode array detector and electrospray ionization-mass spectrometry (UPLC-PDA-ESI-MS). 16 types of isoflavones were obtained in positive mode, but only 12 were obtained in negative mode due to the absence of precursor ions. Malonyldaidzin and malonylgenistin glycosylated at the 4'-O position or malonylated at the 4″-O position of glucose were indicated by their retention behavior and fragmentation pattern. Three possible quantification methods in one run based on UPLC-PDA and UPLC-ESI-MS were validated and compared, suggesting that methods based on UPLC-ESI-MS possess remarkable selectivity and sensitivity. Impermissible quantitative deviations induced by the linearity calibration with 400-fold dynamic range was observed for the first time and was recalibrated with a 20-fold dynamic range. These results suggest that isoflavones and their stereoisomers can be simultaneously determined by positive-ion UPLC-ESI-MS in soymilk. Copyright © 2016. Published by Elsevier Ltd.

Structural Studies of Fucosylated N-Glycans by Ion Mobility Mass Spectrometry and Collision-Induced Fragmentation of Negative Ions

NASA Astrophysics Data System (ADS)

Harvey, David J.; Struwe, Weston B.

2018-05-01

There is considerable potential for the use of ion mobility mass spectrometry in structural glycobiology due in large part to the gas-phase separation attributes not typically observed by orthogonal methods. Here, we evaluate the capability of traveling wave ion mobility combined with negative ion collision-induced dissociation to provide structural information on N-linked glycans containing multiple fucose residues forming the Lewisx and Lewisy epitopes. These epitopes are involved in processes such as cell-cell recognition and are important as cancer biomarkers. Specific information that could be obtained from the intact N-glycans by negative ion CID included the general topology of the glycan such as the presence or absence of a bisecting GlcNAc residue and the branching pattern of the triantennary glycans. Information on the location of the fucose residues was also readily obtainable from ions specific to each antenna. Some isobaric fragment ions produced prior to ion mobility could subsequently be separated and, in some cases, provided additional valuable structural information that was missing from the CID spectra alone.

Interpretation of sucrose gradient sedimentation pattern of deoxyribonucleic acid fragments resulting from random breaks.

PubMed

Litwin, S; Shahn, E; Kozinski, A W

1969-07-01

Mass distribution in a sucrose gradient of deoxyribonucleic acid (DNA) fragments arising as a result of random breaks is predicted by analytical means from which computer evaluations are plotted. The analytical results are compared with the results of verifying experiments: (i) a Monte Carlo computer experiment in which simulated molecules of DNA were individuals of unit length subjected to random "breaks" applied by a random number generator, and (ii) an in vitro experiment in which molecules of T4 DNA, highly labeled with (32)P, were stored in liquid nitrogen for variable periods of time during which a precisely known number of (32)P atoms decayed, causing single-stranded breaks. The distribution of sizes of the resulting fragments was measured in an alkaline sucrose gradient. The profiles obtained in this fashion were compared with the mathematical predictions. Both experiments agree with the analytical approach and thus permit the use of the graphs obtained from the latter as a means of determining the average number of random breaks in DNA from distributions obtained experimentally in a sucrose gradient. An example of the application of this procedure to a previously unresolved problem is provided in the case of DNA from ultraviolet-irradiated phage which undergoes a dose-dependent intracellular breakdown. The relationship between the number of lethal hits and the number of single-stranded breaks was not previously established. A comparison of the calculated number of nicks per strand of DNA with the known dose in phage-lethal hits reveals a relationship closely approximating one lethal hit to one single-stranded break.

The evolution of urban sprawl: evidence of spatial heterogeneity and increasing land fragmentation.

PubMed

Irwin, Elena G; Bockstael, Nancy E

2007-12-26

We investigate the dynamics and spatial distribution of land use fragmentation in a rapidly urbanizing region of the United States to test key propositions regarding the evolution of sprawl. Using selected pattern metrics and data from 1973 and 2000 for the state of Maryland, we find significant increases in developed and undeveloped land fragmentation but substantial spatial heterogeneity as well. Estimated fragmentation gradients that describe mean fragmentation as a function of distance from urban centers confirm the hypotheses that fragmentation rises and falls with distance and that the point of maximum fragmentation shifted outward over time. However, rather than outward increases in sprawl balanced by development infill, we find substantial and significant increases in mean fragmentation values along the entire urban-rural gradient. These findings are in contrast to the results of Burchfield et al. [Burchfield M, Overman HG, Puga D, Turner MA (2006) Q J Econ 121:587-633], who conclude that the extent of sprawl remained roughly unchanged in the Unites States between 1976 and 1992. As demonstrated here, both the data and pattern measure used in their study are systematically biased against recording low-density residential development, the very land use that we find is most strongly associated with fragmentation. Other results demonstrate the association between exurban growth and increasing fragmentation and the systematic variation of fragmentation with nonurban factors. In particular, proximity to the Chesapeake Bay is negatively associated with fragmentation, suggesting that an attraction effect associated with this natural amenity has concentrated development.

The Multiple Impacts of Tropical Forest Fragmentation on Arthropod Biodiversity and on their Patterns of Interactions with Host Plants.

PubMed

Benítez-Malvido, Julieta; Dáttilo, Wesley; Martínez-Falcón, Ana Paola; Durán-Barrón, César; Valenzuela, Jorge; López, Sara; Lombera, Rafael

2016-01-01

Tropical rain forest fragmentation affects biotic interactions in distinct ways. Little is known, however, about how fragmentation affects animal trophic guilds and their patterns of interactions with host plants. In this study, we analyzed changes in biotic interactions in forest fragments by using a multitrophic approach. For this, we classified arthropods associated with Heliconia aurantiaca herbs into broad trophic guilds (omnivores, herbivores and predators) and assessed the topological structure of intrapopulation plant-arthropod networks in fragments and continuous forests. Habitat type influenced arthropod species abundance, diversity and composition with greater abundance in fragments but greater diversity in continuous forest. According to trophic guilds, coleopteran herbivores were more abundant in continuous forest and overall omnivores in fragments. Continuous forest showed a greater diversity of interactions than fragments. Only in fragments, however, did the arthropod community associated with H aurantiaca show a nested structure, suggesting novel and/or opportunistic host-arthropod associations. Plants, omnivores and predators contributed more to nestedness than herbivores. Therefore, Heliconia-arthropod network properties do not appear to be maintained in fragments mainly caused by the decrease of herbivores. Our study contributes to the understanding of the impact of fragmentation on the structure and dynamics of multitrophic arthropod communities associated with a particular plant species of the highly biodiverse tropical forests. Nevertheless, further replication of study sites is needed to strengthen the conclusion that forest fragmentation negatively affects arthropod assemblages.

The Multiple Impacts of Tropical Forest Fragmentation on Arthropod Biodiversity and on their Patterns of Interactions with Host Plants

PubMed Central

Benítez-Malvido, Julieta; Dáttilo, Wesley; Martínez-Falcón, Ana Paola; Durán-Barrón, César; Valenzuela, Jorge; López, Sara; Lombera, Rafael

2016-01-01

Tropical rain forest fragmentation affects biotic interactions in distinct ways. Little is known, however, about how fragmentation affects animal trophic guilds and their patterns of interactions with host plants. In this study, we analyzed changes in biotic interactions in forest fragments by using a multitrophic approach. For this, we classified arthropods associated with Heliconia aurantiaca herbs into broad trophic guilds (omnivores, herbivores and predators) and assessed the topological structure of intrapopulation plant-arthropod networks in fragments and continuous forests. Habitat type influenced arthropod species abundance, diversity and composition with greater abundance in fragments but greater diversity in continuous forest. According to trophic guilds, coleopteran herbivores were more abundant in continuous forest and overall omnivores in fragments. Continuous forest showed a greater diversity of interactions than fragments. Only in fragments, however, did the arthropod community associated with H aurantiaca show a nested structure, suggesting novel and/or opportunistic host-arthropod associations. Plants, omnivores and predators contributed more to nestedness than herbivores. Therefore, Heliconia-arthropod network properties do not appear to be maintained in fragments mainly caused by the decrease of herbivores. Our study contributes to the understanding of the impact of fragmentation on the structure and dynamics of multitrophic arthropod communities associated with a particular plant species of the highly biodiverse tropical forests. Nevertheless, further replication of study sites is needed to strengthen the conclusion that forest fragmentation negatively affects arthropod assemblages. PMID:26731271

Behavioral and physiological responses to fruit availability of spider monkeys ranging in a small forest fragment

PubMed Central

Rimbach, Rebecca; Link, Andrés; Montes-Rojas, Andrés; Di Fiore, Anthony; Heistermann, Michael; Heymann, Eckhard W

2014-01-01

Numerous animal species currently experience habitat loss and fragmentation. This might result in behavioral and dietary adjustments, especially because fruit availability is frequently reduced in fragments. Food scarcity can result in elevated physiological stress levels, and chronic stress often has detrimental effects on individuals. Some animal species exhibit a high degree of fission–fusion dynamics, and theory predicts that these species reduce intragroup feeding competition by modifying their subgroup size according to resource availability. Until now, however, there have been few studies on how species with such fission–fission dynamics adjust their grouping patterns and social behavior in small fragments or on how food availability influences their stress levels. We collected data on fruit availability, feeding behavior, stress hormone levels (measured through fecal glucocorticoid metabolites (FGCM)), subgroup size, and aggression for two groups of brown spider monkeys (Ateles hybridus) in a small forest fragment in Colombia and examined whether fruit availability influences these variables. Contrary to our predictions, spider monkeys ranged in smaller subgroups, had higher FGCM levels and higher aggression rates when fruit availability was high compared to when it was low. The atypical grouping pattern of the study groups seems to be less effective at mitigating contest competition over food resources than more typical fission–fusion patterns. Overall, our findings illustrate that the relationship between resource availability, grouping patterns, aggression rates, and stress levels can be more complex than assumed thus far. Additional studies are needed to investigate the long-term consequences on the health and persistence of spider monkeys in fragmented habitats. PMID:24820229

Self-organized mechano-chemical dynamics in amoeboid locomotion of Physarum fragments

NASA Astrophysics Data System (ADS)

Zhang, Shun; Guy, Robert D.; Lasheras, Juan C.; del Álamo, Juan C.

2017-05-01

The aim of this work is to quantify the spatio-temporal dynamics of flow-driven amoeboid locomotion in small (∼100 μm) fragments of the true slime mold Physarum polycephalum. In this model organism, cellular contraction drives intracellular flows, and these flows transport the chemical signals that regulate contraction in the first place. As a consequence of these non-linear interactions, a diversity of migratory behaviors can be observed in migrating Physarum fragments. To study these dynamics, we measure the spatio-temporal distributions of the velocities of the endoplasm and ectoplasm of each migrating fragment, the traction stresses it generates on the substratum, and the concentration of free intracellular calcium. Using these unprecedented experimental data, we classify migrating Physarum fragments according to their dynamics, finding that they often exhibit spontaneously coordinated waves of flow, contractility and chemical signaling. We show that Physarum fragments exhibiting symmetric spatio-temporal patterns of endoplasmic flow migrate significantly slower than fragments with asymmetric patterns. In addition, our joint measurements of ectoplasm velocity and traction stress at the substratum suggest that forward motion of the ectoplasm is enabled by a succession of stick-slip transitions, which we conjecture are also organized in the form of waves. Combining our experiments with a simplified convection-diffusion model, we show that the convective transport of calcium ions may be key for establishing and maintaining the spatio-temporal patterns of calcium concentration that regulate the generation of contractile forces.

Nonparametric methods in actigraphy: An update

PubMed Central

Gonçalves, Bruno S.B.; Cavalcanti, Paula R.A.; Tavares, Gracilene R.; Campos, Tania F.; Araujo, John F.

2014-01-01

Circadian rhythmicity in humans has been well studied using actigraphy, a method of measuring gross motor movement. As actigraphic technology continues to evolve, it is important for data analysis to keep pace with new variables and features. Our objective is to study the behavior of two variables, interdaily stability and intradaily variability, to describe rest activity rhythm. Simulated data and actigraphy data of humans, rats, and marmosets were used in this study. We modified the method of calculation for IV and IS by modifying the time intervals of analysis. For each variable, we calculated the average value (IVm and ISm) results for each time interval. Simulated data showed that (1) synchronization analysis depends on sample size, and (2) fragmentation is independent of the amplitude of the generated noise. We were able to obtain a significant difference in the fragmentation patterns of stroke patients using an IVm variable, while the variable IV60 was not identified. Rhythmic synchronization of activity and rest was significantly higher in young than adults with Parkinson׳s when using the ISM variable; however, this difference was not seen using IS60. We propose an updated format to calculate rhythmic fragmentation, including two additional optional variables. These alternative methods of nonparametric analysis aim to more precisely detect sleep–wake cycle fragmentation and synchronization. PMID:26483921

Tandem Mass Spectrometry of Modified and Platinated Oligoribonucleotides

NASA Astrophysics Data System (ADS)

Nyakas, Adrien; Stucki, Silvan R.; Schürch, Stefan

2011-05-01

Therapeutic approaches for treatment of various diseases aim at the interruption of transcription or translation. Modified oligonucleotides, such as 2'- O-methyl- and methylphosphonate-derivatives, exhibit high resistance against cellular nucleases, thus rendering application for, e.g., antigene or antisense purposes possible. Other approaches are based on administration of cross-linking agents, such as cis-diamminedichloroplatinum(II) (cisplatin, DDP), which is still the most widely used anticancer drug worldwide. Due to the formation of 1,2-intrastrand cross links at adjacent guanines, replication of the double-strand is disturbed, thus resulting in significant cytotoxicity. Evidence for the gas-phase dissociation mechanism of platinated RNA is given, based on nano-electrospray ionization high-resolution multistage tandem mass spectrometry (MS n ). Confirmation was found by investigating the fragmentation pattern of platinated and unplatinated 2'-methoxy oligoribonucleotide hexamers and their corresponding methylphosphonate derivatives. Platinated 2'-methoxy oligoribonucleotides exhibit a similar gas-phase dissociation behavior as the corresponding DNA and RNA sequences, with the 3'-C-O bond adjacent to the vicinal guanines being cleaved preferentially, leading to wx-ion formation. By examination of the corresponding platinated methylphosphonate derivatives of the 2'-methoxy oligoribonucleotides, the key role of the negatively charged phosphate oxygen atoms in direct proximity to the guanines was proven. The significant alteration of fragmentation due to platination is demonstrated by comparison of the fragment ion patterns of unplatinated and platinated 2'- O-methyl- and 2'- O-methyl methylphosphonate oligoribonucleotides, and the results obtained by H/D exchange experiments.

Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

PubMed

van Agthoven, Maria A; Barrow, Mark P; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B

2015-12-01

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. Graphical Abstract ᅟ.

Development of an accurate and high-throughput methodology for structural comprehension of chlorophylls derivatives. (II) Dephytylated derivatives.

PubMed

Chen, Kewei; Ríos, José Julián; Roca, María; Pérez-Gálvez, Antonio

2015-09-18

Dephytylated chlorophylls (chlorophyllides and pheophorbides) are the starting point of the chlorophyll catabolism in green tissues, components of the chlorophyll pattern in storage/processed food vegetables, as well as the favoured structural arrangement for chlorophyll absorption. In addition, dephytylated native chlorophylls are prone to several modifications of their structure yielding pyro-, 13(2)-hydroxy- and 15(1)-hydroxy-lactone derivatives. Despite of these outstanding remarks only few of them have been analysed by MS(n). Besides new protocols for obtaining standards, we have developed a new high throughput methodology able to determine the fragmentation pathway of 16 dephytylated chlorophyll derivatives, elucidating the structures of the new product ions and new mechanisms of fragmentation. The new methodology combines, by first time, high resolution time-of-flight mass spectrometry and powerful post-processing software. Native chlorophyllides and pheophorbides mainly exhibit product ions that involve the fragmentation of D ring, as well as additional exclusive product ions. The introduction of an oxygenated function at E ring enhances the progress of fragmentation reactions through the β-keto ester group, developing also exclusive product ions for 13(2)-hydroxy derivatives and for 15(1)-hydroxy-lactone ones. Consequently, while MS(2)-based reactions of phytylated chlorophyll derivatives point to fragmentations at the phytyl and propionic chains, dephytylated chlorophyll derivatives behave different as the absence of phytyl makes β-keto ester group and E ring more prone to fragmentation. Proposals of the key reaction mechanisms underlying the origin of new product ions have been made. Copyright © 2015 Elsevier B.V. All rights reserved.

GUIDOS: tools for the assessment of pattern, connectivity, and fragmentation

NASA Astrophysics Data System (ADS)

Vogt, Peter

2013-04-01

Pattern, connectivity, and fragmentation can be considered as pillars for a quantitative analysis of digital landscape images. The free software toolbox GUIDOS (http://forest.jrc.ec.europa.eu/download/software/guidos) includes a variety of dedicated methodologies for the quantitative assessment of these features. Amongst others, Morphological Spatial Pattern Analysis (MSPA) is used for an intuitive description of image pattern structures and the automatic detection of connectivity pathways. GUIDOS includes tools for the detection and quantitative assessment of key nodes and links as well as to define connectedness in raster images and to setup appropriate input files for an enhanced network analysis using Conefor Sensinode. Finally, fragmentation is usually defined from a species point of view but a generic and quantifiable indicator is needed to measure fragmentation and its changes. Some preliminary results for different conceptual approaches will be shown for a sample dataset. Complemented by pre- and post-processing routines and a complete GIS environment the portable GUIDOS Toolbox may facilitate a holistic assessment in risk assessment studies, landscape planning, and conservation/restoration policies. Alternatively, individual analysis components may contribute to or enhance studies conducted with other software packages in landscape ecology.

Care fragmentation, quality, and costs among chronically ill patients.

PubMed

Frandsen, Brigham R; Joynt, Karen E; Rebitzer, James B; Jha, Ashish K

2015-05-01

To assess the relationship between care fragmentation and both quality and costs of care for commercially insured, chronically ill patients. We used claims data from 2004 to 2008 for 506,376 chronically ill, privately insured enrollees of a large commercial insurance company to construct measures of fragmentation. We included patients in the sample if they had chronic conditions in any of the following categories: cardiovascular disease, diabetes, asthma, arthritis, or migraine. We assigned each patient a fragmentation index based on the patterns of care of their primary care provider (PCP), with care patterns spread across a higher number of providers considered to be more fragmented. We used regression analysis to examine the relationship between fragmentation and both quality and cost outcomes. Patients of PCPs in the highest quartile of fragmentation had a higher chance of having a departure from clinical best practice (32.8%, vs 25.9% among patients of PCPs in the lowest quartile of fragmentation; P < .001). Similarly, patients of PCPs with high fragmentation had higher rates of preventable hospitalizations (9.1% in highest quartile vs 7.1% in lowest quartile; P < .001). High fragmentation was associated with $4542 higher healthcare spending ($10,396 in the highest quartile vs $5854 in the lowest quartile; P < .001). We found similar or larger effects on quality and costs among patients when we examined the most frequently occurring disease groups individually. Chronically ill patients whose primary care providers offer highly fragmented care more often experience lapses in care quality and incur greater healthcare costs.

Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Ren, Jianhua; Tian, Yuan; Hossain, Ekram; Connolly, Michael D.

2016-04-01

Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

Characteristic fragment size distributions in dynamic fragmentation

NASA Astrophysics Data System (ADS)

Zhou, Fenghua; Molinari, Jean-François; Ramesh, K. T.

2006-06-01

The one-dimensional fragmentation of a dynamically expanding ring (Mott's problem) is studied numerically to obtain the fragment signatures under different strain rates. An empirical formula is proposed to calculate an average fragment size. Rayleigh distribution is found to describe the statistical properties of the fragment populations.

LC/QTOF-MS fragmentation of N-nitrosodimethylamine precursors in drinking water supplies is predictable and aids their identification.

PubMed

Hanigan, David; Ferrer, Imma; Thurman, E Michael; Herckes, Pierre; Westerhoff, Paul

2017-02-05

N-Nitrosodimethylamine (NDMA) is carcinogenic in rodents and occurs in chloraminated drinking water and wastewater effluents. NDMA forms via reactions between chloramines and mostly unidentified, N-containing organic matter. We developed a mass spectrometry technique to identify NDMA precursors by analyzing 25 model compounds with LC/QTOF-MS. We searched isolates of 11 drinking water sources and 1 wastewater using a custom MATLAB ® program and extracted ion chromatograms for two fragmentation patterns that were specific to the model compounds. Once a diagnostic fragment was discovered, we conducted MS/MS during a subsequent injection to confirm the precursor ion. Using non-target searches and two diagnostic fragmentation patterns, we discovered 158 potential NDMA precursors. Of these, 16 were identified using accurate mass combined with fragment and retention time matches of analytical standards when available. Five of these sixteen NDMA precursors were previously unidentified in the literature, three of which were metabolites of pharmaceuticals. Except methadone, the newly identified precursors all had NDMA molar yields of less than 5%, indicating that NDMA formation could be additive from multiple compounds, each with low yield. We demonstrate that the method is applicable to other disinfection by-product precursors by predicting and verifying the fragmentation patterns for one nitrosodiethylamine precursor. Copyright © 2016. Published by Elsevier B.V.

Structural and metabolic relationships between goldfish brain glycoproteins participating in functional plasticity of the central nervous system.

PubMed

Schmidt, R; Shashoua, V E

1983-03-01

Ependymins beta and gamma (MW 32,000 and 26,000 daltons) are two secreted goldfish brain glycoproteins that exhibit a specifically enhanced turnover rate when the animals successfully acquire a new pattern of swimming behaviour. Both proteins are bound identically to concanavalin A and can be isolated from brain extracellular fluid and from brain cytoplasm by lectin affinity chromatography. Radioimmunoassay data, using purified 125I-labeled ependymins and antisera directed against ependymin beta or ependymin gamma, show complete cross-reactivity between the two proteins. It is demonstrated by Scatchard-plot analysis that the antisera recognize identical immunological determinants in both proteins. The amino acid composition of the ependymins is similar, and several identical polypeptide fragments are obtained after limited proteolysis with Staphylococcus aureus protease. The proteins are capable of forming complexes of the compositions gamma 2, beta gamma, and beta 2. A protease present in the extracellular fluid of goldfish brain promotes proteolysis of ependymin beta to ependymin gamma. The finding that ependymin gamma is physiologically derived from ependymin beta suggests the possibility that ependymin beta might exert its biological function during consolidation of new behavioural patterns via smaller polypeptide fragments.

Tropical forest fragmentation affects floral visitors but not the structure of individual-based palm-pollinator networks.

PubMed

Dáttilo, Wesley; Aguirre, Armando; Quesada, Mauricio; Dirzo, Rodolfo

2015-01-01

Despite increasing knowledge about the effects of habitat loss on pollinators in natural landscapes, information is very limited regarding the underlying mechanisms of forest fragmentation affecting plant-pollinator interactions in such landscapes. Here, we used a network approach to describe the effects of forest fragmentation on the patterns of interactions involving the understory dominant palm Astrocaryum mexicanum (Arecaceae) and its floral visitors (including both effective and non-effective pollinators) at the individual level in a Mexican tropical rainforest landscape. Specifically, we asked: (i) Does fragment size affect the structure of individual-based plant-pollinator networks? (ii) Does the core of highly interacting visitor species change along the fragmentation size gradient? (iii) Does forest fragment size influence the abundance of effective pollinators of A. mexicanum? We found that fragment size did not affect the topological structure of the individual-based palm-pollinator network. Furthermore, while the composition of peripheral non-effective pollinators changed depending on fragment size, effective core generalist species of pollinators remained stable. We also observed that both abundance and variance of effective pollinators of male and female flowers of A. mexicanum increased with forest fragment size. These findings indicate that the presence of effective pollinators in the core of all forest fragments could keep the network structure stable along the gradient of forest fragmentation. In addition, pollination of A. mexicanum could be more effective in larger fragments, since the greater abundance of pollinators in these fragments may increase the amount of pollen and diversity of pollen donors between flowers of individual plants. Given the prevalence of fragmentation in tropical ecosystems, our results indicate that the current patterns of land use will have consequences on the underlying mechanisms of pollination in remnant forests.

The evolution of urban sprawl: Evidence of spatial heterogeneity and increasing land fragmentation

PubMed Central

Irwin, Elena G.; Bockstael, Nancy E.

2007-01-01

We investigate the dynamics and spatial distribution of land use fragmentation in a rapidly urbanizing region of the United States to test key propositions regarding the evolution of sprawl. Using selected pattern metrics and data from 1973 and 2000 for the state of Maryland, we find significant increases in developed and undeveloped land fragmentation but substantial spatial heterogeneity as well. Estimated fragmentation gradients that describe mean fragmentation as a function of distance from urban centers confirm the hypotheses that fragmentation rises and falls with distance and that the point of maximum fragmentation shifted outward over time. However, rather than outward increases in sprawl balanced by development infill, we find substantial and significant increases in mean fragmentation values along the entire urban–rural gradient. These findings are in contrast to the results of Burchfield et al. [Burchfield M, Overman HG, Puga D, Turner MA (2006) Q J Econ 121:587–633], who conclude that the extent of sprawl remained roughly unchanged in the Unites States between 1976 and 1992. As demonstrated here, both the data and pattern measure used in their study are systematically biased against recording low-density residential development, the very land use that we find is most strongly associated with fragmentation. Other results demonstrate the association between exurban growth and increasing fragmentation and the systematic variation of fragmentation with nonurban factors. In particular, proximity to the Chesapeake Bay is negatively associated with fragmentation, suggesting that an attraction effect associated with this natural amenity has concentrated development. PMID:18093930

MS/MS studies on the selective on-line detection of sesquiterpenes using a Flowing Afterglow-Tandem Mass Spectrometer (FA-TMS)

NASA Astrophysics Data System (ADS)

Rimetz-Planchon, J.; Dhooghe, F.; Schoon, N.; Vanhaecke, F.; Amelynck, C.

2011-04-01

A Flowing Afterglow-Tandem Mass Spectrometer (FA-TMS) was used to investigate the feasibility of selective on-line detection of a series of seven sesquiterpenes (SQTs). These SQTs were chemically ionized by either H3O+ or NO+ reagent ions in the FA, resulting among others in protonated SQT and SQT molecular ions, respectively. These and other Chemical Ionization (CI) product ions were subsequently subjected to dissociation by collisions with Ar atoms in the collision cell of the tandem mass spectrometer. The fragmentation spectra show similarities with mass spectra obtained for these compounds with other instruments such as a Proton Transfer Reaction-Linear Ion Trap (PTR-LIT), a Proton Transfer Reaction-Mass Spectrometer (PTR-MS), a Triple Quadrupole-Mass Spectrometer (QqQ-MS) and a Selected Ion Flow Tube-Mass Spectrometer (SIFT-MS). Fragmentation of protonated SQT is characterized by fragment ions at the same masses but with different intensities for the individual SQT. Distinction of SQTs is based on well-chosen intensity ratios and collision energies. The fragmentation patterns of SQT molecular ions show specific fragment ion tracers at m/z 119, m/z162, m/z 137 and m/z 131 for α-cedrene, δ-neoclovene, isolongifolene and α-humulene, respectively. Consequently, chemical ionization of SQT by NO+, followed by MS/MS of SQT+ seems to open a way for selective quantification of SQTs in mixtures.

Human impacts affect tree community features of 20 forest fragments of a vanishing neotropical hotspot.

PubMed

Pereira, José Aldo Alves; de Oliveira-Filho, Ary Teixeira; Eisenlohr, Pedro V; Miranda, Pedro L S; de Lemos Filho, José Pires

2015-02-01

The loss in forest area due to human occupancy is not the only threat to the remaining biodiversity: forest fragments are susceptible to additional human impact. Our aim was to investigate the effect of human impact on tree community features (species composition and abundance, and structural descriptors) and check if there was a decrease in the number of slender trees, an increase in the amount of large trees, and also a reduction in the number of tree species that occur in 20 fragments of Atlantic montane semideciduous forest in southeastern Brazil. We produced digital maps of each forest fragment using Landsat 7 satellite images and processed the maps to obtain morphometric variables. We used investigative questionnaires and field observations to survey the history of human impact. We then converted the information into scores given to the extent, severity, and duration of each impact, including proportional border area, fire, trails, coppicing, logging, and cattle, and converted these scores into categorical levels. We used linear models to assess the effect of impacts on tree species abundance distribution and stand structural descriptors. Part of the variation in floristic patterns was significantly correlated to the impacts of fire, logging, and proportional border area. Structural descriptors were influenced by cattle and outer roads. Our results provided, for the first time, strong evidence that tree species occurrence and abundance, and forest structure of Atlantic seasonal forest fragments respond differently to various modes of disturbance by humans.

Global patterns of fragmentation and connectivity of mammalian carnivore habitat.

PubMed

Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; Rondinini, Carlo; Boitani, Luigi

2011-09-27

Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges, a greater proportion of habitat within their range, greater habitat connectivity and a lower risk of extinction. Species with higher connectivity (i.e. less habitat isolation) also had a greater proportion of high-quality habitat, but had smaller, not larger, ranges, probably reflecting shorter distances between habitat patches for species with restricted distributions; such species were also more threatened, as would be expected given the negative relationship between range size and extinction risk. Fragmentation and connectivity did not differ among Carnivora families, and body mass was associated with connectivity but not fragmentation. On average, only 54.3 per cent of a species' geographical range comprised high-quality habitat, and more troubling, only 5.2 per cent of the range comprised such habitat within protected areas. Identification of global hotspots of fragmentation and connectivity will help guide strategic priorities for carnivore conservation.

Geometry analysis for landscape fragmentation in coastal areas of China

NASA Astrophysics Data System (ADS)

Zhang, Tianhai; Yu, Ning; Mu, Hongdu; Tuo, Tao

2017-08-01

In recent years, the continuous expansion of urban-transport networks in China has aggravated the fragmentation of regional landscapes and led to the degradation of multiple ecological functions. In this study, Geographic Information System (GIS) techniques, patch size of fragmentation geometry were used to identify and monitor spatial distribution patterns of landscape fragmentation due to urban-transport networks in Fujian Province. This network has caused serious damage to regional ecological functions, and risks to the persistence of animal populations and biodiversity. This analysis revealed that the smallest patch class (0-15 km2) occurred with a much greater frequency than all other larger patch sizes. In the coastal cities of Xiamen, Zhangzhou and Quanzhou, the percentage of the number of patches less than 300 km2 was higher than in the western cities of Nanping, Sanming and Longyan, and the percentage of the area of patches less than 300 km2 was also higher. Based on a holistic identification of the structure of the network and its landscape division, we found that: Fujian Province has a spatial pattern of landscape fragmentation, with less fragmentation in western and northern regions, and most fragmentation in southern and eastern regions. Coastal regions and areas close to the main transport routes were more seriously fragmented and contained most of the small patches.

Global patterns of fragmentation and connectivity of mammalian carnivore habitat

PubMed Central

Crooks, Kevin R.; Burdett, Christopher L.; Theobald, David M.; Rondinini, Carlo; Boitani, Luigi

2011-01-01

Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges, a greater proportion of habitat within their range, greater habitat connectivity and a lower risk of extinction. Species with higher connectivity (i.e. less habitat isolation) also had a greater proportion of high-quality habitat, but had smaller, not larger, ranges, probably reflecting shorter distances between habitat patches for species with restricted distributions; such species were also more threatened, as would be expected given the negative relationship between range size and extinction risk. Fragmentation and connectivity did not differ among Carnivora families, and body mass was associated with connectivity but not fragmentation. On average, only 54.3 per cent of a species' geographical range comprised high-quality habitat, and more troubling, only 5.2 per cent of the range comprised such habitat within protected areas. Identification of global hotspots of fragmentation and connectivity will help guide strategic priorities for carnivore conservation. PMID:21844043

Fission of actinide nuclei using multi-nucleon transfer reactions

NASA Astrophysics Data System (ADS)

Léguillon, Romain; Nishio, Katsuhisa; Hirose, Kentaro; Orlandi, Riccardo; Makii, Hiroyuki; Nishinaka, Ichiro; Ishii, Tetsuro; Tsukada, Kazuaki; Asai, Masato; Chiba, Satoshi; Ohtsuki, Tsutomu; Araki, Shohei; Watanabe, Yukinobu; Tatsuzawa, Ryotaro; Takaki, Naoyuki

2014-09-01

We are promoting a campaign to measure fission-fragment mass distributions for neutron-rich actinide nuclei populated by transfer reactions from their ground state up to an excitation energy of several tens MeV. We thus obtain the excitation energy dependence of the mass distribution. The experiment was carried out at the 20 MV JAEA tandem facility at Tokai. We report on the data obtained in the direct reaction 18 O + 232 Th . Transfer-channels and excitation energies of the fissioning nuclei were identified using silicon dE-E detectors located at forward angle. Two fission fragments were detected in coincidence using multi-wire proportional counters. Fission fragment masses were determined by kinematic consideration. We obtained the fission fragment mass distributions for 13 nuclei from actinium to uranium and some fission barrier heights. We are promoting a campaign to measure fission-fragment mass distributions for neutron-rich actinide nuclei populated by transfer reactions from their ground state up to an excitation energy of several tens MeV. We thus obtain the excitation energy dependence of the mass distribution. The experiment was carried out at the 20 MV JAEA tandem facility at Tokai. We report on the data obtained in the direct reaction 18 O + 232 Th . Transfer-channels and excitation energies of the fissioning nuclei were identified using silicon dE-E detectors located at forward angle. Two fission fragments were detected in coincidence using multi-wire proportional counters. Fission fragment masses were determined by kinematic consideration. We obtained the fission fragment mass distributions for 13 nuclei from actinium to uranium and some fission barrier heights. Present study is supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan.

Peptide Fragmentation Induced by Radicals at Atmospheric Pressure

PubMed Central

Vilkov, Andrey N.; Laiko, Victor V.; Doroshenko, Vladimir M.

2009-01-01

A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essentially atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to ECD/ETD, along with the y-/b- fragments that are specific to CAD. In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer. According to a proposed mechanism, the fragmentation results from the interaction of ESI-generated analyte ions with the gas-phase radical species produced by a corona discharge source. PMID:19034885

Mass Spectra of Some Perfluoroalkyl and Perfluoroalkylether Substituted 1,2,4-Oxadiazoles

NASA Technical Reports Server (NTRS)

Paciorek, Kazimiera J. L.; Nakahara, James H.; Kratzer, Reinhold H.; Rosser, Robert W.

1977-01-01

Electron impact fragmentation patterns were obtained for 1,4-bis[(5-perfluoro-n-heptyl)-1,2,4-oxadiazolyl- benzene, its perfluoroalkylether substituted analogue, 3,5-bis(perfluoroalkyl)-, 3,5-bis(perfluoroalkylether)- and 3-perfluoroalkylether-5-perfluoroalkyl-1,2,4-oxadiazoles. In the compounds containing the phenylene group the molecular ion constituted the base peak; the main process was the breakdown of the oxadiazole ring with concurrent liberation of the perfluoroalkyl or perfluoroalkylether nitrile molecule; cleavage of the fluorinated chain ot to the oxadiazole ring was found to take place to a considerable degree. In the perfluorinated 1,2,4-oxadiazoles cleavage beta to the oxadiazole ring occurred preferentially; fragmentation of the ring itself took place to a limited degree only. The 3-perfluoroalkylether-5-perfluoroalkyl-1,2,4-oxadiazole appeared to undergo the primary beta-cleavage exclusively at the perfluoroalkylether sidechain.

The role of attention during encoding in implicit and explicit memory.

PubMed

Mulligan, N W

1998-01-01

In 5 experiments, participants read study words under conditions of divided or full attention. Dividing attention reduced performance on the general knowledge test, a conceptual implicit test of memory. Likewise, dividing attention reduced conceptual priming on the word--association task, as well as on a matched explicit test, associate-cued recall. In contrast, even very strong division of attention did not reduce perceptual priming on word-fragment completion, although it did reduce recall on the matched explicit test of word-fragment-cued recall. Finally, dividing attention reduced recall on the perceptual explicit tests of graphemic-cued recall and graphemic recognition. The results indicate that perceptual implicit tests rely minimally on attention-demanding encoding processes relative to other types of memory tests. The obtained pattern of dissociations is not readily accommodated by the transfer-appropriate-processing (TAP) account of implicit and explicit memory. Potential extensions of the TAP view are discussed.

Consequences of Landscape Fragmentation on Lyme Disease Risk: A Cellular Automata Approach

PubMed Central

Li, Sen; Hartemink, Nienke; Speybroeck, Niko; Vanwambeke, Sophie O.

2012-01-01

The abundance of infected Ixodid ticks is an important component of human risk of Lyme disease, and various empirical studies have shown that this is associated, at least in part, to landscape fragmentation. In this study, we aimed at exploring how varying woodland fragmentation patterns affect the risk of Lyme disease, through infected tick abundance. A cellular automata model was developed, incorporating a heterogeneous landscape with three interactive components: an age-structured tick population, a classical disease transmission function, and hosts. A set of simplifying assumptions were adopted with respect to the study objective and field data limitations. In the model, the landscape influences both tick survival and host movement. The validation of the model was performed with an empirical study. Scenarios of various landscape configurations (focusing on woodland fragmentation) were simulated and compared. Lyme disease risk indices (density and infection prevalence of nymphs) differed considerably between scenarios: (i) the risk could be higher in highly fragmented woodlands, which is supported by a number of recently published empirical studies, and (ii) grassland could reduce the risk in adjacent woodland, which suggests landscape fragmentation studies of zoonotic diseases should not focus on the patch-level woodland patterns only, but also on landscape-level adjacent land cover patterns. Further analysis of the simulation results indicated strong correlations between Lyme disease risk indices and the density, shape and aggregation level of woodland patches. These findings highlight the strong effect of the spatial patterns of local host population and movement on the spatial dynamics of Lyme disease risks, which can be shaped by woodland fragmentation. In conclusion, using a cellular automata approach is beneficial for modelling complex zoonotic transmission systems as it can be combined with either real world landscapes for exploring direct spatial effects or artificial representations for outlining possible empirical investigations. PMID:22761842

Age-related differences in human skin proteoglycans.

PubMed

Carrino, David A; Calabro, Anthony; Darr, Aniq B; Dours-Zimmermann, Maria T; Sandy, John D; Zimmermann, Dieter R; Sorrell, J Michael; Hascall, Vincent C; Caplan, Arnold I

2011-02-01

Previous work has shown that versican, decorin and a catabolic fragment of decorin, termed decorunt, are the most abundant proteoglycans in human skin. Further analysis of versican indicates that four major core protein species are present in human skin at all ages examined from fetal to adult. Two of these are identified as the V0 and V1 isoforms, with the latter predominating. The other two species are catabolic fragments of V0 and V1, which have the amino acid sequence DPEAAE as their carboxyl terminus. Although the core proteins of human skin versican show no major age-related differences, the glycosaminoglycans (GAGs) of adult skin versican are smaller in size and show differences in their sulfation pattern relative to those in fetal skin versican. In contrast to human skin versican, human skin decorin shows minimal age-related differences in its sulfation pattern, although, like versican, the GAGs of adult skin decorin are smaller than those of fetal skin decorin. Analysis of the catabolic fragments of decorin from adult skin reveals the presence of other fragments in addition to decorunt, although the core proteins of these additional decorin catabolic fragments have not been identified. Thus, versican and decorin of human skin show age-related differences, versican primarily in the size and the sulfation pattern of its GAGs and decorin in the size of its GAGs. The catabolic fragments of versican are detected at all ages examined, but appear to be in lower abundance in adult skin compared with fetal skin. In contrast, the catabolic fragments of decorin are present in adult skin, but are virtually absent from fetal skin. Taken together, these data suggest that there are age-related differences in the catabolism of proteoglycans in human skin. These age-related differences in proteoglycan patterns and catabolism may play a role in the age-related changes in the physical properties and injury response of human skin.

Urbanization-induced habitat fragmentation erodes multiple components of temporal diversity in a Southern California native bee assemblage

PubMed Central

Ascher, John S.; Holway, David A.

2017-01-01

Despite a large number of ecological studies that document diversity loss resulting from anthropogenic disturbance, surprisingly few consider how disturbance affects temporal patterns of diversity that result from seasonal turnover of species. Temporal dynamics can play an important role in the structure and function of biological assemblages. Here, we investigate the temporal diversity patterns of bee faunas in Southern California coastal sage scrub ecosystems that have been extensively fragmented by urbanization. Using a two-year dataset of 235 bee species (n = 12,036 specimens), we compared 1-ha plots in scrub fragments and scrub reserves with respect to three components of temporal diversity: overall plot-level diversity pooled over time (temporal gamma diversity), diversity at discrete points in time (temporal alpha diversity), and seasonal turnover in assemblage composition (temporal beta diversity). Compared to reserves, fragments harbored bee assemblages with lower species richness and assemblage evenness both when summed across temporal samples (i.e., lower temporal gamma diversity) and at single points in time (i.e., lower temporal alpha diversity). Bee assemblages in fragments also exhibited reduced seasonal turnover (i.e., lower temporal beta diversity). While fragments and reserves did not differ in overall bee abundance, bee abundance in fragments peaked later in the season compared to that in reserves. Our results argue for an increased awareness of temporal diversity patterns, as information about the distinct components of temporal diversity is essential both for characterizing the assemblage dynamics of seasonal organisms and for identifying potential impacts of anthropogenic disturbance on ecosystem function through its effects on assemblage dynamics. PMID:28854229

Habitat fragmentation and the Burrowing Owls (Speotyto cunicularia) in Saskatchewan

Treesearch

Robert G. Warnock; Paul C. James

1997-01-01

The relationship between landscape (125,664 ha circular plots) fragmentation patterns and the spatial distribution of Burrowing Owls (Speotyto cunicularia) was investigated in the heavily fragmented grasslands of Saskatchewan. Data were collected from 152 Burrowing Owl sites and 250 random sites located on 1990 LANDSAT-TM satellite images and 1:250,...

The influence of impact direction and axial loading on the bone fracture pattern.

PubMed

Cohen, Haim; Kugel, Chen; May, Hila; Medlej, Bahaa; Stein, Dan; Slon, Viviane; Brosh, Tamar; Hershkovitz, Israel

2017-08-01

The effect of the direction of the impact and the presence of axial loading on fracture patterns have not yet been established in experimental 3-point bending studies. To reveal the association between the direction of the force and the fracture pattern, with and without axial loading. A Dynatup Model POE 2000 (Instron Co.) low energy pendulum impact machine was utilized to apply impact loading on fresh pig femoral bones (n=50). The bone clamp shaft was adjusted to position the bone for three-point bending with and without additional bone compression. Four different directions of the force were applied: anterior, posterior, lateral, and medial. The impacted aspect can be distinguished from the non-impacted aspects based on the fracture pattern alone (the most fractured one); the impact point can be identified on bare bones (the area from which all oblique lines radiate and/or the presence of a chip fragment). None of our experiments (with and without compression) yielded a "true" butterfly fracture, but instead, oblique radiating lines emerged from the point of impact (also known as "false" butterfly). Impacts on the lateral and anterior aspects of the bones produce more and longer fracture lines than impacts on the contralateral side; bones subjected to an impact with axial loading are significantly more comminuted and fragmented. Under axial loading, the number of fracture lines is independent of the impact direction. Our study presents an experimental model for fracture analysis and shows that the impact direction and the presence of axial loading during impact significantly affect the fracture pattern obtained. Copyright © 2017 Elsevier B.V. All rights reserved.

Heart Rate Fragmentation: A Symbolic Dynamical Approach.

PubMed

Costa, Madalena D; Davis, Roger B; Goldberger, Ary L

2017-01-01

Background: We recently introduced the concept of heart rate fragmentation along with a set of metrics for its quantification. The term was coined to refer to an increase in the percentage of changes in heart rate acceleration sign, a dynamical marker of a type of anomalous variability. The effort was motivated by the observation that fragmentation, which is consistent with the breakdown of the neuroautonomic-electrophysiologic control system of the sino-atrial node, could confound traditional short-term analysis of heart rate variability. Objective: The objectives of this study were to: (1) introduce a symbolic dynamical approach to the problem of quantifying heart rate fragmentation; (2) evaluate how the distribution of the different dynamical patterns ("words") varied with the participants' age in a group of healthy subjects and patients with coronary artery disease (CAD); and (3) quantify the differences in the fragmentation patterns between the two sample populations. Methods: The symbolic dynamical method employed here was based on a ternary map of the increment NN interval time series and on the analysis of the relative frequency of symbolic sequences (words) with a pre-defined set of features. We analyzed annotated, open-access Holter databases of healthy subjects and patients with CAD, provided by the University of Rochester Telemetric and Holter ECG Warehouse (THEW). Results: The degree of fragmentation was significantly higher in older individuals than in their younger counterparts. However, the fragmentation patterns were different in the two sample populations. In healthy subjects, older age was significantly associated with a higher percentage of transitions from acceleration/deceleration to zero acceleration and vice versa (termed "soft" inflection points). In patients with CAD, older age was also significantly associated with higher percentages of frank reversals in heart rate acceleration (transitions from acceleration to deceleration and vice versa , termed "hard" inflection points). Compared to healthy subjects, patients with CAD had significantly higher percentages of soft and hard inflection points, an increased percentage of words with a high degree of fragmentation and a decreased percentage of words with a lower degree of fragmentation. Conclusion: The symbolic dynamical method employed here was useful to probe the newly recognized property of heart rate fragmentation. The findings from these cross-sectional studies confirm that CAD and older age are associated with higher levels of heart rate fragmentation. Furthermore, fragmentation with healthy aging appears to be phenotypically different from fragmentation in the context of CAD.

First ancient DNA sequences from the Late Pleistocene red deer (Cervus elaphus) in the Crimea, Ukraine

NASA Astrophysics Data System (ADS)

Stanković, Ana; Nadachowski, Adam; Doan, Karolina; Stefaniak, Krzysztof; Baca, Mateusz; Socha, Paweł; Wegleński, Piotr; Ridush, Bogdan

2010-05-01

The Late Pleistocene has been a period of significant population and species turnover and extinctions among the large mammal fauna. Massive climatic and environmental changes during Pleistocene significantly influenced the distribution and also genetic diversity of plants and animals. The model of glacial refugia and habitat contraction to southern peninsulas in Europe as areas for the survival of temperate animal species during unfavourable Pleistocene glaciations is at present widely accepted. However, both molecular data and the fossil record indicate the presence of northern and perhaps north-eastern refugia in Europe. In recent years, much new palaeontological data have been obtained in the Crimean Peninsula, Ukraine, following extensive investigations. The red deer (Cervus elaphus) samples for aDNA studies were collected in Emine-Bair-Khosar Cave, situated on the north edge of Lower Plateau of the Chatyrdag Massif (Crimean Mountains). The cave is a vertical shaft, which functioned as a huge mega-trap over a long period of time (probably most of the Pleistocene). The bone assemblages provided about 5000 bones belonging to more than 40 species. The C. elaphus bones were collected from three different stratigraphical levels, radiocarbon dated by accelerator mass spectrometry (AMS) method. The bone fragments of four specimens of red deer were used for the DNA isolation and analysis. The mtDNA (Cytochome b) was successfully isolated from three bone fragments and the cytochrome b sequences were amplified by multiplex PCR. The sequences obtained so far allowed for the reconstruction of only preliminary phylogenetic trees. A fragment of metatarsus from level dated to ca. 48,500±2,000 years BP, yielded a sequence of 513 bp, allowing to locate the specimen on the phylogenetic tree within modern C. elaphus specimens from southern and middle Europe. The second bone fragment, a fragment of mandible, collected from level dated approximately to ca. 33,500±400 years BP, yielded a sequence (696 bp) locating this specimen much closer to the modern C. elaphus specimens from China and Far East. From the third bone fragment (metatarsus), dated between ca. 12,000 years BP and 30,000 years BP, the sequence of only 346 bp has been obtained. It locates this specimen between European and Asiatic haplogroups. The preliminary results of analysis of the DNA from Crimean C. elaphus fossils reveal the great genetic heterogeneity and a complex phylogeographical pattern of the material studied. The obtained results support the opinion that Crimean Peninsula was the most north-eastern refugium in Europe during Late Pleistocene playing a major role in recolonization and dispersal processes of temperate species during and after the Late Pleistocene in this part of the Euro-Asian continent.

Measuring forest landscape patterns in the Cascade Range of Oregon, USA

NASA Technical Reports Server (NTRS)

Ripple, William J.; Bradshaw, G. A.; Spies, Thomas A.

1995-01-01

This paper describes the use of a set of spatial statistics to quantify the landscape pattern caused by the patchwork of clearcuts made over a 15-year period in the western Cascades of Oregon. Fifteen areas were selected at random to represent a diversity of landscape fragmentation patterns. Managed forest stands (patches) were digitized and analyzed to produce both tabular and mapped information describing patch size, shape, abundance and spacing, and matrix characteristics of a given area. In addition, a GIS fragmentation index was developed which was found to be sensitive to patch abundance and to the spatial distribution of patches. Use of the GIS-derived index provides an automated method of determining the level of forest fragmentation and can be used to facilitate spatial analysis of the landscape for later coordination with field and remotely sensed data. A comparison of the spatial statistics calculated for the two years indicates an increase in forest fragmentation as characterized by an increase in mean patch abundance and a decrease in interpatch distance, amount of interior natural forest habitat, and the GIS fragmentation index. Such statistics capable of quantifying patch shape and spatial distribution may prove important in the evaluation of the changing character of interior and edge habitats for wildlife.

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens.

PubMed

Weiß, Clemens L; Schuenemann, Verena J; Devos, Jane; Shirsekar, Gautam; Reiter, Ella; Gould, Billie A; Stinchcombe, John R; Krause, Johannes; Burbano, Hernán A

2016-06-01

Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

Isoschizomers and amplified fragment length polymorphism for the detection of specific cytosine methylation changes.

PubMed

Ruiz-García, Leonor; Cabezas, Jose Antonio; de María, Nuria; Cervera, María-Teresa

2010-01-01

Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is a modification of the Amplified Fragment Length Polymorphism (AFLP) technique that has been used to study methylation of anonymous CCGG sequences in different fungi, plant and animal species. The main variation of this technique is based on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent cutter restriction enzyme. For each sample, AFLP analysis is performed using both EcoRI/HpaII and EcoRI/MspI digested samples. Comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) "Methylation-insensitive polymorphisms" that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples; and (2) "Methylation-sensitive polymorphisms" that are associated with amplified fragments differing in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses modifications that can be applied to adjust the technology to different species of interest.

Consequences of extensive habitat fragmentation in landscape-level patterns of genetic diversity and structure in the Mediterranean esparto grasshopper

PubMed Central

Ortego, Joaquín; Aguirre, María P; Noguerales, Víctor; Cordero, Pedro J

2015-01-01

Anthropogenic habitat fragmentation has altered the distribution and population sizes in many organisms worldwide. For this reason, understanding the demographic and genetic consequences of this process is necessary to predict the fate of populations and establish management practices aimed to ensure their viability. In this study, we analyse whether the spatial configuration of remnant semi-natural habitat patches within a chronically fragmented landscape has shaped the patterns of genetic diversity and structure in the habitat-specialist esparto grasshopper (Ramburiella hispanica). In particular, we predict that agricultural lands constitute barriers to gene flow and hypothesize that fragmentation has restricted interpopulation dispersal and reduced local levels of genetic diversity. Our results confirmed the expectation that isolation and habitat fragmentation have reduced the genetic diversity of local populations. Landscape genetic analyses based on circuit theory showed that agricultural land offers ∽1000 times more resistance to gene flow than semi-natural habitats, indicating that patterns of dispersal are constrained by the spatial configuration of remnant patches of suitable habitat. Overall, this study shows that semi-natural habitat patches act as corridors for interpopulation gene flow and should be preserved due to the disproportionately large ecological function that they provide considering their insignificant area within these human-modified landscapes. PMID:26136826

Global patterns of tropical forest fragmentation

NASA Astrophysics Data System (ADS)

Taubert, Franziska; Fischer, Rico; Groeneveld, Jürgen; Lehmann, Sebastian; Müller, Michael S.; Rödig, Edna; Wiegand, Thorsten; Huth, Andreas

2018-02-01

Remote sensing enables the quantification of tropical deforestation with high spatial resolution. This in-depth mapping has led to substantial advances in the analysis of continent-wide fragmentation of tropical forests. Here we identified approximately 130 million forest fragments in three continents that show surprisingly similar power-law size and perimeter distributions as well as fractal dimensions. Power-law distributions have been observed in many natural phenomena such as wildfires, landslides and earthquakes. The principles of percolation theory provide one explanation for the observed patterns, and suggest that forest fragmentation is close to the critical point of percolation; simulation modelling also supports this hypothesis. The observed patterns emerge not only from random deforestation, which can be described by percolation theory, but also from a wide range of deforestation and forest-recovery regimes. Our models predict that additional forest loss will result in a large increase in the total number of forest fragments—at maximum by a factor of 33 over 50 years—as well as a decrease in their size, and that these consequences could be partly mitigated by reforestation and forest protection.

Loggers and Forest Fragmentation: Behavioral Models of Road Building in the Amazon Basin

NASA Technical Reports Server (NTRS)

Arima, Eugenio Y.; Walker, Robert T.; Perz, Stephen G.; Caldas, Marcellus

2005-01-01

Although a large literature now exists on the drivers of tropical deforestation, less is known about its spatial manifestation. This is a critical shortcoming in our knowledge base since the spatial pattern of land-cover change and forest fragmentation, in particular, strongly affect biodiversity. The purpose of this article is to consider emergent patterns of road networks, the initial proximate cause of fragmentation in tropical forest frontiers. Specifically, we address the road-building processes of loggers who are very active in the Amazon landscape. To this end, we develop an explanation of road expansions, using a positive approach combining a theoretical model of economic behavior with geographic information systems (GIs) software in order to mimic the spatial decisions of road builders. We simulate two types of road extensions commonly found in the Amazon basin in a region: showing the fishbone pattern of fragmentation. Although our simulation results are only partially successful, they call attention to the role of multiple agents in the landscape, the importance of legal and institutional constraints on economic behavior, and the power of GIs as a research tool.

Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP).

PubMed

Guevara, María Ángeles; de María, Nuria; Sáez-Laguna, Enrique; Vélez, María Dolores; Cervera, María Teresa; Cabezas, José Antonio

2017-01-01

Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.

Discerning fragmentation dynamics of tropical forest and wetland during reforestation, urban sprawl, and policy shifts.

PubMed

Gao, Qiong; Yu, Mei

2014-01-01

Despite the overall trend of worldwide deforestation over recent decades, reforestation has also been found and is expected in developing countries undergoing fast urbanization and agriculture abandonment. The consequences of reforestation on landscape patterns are seldom addressed in the literature, despite their importance in evaluating biodiversity and ecosystem functions. By analyzing long-term land cover changes in Puerto Rico, a rapidly reforested (6 to 42% during 1940-2000) and urbanized tropical island, we detected significantly different patterns of fragmentation and underlying mechanisms among forests, urban areas, and wetlands. Forest fragmentation is often associated with deforestation. However, we also found significant fragmentation during reforestation. Urban sprawl and suburb development have a dominant impact on forest fragmentation. Reforestation mostly occurs along forest edges, while significant deforestation occurs in forest interiors. The deforestation process has a much stronger impact on forest fragmentation than the reforestation process due to their different spatial configurations. In contrast, despite the strong interference of coastal urbanization, wetland aggregation has occurred due to the effective implementation of laws/regulations for wetland protection. The peak forest fragmentation shifted toward rural areas, indicating progressively more fragmentation in forest interiors. This shift is synchronous with the accelerated urban sprawl as indicated by the accelerated shift of the peak fragmentation index of urban cover toward rural areas, i.e., 1.37% yr-1 in 1977-1991 versus 2.17% yr-1 in 1991-2000. Based on the expected global urbanization and the regional forest transition from deforested to reforested, the fragmented forests and aggregated wetlands in this study highlight possible forest fragmentation processes during reforestation in an assessment of biodiversity and functions and suggest effective laws/regulations in land planning to reduce future fragmentation.

Discerning Fragmentation Dynamics of Tropical Forest and Wetland during Reforestation, Urban Sprawl, and Policy Shifts

PubMed Central

Gao, Qiong; Yu, Mei

2014-01-01

Despite the overall trend of worldwide deforestation over recent decades, reforestation has also been found and is expected in developing countries undergoing fast urbanization and agriculture abandonment. The consequences of reforestation on landscape patterns are seldom addressed in the literature, despite their importance in evaluating biodiversity and ecosystem functions. By analyzing long-term land cover changes in Puerto Rico, a rapidly reforested (6 to 42% during 1940–2000) and urbanized tropical island, we detected significantly different patterns of fragmentation and underlying mechanisms among forests, urban areas, and wetlands. Forest fragmentation is often associated with deforestation. However, we also found significant fragmentation during reforestation. Urban sprawl and suburb development have a dominant impact on forest fragmentation. Reforestation mostly occurs along forest edges, while significant deforestation occurs in forest interiors. The deforestation process has a much stronger impact on forest fragmentation than the reforestation process due to their different spatial configurations. In contrast, despite the strong interference of coastal urbanization, wetland aggregation has occurred due to the effective implementation of laws/regulations for wetland protection. The peak forest fragmentation shifted toward rural areas, indicating progressively more fragmentation in forest interiors. This shift is synchronous with the accelerated urban sprawl as indicated by the accelerated shift of the peak fragmentation index of urban cover toward rural areas, i.e., 1.37% yr−1 in 1977–1991 versus 2.17% yr−1 in 1991–2000. Based on the expected global urbanization and the regional forest transition from deforested to reforested, the fragmented forests and aggregated wetlands in this study highlight possible forest fragmentation processes during reforestation in an assessment of biodiversity and functions and suggest effective laws/regulations in land planning to reduce future fragmentation. PMID:25409016

Embedded fragments from U.S. military personnel--chemical analysis and potential health implications.

PubMed

Centeno, José A; Rogers, Duane A; van der Voet, Gijsbert B; Fornero, Elisa; Zhang, Lingsu; Mullick, Florabel G; Chapman, Gail D; Olabisi, Ayodele O; Wagner, Dean J; Stojadinovic, Alexander; Potter, Benjamin K

2014-01-23

The majority of modern war wounds are characterized by high-energy blast injuries containing a wide range of retained foreign materials of a metallic or composite nature. Health effects of retained fragments range from local or systemic toxicities to foreign body reactions or malignancies, and dependent on the chemical composition and corrosiveness of the fragments in vivo. Information obtained by chemical analysis of excised fragments can be used to guide clinical decisions regarding the need for fragment removal, to develop therapeutic interventions, and to better anticipate future medical problems from retained fragment related injuries. In response to this need, a new U.S Department of Defense (DoD) directive has been issued requiring characterization of all removed fragments to provide a database of fragment types occurring in combat injuries. The objective of this study is to determine the chemical composition of retained embedded fragments removed from injured military personnel, and to relate results to histological findings in tissue adjacent to fragment material. We describe an approach for the chemical analysis and characterization of retained fragments and adjacent tissues, and include case examples describing fragments containing depleted uranium (DU), tungsten (W), lead (Pb), and non-metal foreign bodies composed of natural and composite materials. Fragments obtained from four patients with penetrating blast wounds to the limbs were studied employing a wide range of chemical and microscopy techniques. Available adjacent tissues from three of the cases were histologically, microscopically, and chemically examined. The physical and compositional properties of the removed foreign material surfaces were examined with energy dispersive x-ray fluorescence spectrometry (EDXRF), scanning electron microscopy (SEM), laser ablation inductively-coupled plasma mass-spectrometry (LA-ICP-MS), and confocal laser Raman microspectroscopy (CLRM). Quantitative chemical analysis of both fragments and available tissues was conducted employing ICP-MS. Over 800 fragments have been characterized and included as part of the Joint Pathology Center Embedded Fragment Registry. Most fragments were obtained from penetrating wounds sustained to the extremities, particularly soft tissue injuries. The majority of the fragments were primarily composed of a single metal such as iron, copper, or aluminum with traces of antimony, titanium, uranium, and lead. One case demonstrated tungsten in both the fragment and the connected tissue, together with lead. Capsular tissue and fragments from a case from the 1991 Kuwait conflict showed evidence of uranium that was further characterized by uranium isotopic ratios analysis to contain depleted uranium. The present study provides a systematic approach for obtaining a full chemical characterization of retained embedded fragments. Given the vast number of combat casualties with retained fragments, it is expected that fragment analysis will have significant implications for the optimal short and long-term care of wounded service members.

Embedded Fragments from U.S. Military Personnel—Chemical Analysis and Potential Health Implications

PubMed Central

Centeno, José A.; Rogers, Duane A.; van der Voet, Gijsbert B.; Fornero, Elisa; Zhang, Lingsu; Mullick, Florabel G.; Chapman, Gail D.; Olabisi, Ayodele O.; Wagner, Dean J.; Stojadinovic, Alexander; Potter, Benjamin K.

2014-01-01

Background: The majority of modern war wounds are characterized by high-energy blast injuries containing a wide range of retained foreign materials of a metallic or composite nature. Health effects of retained fragments range from local or systemic toxicities to foreign body reactions or malignancies, and dependent on the chemical composition and corrosiveness of the fragments in vivo. Information obtained by chemical analysis of excised fragments can be used to guide clinical decisions regarding the need for fragment removal, to develop therapeutic interventions, and to better anticipate future medical problems from retained fragment related injuries. In response to this need, a new U.S Department of Defense (DoD) directive has been issued requiring characterization of all removed fragments to provide a database of fragment types occurring in combat injuries. Objectives: The objective of this study is to determine the chemical composition of retained embedded fragments removed from injured military personnel, and to relate results to histological findings in tissue adjacent to fragment material. Methods: We describe an approach for the chemical analysis and characterization of retained fragments and adjacent tissues, and include case examples describing fragments containing depleted uranium (DU), tungsten (W), lead (Pb), and non-metal foreign bodies composed of natural and composite materials. Fragments obtained from four patients with penetrating blast wounds to the limbs were studied employing a wide range of chemical and microscopy techniques. Available adjacent tissues from three of the cases were histologically, microscopically, and chemically examined. The physical and compositional properties of the removed foreign material surfaces were examined with energy dispersive x-ray fluorescence spectrometry (EDXRF), scanning electron microscopy (SEM), laser ablation inductively-coupled plasma mass-spectrometry (LA-ICP-MS), and confocal laser Raman microspectroscopy (CLRM). Quantitative chemical analysis of both fragments and available tissues was conducted employing ICP-MS. Results: Over 800 fragments have been characterized and included as part of the Joint Pathology Center Embedded Fragment Registry. Most fragments were obtained from penetrating wounds sustained to the extremities, particularly soft tissue injuries. The majority of the fragments were primarily composed of a single metal such as iron, copper, or aluminum with traces of antimony, titanium, uranium, and lead. One case demonstrated tungsten in both the fragment and the connected tissue, together with lead. Capsular tissue and fragments from a case from the 1991 Kuwait conflict showed evidence of uranium that was further characterized by uranium isotopic ratios analysis to contain depleted uranium. Conclusions: The present study provides a systematic approach for obtaining a full chemical characterization of retained embedded fragments. Given the vast number of combat casualties with retained fragments, it is expected that fragment analysis will have significant implications for the optimal short and long-term care of wounded service members. PMID:24464236

Study of the Cross-Reactions of Hen and Duck Ovalbumins. Immunochemical Relationship between Native Proteins and Precipitating Fragments obtained after Proteolysis

PubMed Central

Kaminski, Marie

1962-01-01

The enzymatic digestion of duck ovalbumin yields precipitating fragments similar to those obtained with hen ovalbumin. In an anti-ovalbumin serum, the amount of antibody precipitating with the two fragments of degraded homologous ovalbumin and the amount of antibody precipitating with the heterologous ovalbumin are independent. The absorption of an anti-ovalbumin serum with the heterologous ovalbumin does not remove selectively the antibodies against one or another fragment of the degraded homologous antigen. The corresponding fragments obtained by digestion of hen and duck ovalbumins give cross-reactions when tested with anti-hen-ovalbumin serum, anti-duck-ovalbumin serum and anti-degraded-hen-ovalbumin serum. On double diffusion in agar, the cross-reaction between the native ovalbumin and its fragment yields a spur which is shorter than the spur formed by the two native ovalbumins or by the two corresponding fragments. ImagesFIG. 1FIG. 2FIG. 3FIG. 4FIG. 5FIG. 6FIG. 7FIG. 8FIG. 9FIG. 11FIG. 12FIG. 13 PMID:14453463

Characterisation of homoflavonoids from three Ophioglossum species using liquid chromatography with diode array detection and electrospray ionisation tandem mass spectrometry.

PubMed

Wan, Chuan-Xing; Luo, Jian-Guang; Gu, Yu-Cheng; Xu, De-Ran; Kong, Ling-Yi

2013-01-01

Homoflavonoids, characterised by one more carbon atom directly added to C6 -C3 -C6 backbone of flavonoids, are rich in the species of genus Ophioglossum. Up to now we have little knowledge about their MS fragmentation patterns. It is therefore necessary to investigate their MS fragmentation pathways so as to distinguish them from other types of flavonoids. To develop a rapid method for identifying homoflavonoids from Ophioglossum based on their characteristic MS fragmentation. Mass spectrometry fragmentation pathways and qualitative analysis of homoflavonoids in three ferns of Ophioglosssum were investigated by using high-performance liquid chromatography coupled with diode-array detection and electrospray ionisation tandem mass spectrometry (HPLC-DAD-ESI/MS(n) ). The analyses of the MS(n) spectra of the homoflavonoids allowed us to classify them into two types according to their fragmentation characteristics. The type I homoflavonoids, with an attached additional carbon atom to the C-3 position of the C-ring, presented the initial competing loss of H2 O and CH2 O from their aglycone ions, compared to the initial removal of H2 O or CO in the case of the type II homoflavonoids, which bear the additional carbon atom at the C-2' site of the B-ring and forming ring D. The above characteristic fragmentations of homoflavonoids were quite different from those of other flavonoids, and were successfully applied to identify homoflavonoids in the crude extracts of three Ophioglossum species. The HPLC-DAD-ESI/MS(n) method obtained in the present study provided a powerful tool for identifying homoflavonoids from ferns in the genus Ophioglossum. Copyright © 2013 John Wiley & Sons, Ltd.

Geographic variation in cowbird distribution, abundance, and parasitism

USGS Publications Warehouse

Morrison, M.L.; Hahn, D.C.; George, T. Luke; Dobkin, David S.

2002-01-01

We evaluated geographical patterns in the abundance and distribution of Brown-headed Cowbirds (Molothrus ater), and in the frequency of cowbird parasitism, across North America in relation to habitat fragmentation. We found no distinctive parasitism patterns at the national or even regional scales, but the species is most abundant in the Great Plains, the heart of their original range, and least common in the southeastern U.S. This situation is dynamic, because both the Brown-headed and two other cowbird species are actively expanding their ranges in the southern U.S. We focused almost entirely in this paper on the Brown-headed Cowbird, because it is the only endemic North American cowbird, its distribution is much wider, and it has been much more intensively studied. We determined that landscape is the most meaningful unit of scale for comparing cowbird parasitism patterns as, for example, in comparisons of northeastern and central hardwood forests within agricultural matrices, and suburbanized areas versus western coniferous forests. We concluded that cowbird parasitism patterns were broadly similar within all landscapes. Even comparisons between prominently dissimilar landscapes, such as hardwoods in agriculture and suburbia versus coniferous forest, display a striking similarity in the responses of cowbirds. Our review clearly indicated that proximity of feeding areas is the key factor influencing presence and parasitism patterns within the landscape. We considered intensity of landscape fragmentation from forest-dominated landscapes altered in a forest management context to fragmentation characterized by mixed suburbanization or agricultural development. Our review consistently identified an inverse relationship between extent of forest cover across the landscape and cowbird presence. Invariably, the variation seen in parasitism frequencies within a region was at least partially explained as a response to changes in forest cover. The most salient geographic aspect of cowbirds' response to landscape fragmentation is the time since fragmentation occurred. Eastern landscapes generally experienced 200 years ago the development and fragmentation that western landscapes experienced less than 75 years ago. Consequently, there is a broad east-west contrast in which more numerous human settlements and smaller unbroken forest stands are found in the East, a difference that permits cowbirds to be more pervasive and ubiquitous. The locality of suitable feeding areas is a hallmark trait of the cowbirds' strategy in exploiting specific forest fragments. Host abundance influences parasitism patterns only secondarily at the landscape scale. These two limiting factors come into play differently in different landscapes. For example, cowbird abundance in unbroken forested landscapes are limited primarily by the availability of foraging areas rather than by host density, whereas cowbirds are limited primarily by host availability in landscapes that are extensively fragmented with feeding areas.

Pattern Recognition-Assisted Infrared Library Searching of the Paint Data Query Database to Enhance Lead Information from Automotive Paint Trace Evidence.

PubMed

Lavine, Barry K; White, Collin G; Allen, Matthew D; Weakley, Andrew

2017-03-01

Multilayered automotive paint fragments, which are one of the most complex materials encountered in the forensic science laboratory, provide crucial links in criminal investigations and prosecutions. To determine the origin of these paint fragments, forensic automotive paint examiners have turned to the paint data query (PDQ) database, which allows the forensic examiner to compare the layer sequence and color, texture, and composition of the sample to paint systems of the original equipment manufacturer (OEM). However, modern automotive paints have a thin color coat and this layer on a microscopic fragment is often too thin to obtain accurate chemical and topcoat color information. A search engine has been developed for the infrared (IR) spectral libraries of the PDQ database in an effort to improve discrimination capability and permit quantification of discrimination power for OEM automotive paint comparisons. The similarity of IR spectra of the corresponding layers of various records for original finishes in the PDQ database often results in poor discrimination using commercial library search algorithms. A pattern recognition approach employing pre-filters and a cross-correlation library search algorithm that performs both a forward and backward search has been used to significantly improve the discrimination of IR spectra in the PDQ database and thus improve the accuracy of the search. This improvement permits inter-comparison of OEM automotive paint layer systems using the IR spectra alone. Such information can serve to quantify the discrimination power of the original automotive paint encountered in casework and further efforts to succinctly communicate trace evidence to the courts.

DNA damage and genetic methylation changes caused by Cd in Arabidopsis thaliana seedlings.

PubMed

Li, Zhaoling; Liu, Zhihong; Chen, Ruijuan; Li, Xiaojun; Tai, Peidong; Gong, Zongqiang; Jia, Chunyun; Liu, Wan

2015-09-01

Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MASP) techniques are sensitive to deoxyribonucleic acid (DNA) damage and genetic methylation, respectively. Using these 2 techniques, Arabidopsis thaliana cultured with 0 mg/L (control), 0.5 mg/L, 1.5 mg/L, and 5.0 mg/L Cd(2+) for 16 d was used to analyze the DNA damage and methylation changes as a result of cadmium (Cd). The DNA was amplified by 14 AFLP primer pairs and 13 MSAP primer combinations. In the AFLP experiment, 62 polymorphic sites were found in the patterns of 11 primer combinations and a total of 1116 fragments were obtained in these patterns. There were no polymorphic bands in the remaining 3 pairs. The proportions of polymorphic sites in the 0.5-mg/L Cd(2+) and 5.0-mg/L Cd(2+) treatments were significantly different. Seven polymorphic fragments were then separated and successfully sequenced, yielding 6 nucleobase substitutions and 1 nucleobase deletion. Similarly, in the MSAP experiment, the MSAP% and number of demethylated-type bands were unchanged after Cd treatment, but the number of methylated-type bands was increased significantly in the 5.0-mg/L Cd(2+) treatment group, a finding that may be associated with the AFLP results. The polymorphic bands were also sequenced and the functions of their homologous genes were determined. The DNA damage and methylation changes may be the primary cause of certain pathology changes as a result of Cd uptake in plants. © 2015 SETAC.

Molecular identification and genetic variation of varieties of Styphnolobium japonicum (Fabaceae) using SRAP markers.

PubMed

Sun, R X; Zhang, C H; Zheng, Y Q; Zong, Y C; Yu, X D; Huang, P

2016-05-06

Thirty-four Styphnolobium japonicum varieties were analyzed using sequence-related amplified polymorphism (SRAP) markers, to investigate genetic variation and test the effectiveness of SRAP markers in DNA fingerprint establishment. Twelve primer pairs were selected from 120 primer combinations for their reproducibility and high polymorphism. We found a total of 430 amplified fragments, of which 415 fragments were considered polymorphic with an average of 34.58 polymorphic fragments for each primer combination. The percentage of polymorphic fragments was 96.60%, and four primer pairs showed 100% polymorphism. Moreover, simple matched coefficients ranged between 0.68 and 0.89, with an average of 0.785, indicating that the genetic variation among varieties was relatively low. This could be because of the narrow genetic basis of the selected breeding material. Based on the similarity coefficient value of 0.76, the varieties were divided into four major groups. In addition, abundant and clear SRAP fingerprints were obtained and could be used to establish DNA fingerprints. In the DNA fingerprints, each variety had its unique pattern that could be easily distinguished from others. The results demonstrated that 34 varieties of S. japonicum had a relatively narrow genetic variation. Hence, a broadening of the genetic basis of breeding material is necessary. We conclude that establishment of DNA fingerprint is feasible by means of SRAP markers.

Design Fragments

DTIC Science & Technology

2007-04-19

define the patterns and are better at analyzing behavior. SPQR (System for Pattern Query and Recognition) [18, 58] can recognize pattern vari- ants...Stotts. SPQR : Flexible automated design pattern extraction from source code. ase, 00:215, 2003. ISSN 1527-1366. doi: http://doi.ieeecomputersociety. org

Proteomic Analysis of Tendon Extracellular Matrix Reveals Disease Stage-specific Fragmentation and Differential Cleavage of COMP (Cartilage Oligomeric Matrix Protein)*

PubMed Central

Dakin, Stephanie Georgina; Smith, Roger Kenneth Whealands; Heinegård, Dick; Önnerfjord, Patrik; Khabut, Areej; Dudhia, Jayesh

2014-01-01

During inflammatory processes the extracellular matrix (ECM) is extensively remodeled, and many of the constituent components are released as proteolytically cleaved fragments. These degradative processes are better documented for inflammatory joint diseases than tendinopathy even though the pathogenesis has many similarities. The aims of this study were to investigate the proteomic composition of injured tendons during early and late disease stages to identify disease-specific cleavage patterns of the ECM protein cartilage oligomeric matrix protein (COMP). In addition to characterizing fragments released in naturally occurring disease, we hypothesized that stimulation of tendon explants with proinflammatory mediators in vitro would induce fragments of COMP analogous to natural disease. Therefore, normal tendon explants were stimulated with IL-1β and prostaglandin E2, and their effects on the release of COMP and its cleavage patterns were characterized. Analyses of injured tendons identified an altered proteomic composition of the ECM at all stages post injury, showing protein fragments that were specific to disease stage. IL-1β enhanced the proteolytic cleavage and release of COMP from tendon explants, whereas PGE2 had no catabolic effect. Of the cleavage fragments identified in early stage tendon disease, two fragments were generated by an IL-1-mediated mechanism. These fragments provide a platform for the development of neo-epitope assays specific to injury stage for tendon disease. PMID:24398684

Quantitative analysis of forest fragmentation in the atlantic forest reveals more threatened bird species than the current red list.

PubMed

Schnell, Jessica K; Harris, Grant M; Pimm, Stuart L; Russell, Gareth J

2013-01-01

Habitat loss and attendant fragmentation threaten the existence of many species. Conserving these species requires a straightforward and objective method that quantifies how these factors affect their survival. Therefore, we compared a variety of metrics that assess habitat fragmentation in bird ranges, using the geographical ranges of 127 forest endemic passerine birds inhabiting the Atlantic Forest of Brazil. A common, non-biological metric - cumulative area of size-ranked fragments within a species range - was misleading, as the least threatened species had the most habitat fragmentation. Instead, we recommend a modified version of metapopulation capacity. The metric links detailed spatial information on fragment sizes and spatial configuration to the birds' abilities to occupy and disperse across large areas (100,000+ km(2)). In the Atlantic Forest, metapopulation capacities were largely bimodal, in that most species' ranges had either low capacity (high risk of extinction) or high capacity (very small risk of extinction). This pattern persisted within taxonomically and ecologically homogenous groups, indicating that it is driven by fragmentation patterns and not differences in species ecology. Worryingly, we found IUCN considers some 28 of 58 species in the low metapopulation capacity cluster to not be threatened. We propose that assessing the effect of fragmentation will separate species more clearly into distinct risk categories than does a simple assessment of remaining habitat.

Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization.

PubMed

Neustetter, M; Jabbour Al Maalouf, E; Limão-Vieira, P; Denifl, S

2016-08-07

Electron ionization of neat tungsten hexacarbonyl (W(CO)6) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO)6 clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO)n (+) (0 ≤ n ≤ 6) and W2(CO)n (+) (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO)n (+) (0 ≤ n ≤ 3) and W2C(CO)n (+) (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.

Effect of palladium doping on the stability and fragmentation patterns of cationic gold clusters

NASA Astrophysics Data System (ADS)

Ferrari, P.; Hussein, H. A.; Heard, C. J.; Vanbuel, J.; Johnston, R. L.; Lievens, P.; Janssens, E.

2018-05-01

We analyze in detail how the interplay between electronic structure and cluster geometry determines the stability and the fragmentation channels of single Pd-doped cationic Au clusters, PdA uN-1+ (N =2 -20 ). For this purpose, a combination of photofragmentation experiments and density functional theory calculations was employed. A remarkable agreement between the experiment and the calculations is obtained. Pd doping is found to modify the structure of the Au clusters, in particular altering the two-dimensional to three-dimensional transition size, with direct consequences on the stability of the clusters. Analysis of the electronic density of states of the clusters shows that depending on cluster size, Pd delocalizes one 4 d electron, giving an enhanced stability to PdA u6 + , or remains with all 4 d10 electrons localized, closing an electronic shell in PdA u9 + . Furthermore, it is observed that for most clusters, Au evaporation is the lowest-energy decay channel, although for some sizes Pd evaporation competes. In particular, PdA u7 + and PdA u9 + decay by Pd evaporation due to the high stability of the A u7 + and A u9 + fragmentation products.

LIAD-fs scheme for studies of ultrafast laser interactions with gas phase biomolecules.

PubMed

Calvert, C R; Belshaw, L; Duffy, M J; Kelly, O; King, R B; Smyth, A G; Kelly, T J; Costello, J T; Timson, D J; Bryan, W A; Kierspel, T; Rice, P; Turcu, I C E; Cacho, C M; Springate, E; Williams, I D; Greenwood, J B

2012-05-14

Laser induced acoustic desorption (LIAD) has been used for the first time to study the parent ion production and fragmentation mechanisms of a biological molecule in an intense femtosecond (fs) laser field. The photoacoustic shock wave generated in the analyte substrate (thin Ta foil) has been simulated using the hydrodynamic HYADES code, and the full LIAD process has been experimentally characterised as a function of the desorption UV-laser pulse parameters. Observed neutral plumes of densities >10(9) cm(-3) which are free from solvent or matrix contamination demonstrate the suitability and potential of the source for studying ultrafast dynamics in the gas phase using fs laser pulses. Results obtained with phenylalanine show that through manipulation of fundamental femtosecond laser parameters (such as pulse length, intensity and wavelength), energy deposition within the molecule can be controlled to allow enhancement of parent ion production or generation of characteristic fragmentation patterns. In particular by reducing the pulse length to a timescale equivalent to the fastest vibrational periods in the molecule, we demonstrate how fragmentation of the molecule can be minimised whilst maintaining a high ionisation efficiency. This journal is © the Owner Societies 2012

Anthropogenic fragmentation may not alter pre-existing patterns of genetic diversity and differentiation in perennial shrubs.

PubMed

Llorens, Tanya M; Ayre, David J; Whelan, Robert J

2018-04-01

Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird-pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F' ST  = 0.615 and 0.454; S p  = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long-term effects of inbreeding in self-compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self-compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation. © 2018 John Wiley & Sons Ltd.

Recent (2000-2015) developments in the analysis of minor unknown natural products based on characteristic fragment information using LC-MS.

PubMed

Cai, Tian; Guo, Ze-Qin; Xu, Xiao-Ying; Wu, Zhi-Jun

2018-03-01

Liquid chromatography-Mass Spectrometry (LC-MS) has been widely used in natural product analysis. Global detection and identification of nontargeted components are desirable in natural product research, for example, in quality control of Chinese herbal medicine. Nontargeted components analysis continues to expand to exciting life science application domains such as metabonomics. With this background, the present review summarizes recent developments in the analysis of minor unknown natural products using LC-MS and mainly focuses on the determination of the molecular formulae, selection of precursor ions, and characteristic fragmentation patterns of the known compounds. This review consists of three parts. Firstly, the methods used to determine unique molecular formula of unknown compounds such as accurate mass measurements, MS n spectra, or relative isotopic abundance information, are introduced. Secondly, the methods improving signal-to-noise ratio of MS/MS spectra by manual-MS/MS or workflow targeting-only signals were elucidated; pure precursor ions can be selected by changing the precursor ion isolated window. Lastly, characteristic fragmentation patterns such as Retro-Diels-Alder (RDA), McLafferty rearrangements, "internal residue loss," and so on, occurring in the molecular ions of natural products are summarized. Classical application of characteristic fragmentation patterns in identifying unknown compounds in extracts and relevant fragmentation mechanisms are presented (RDA reactions occurring readily in the molecular ions of flavanones or isoflavanones, McLafferty-type fragmentation reactions of some natural products such as epipolythiodioxopiperazines; fragmentation by "internal residue loss" possibly involving ion-neutral complex intermediates). © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:202-216, 2018. © 2016 Wiley Periodicals, Inc.

Enterobacterial repetitive intergenic consensus sequences and the PCR to generate fingerprints of genomic DNAs from Vibrio cholerae O1, O139, and non-O1 strains.

PubMed

Rivera, I G; Chowdhury, M A; Huq, A; Jacobs, D; Martins, M T; Colwell, R R

1995-08-01

Enterobacterial repetitive intergenic consensus (ERIC) sequence polymorphism was studied in Vibrio Cholerae strains isolated before and after the cholera epidemic in Brazil (in 1991), along with epidemic strains from Peru, Mexico, and India, by PCR. A total of 17 fingerprint patterns (FPs) were detected in the V. cholerae strains examined; 96.7% of the toxigenic V. cholerae O1 strains and 100% of the O139 serogroup strains were found to belong to the same FP group comprising four fragments (FP1). The nontoxigenic V. cholerae O1 also yielded four fragments but constituted a different FP group (FP2). A total of 15 different patterns were observed among the V. cholerae non-O1 strains. Two patterns were observed most frequently for V. cholerae non-01 strains, 25% of which have FP3, with five fragments, and 16.7% of which have FP4, with two fragments. Three fragments, 1.75, 0.79, and 0.5 kb, were found to be common to both toxigenic and nontoxigenic V. cholerae O1 strains as well as to group FP3, containing V. cholerae non-O1 strains. Two fragments of group FP3, 1.3 and 1.0 kb, were present in FP1 and FP2 respectively. The 0.5-kb fragment was common to all strains and serogroups of V. cholerae analyzed. It is concluded from the results of this study, based on DNA FPs of environmental isolates, that it is possible to detect an emerging virulent strain in a cholera-endemic region. ERIC-PCR constitutes a powerful tool for determination of the virulence potential of V. cholerae O1 strains isolated in surveillance programs and for molecular epidemiological investigations.

Implications of discontinuous elevation gradients on fragmentation and restoration in patterned wetlands

USGS Publications Warehouse

Zweig, Christa L.; Reichert, Brian E.; Kitchens, Wiley M.

2011-01-01

Large wetlands around the world face the possibility of degradation, not only from complete conversion, but also from subtle changes in their structure and function. While fragmentation and isolation of wetlands within heterogeneous landscapes has received much attention, the disruption of spatial patterns/processes within large wetland systems and the resulting fragmentation of community components are less well documented. A greater understanding of pattern/process relationships and landscape gradients, and what occurs when they are altered, could help avoid undesirable consequences of restoration actions. The objective of this study is to determine the amount of fragmentation of sawgrass ridges due to artificial impoundment of water and how that may be differentially affected by spatial position relative to north and south levees. We also introduce groundbreaking evidence of landscape-level discontinuous elevation gradients within WCA3AS by comparing generalized linear and generalized additive models. These relatively abrupt breaks in elevation may have non-linear effects on hydrology and vegetation communities and would be crucial in restoration considerations. Modeling suggests there are abrupt breaks in elevation as a function of northing (Y-coordinate). Fragmentation indices indicate that fragmentation is a function of elevation and easting (X-coordinate), and that fragmentation has increased from 1988-2002. When landscapes change and the changes are compounded by non-linear landscape variables that are described herein, the maintenance processes change with them, creating a degraded feedback loop that alters the system's response to structuring variables and diminishes our ability to predict the effects of restoration projects or climate change. Only when these landscape variables and linkages are clearly defined can we predict the response to potential perturbations and apply the knowledge to other landscape-level wetland systems in need of future restoration.

Ecological impacts of tropical forest fragmentation: how consistent are patterns in species richness and nestedness?

PubMed

Hill, Jane K; Gray, Michael A; Khen, Chey Vun; Benedick, Suzan; Tawatao, Noel; Hamer, Keith C

2011-11-27

Large areas of tropical forest now exist as remnants scattered across agricultural landscapes, and so understanding the impacts of forest fragmentation is important for biodiversity conservation. We examined species richness and nestedness among tropical forest remnants in birds (meta-analysis of published studies) and insects (field data for fruit-feeding Lepidoptera (butterflies and moths) and ants). Species-area relationships were evident in all four taxa, and avian and insect assemblages in remnants typically were nested subsets of those in larger areas. Avian carnivores and nectarivores and predatory ants were more nested than other guilds, implying that the sequential loss of species was more predictable in these groups, and that fragmentation alters the trophic organization of communities. For butterflies, the ordering of fragments to achieve maximum nestedness was by fragment area, suggesting that differences among fragments were driven mainly by extinction. In contrast for moths, maximum nestedness was achieved by ordering species by wing length; species with longer wings (implying better dispersal) were more likely to occur at all sites, including low diversity sites, suggesting that differences among fragments were driven more strongly by colonization. Although all four taxa exhibited high levels of nestedness, patterns of species turnover were also idiosyncratic, and thus even species-poor sites contributed to landscape-scale biodiversity, particularly for insects.

Ecological impacts of tropical forest fragmentation: how consistent are patterns in species richness and nestedness?

PubMed Central

Hill, Jane K.; Gray, Michael A.; Khen, Chey Vun; Benedick, Suzan; Tawatao, Noel; Hamer, Keith C.

2011-01-01

Large areas of tropical forest now exist as remnants scattered across agricultural landscapes, and so understanding the impacts of forest fragmentation is important for biodiversity conservation. We examined species richness and nestedness among tropical forest remnants in birds (meta-analysis of published studies) and insects (field data for fruit-feeding Lepidoptera (butterflies and moths) and ants). Species–area relationships were evident in all four taxa, and avian and insect assemblages in remnants typically were nested subsets of those in larger areas. Avian carnivores and nectarivores and predatory ants were more nested than other guilds, implying that the sequential loss of species was more predictable in these groups, and that fragmentation alters the trophic organization of communities. For butterflies, the ordering of fragments to achieve maximum nestedness was by fragment area, suggesting that differences among fragments were driven mainly by extinction. In contrast for moths, maximum nestedness was achieved by ordering species by wing length; species with longer wings (implying better dispersal) were more likely to occur at all sites, including low diversity sites, suggesting that differences among fragments were driven more strongly by colonization. Although all four taxa exhibited high levels of nestedness, patterns of species turnover were also idiosyncratic, and thus even species-poor sites contributed to landscape-scale biodiversity, particularly for insects. PMID:22006967

Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: Phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus)

USGS Publications Warehouse

Vandergast, A.G.; Bohonak, A.J.; Weissman, D.B.; Fisher, R.N.

2007-01-01

Habitat loss and fragmentation due to urbanization are the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. However, it may be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric fragmentation due to previous natural geological and climatic changes. To address these challenges, we examined the phylogenetic and population genetic structure of a flightless insect endemic to cismontane southern California, Stenopelmatus 'mahogani' (Orthoptera: Stenopelmatidae). Analyses of mitochondrial DNA sequence data suggest that diversification across southern California began during the Pleistocene, with most haplotypes currently restricted to a single population. Patterns of genetic divergence correlate with contemporary urbanization, even after correcting for (geographical information system) GIS-based reconstructions of fragmentation during the Pleistocene. Theoretical simulations confirm that contemporary patterns of genetic structure could be produced by recent urban fragmentation using biologically reasonable assumptions about model parameters. Diversity within populations was positively correlated with current fragment size, but not prehistoric fragment size, suggesting that the effects of increased drift following anthropogenic fragmentation are already being seen. Loss of genetic connectivity and diversity can hinder a population's ability to adapt to ecological perturbations commonly associated with urbanization, such as habitat degradation, climatic changes and introduced species. Consequently, our results underscore the importance of preserving and restoring landscape connectivity for long-term persistence of low vagility native species. Journal compilation ?? 2006 Blackwell Publishing Ltd.

Characterizing the forest fragmentation of Canada's national parks.

PubMed

Soverel, Nicholas O; Coops, Nicholas C; White, Joanne C; Wulder, Michael A

2010-05-01

Characterizing the amount and configuration of forests can provide insights into habitat quality, biodiversity, and land use. The establishment of protected areas can be a mechanism for maintaining large, contiguous areas of forests, and the loss and fragmentation of forest habitat is a potential threat to Canada's national park system. Using the Earth Observation for Sustainable Development of Forests (EOSD) land cover product (EOSD LC 2000), we characterize the circa 2000 forest patterns in 26 of Canada's national parks and compare these to forest patterns in the ecological units surrounding these parks, referred to as the greater park ecosystem (GPE). Five landscape pattern metrics were analyzed: number of forest patches, mean forest patch size (hectare), standard deviation of forest patch size (hectare), mean forest patch perimeter-to-area ratio (meters per hectare), and edge density of forest patches (meters per hectare). An assumption is often made that forests within park boundaries are less fragmented than the surrounding GPE, as indicated by fewer forest patches, a larger mean forest patch size, less variability in forest patch size, a lower perimeter-to-area ratio, and lower forest edge density. Of the 26 national parks we analyzed, 58% had significantly fewer patches, 46% had a significantly larger mean forest patch size (23% were not significantly different), and 46% had a significantly smaller standard deviation of forest patch size (31% were not significantly different), relative to their GPEs. For forest patch perimeter-to-area ratio and forest edge density, equal proportions of parks had values that were significantly larger or smaller than their respective GPEs and no clear trend emerged. In summary, all the national parks we analyzed, with the exception of the Georgian Bay Islands, were found to be significantly different from their corresponding GPE for at least one of the five metrics assessed, and 50% of the 26 parks were significantly different from their respective GPEs for all of the metrics assessed. The EOSD LC 2000 provides a heretofore unavailable dataset for characterizing broad trends in forest fragmentation in Canada's national parks and in their surrounding GPEs. The interpretation of forest fragmentation metrics must be guided by the underlying land cover context, as many forested ecosystems in Canada are naturally fragmented due to wetlands and topography. Furthermore, interpretation must also consider the management context, as some parks are designed to preserve fragmented habitats. An analysis of forest pattern such as that described herein provides a baseline, from which changes in fragmentation patterns over time could be monitored, enabled by earth observation data.

Filetype Identification Using Long, Summarized N-Grams

DTIC Science & Technology

2011-03-01

compressed or encrypted data . If the algorithm used to compress or encrypt the data can be determined, then it is frequently possible to uncom- press...fragments. His implementation utilized the bzip2 library to compress the file fragments. The bzip2 library is based off the Lempel - Ziv -Markov chain... algorithm that uses a dictionary compression scheme to remove repeating data patterns within a set of data . The removed patterns are listed within the

Conformational Specific Infrared and Ultraviolet Spectroscopy of Cold YA(D-Pro)AA\\cdotH+ Ions: a Sterochemical "twist" on the Proline Effect

NASA Astrophysics Data System (ADS)

Harrilal, Christopher P.; DeBlase, Andrew F.; Burke, Nicole L.; McLuckey, Scott A.; Zwier, Timothy S.

2016-06-01

The "proline effect" is a well-known fragmentation phenomenon in mass spectrometry, in which y-fragments are produced preferentially over b-fragments during the collision induced dissociation of protonated L-proline containing peptide ions. This specific fragmentation channel is favored because of the high basicity of the secondary amine intermediate and the ring instability in alternative bn+ products [ASMS 2014, 25, 1705]. In contrast, peptides containing the D-Pro stereoisomer have been shown to largely favor the production of b4+ ions over y3+ ions. This strongly suggests that differences in the conformational preferences between the D-Pro and L-Pro diastereomers are likely to be responsible but structural evidence has been lacking to date. Using tandem mass spectrometry and IR-UV double resonant action spectroscopy we are able to compare the 3D structures of cold [YA(D-Pro)AA+H]+ to [YA(L-Pro)AA+H]+ ions. The UV action spectra reveals two major conformers in [YA(D-Pro)AA+H]+ and one major conformer in [YA(L-Pro)AA+H]+. Clear differences in the hydrogen bonding patterns are apparent between the two conformers observed in the D-Pro specie which are both distinct from the L-Pro diastereomer. Furthermore, conformer and diastereomer specific photofragmentation patterns are observed. It is also noted that a ten-fold photofragment enhancement unique to one of the D-Pro conformers is observed upon absorption of a resonant IR photon after UV excitation. Differences in the excited state photophysics between the two D-Pro conformers suggest that vibrational excitation of S1 turns on coupling to the dissociative -Tyr channel in one conformer, while this coupling is already present in the vibronic ground state of the other. Calculated harmonic spectra (M052X/6-31+G*) of conformers obtained from Monte Carlo searches to the experimental spectra.

Integrating vegetation index time series and meteorological data to understand the effect of the land use/land cover (LULC) in the climatic seasonality of the Brazilian Cerrado

NASA Astrophysics Data System (ADS)

Lins, D. B.; Zullo, J.; Friedel, M. J.

2013-12-01

The Cerrado (savanna ecosystem) of São Paulo state (Brazil) represent a complex mosaic of different typologies of uses, actors and biophysical and social restrictions. Originally, 14% of the state of São Paulo area was covered by the diversity of Cerrado phytophysiognomies. Currently, only 1% of this original composition remains fragmented into numerous relicts of biodiversity, mainly concentrated in the central-eastern of the state. A relevant part of the fragments are found in areas of intense coverage change by human activities, whereas the greatest pressure comes from sugar cane cultivation, either by direct replacement of Cerrado vegetation or occupying pasture areas in the fragments edges. As a result, new local level dynamics has been introduced, directly or indirectly, affecting the established of processes in climate systems. In this study, the main goal is analyzing the relationship between the Cerrado landscape changing and the climate dynamics in regional and local areas. The multi-temporal MODIS 250 m Vegetation Index (VI) datasets (period of 2000 to 2012) are integrated with precipitation data of the correspondent period (http://www.agritempo.gov.br/),one of the most important variable of the spatial phytophysiognomies distribution. The integration of meteorological data enable the development of an integrated approach to understand the relationship between climatic seasonality and the changes in the spatial patterns. A procedure to congregated diverse dynamics information is the Self Organizing Map (SOM, Kohonen, 2001), a technique that relies on unsupervised competitive learning (Kohonen and Somervuo 2002) to recognize patterns. In this approach, high-dimensional data are represented on two dimensions, making possible to obtain patterns that takes into account information from different natures. Observed advances will contribute to bring machine-learning techniques as a valid tool to provide improve in land use/land cover (LULC) analyzes at different hierarchical scales to support numerous science and policy applications.

Building patterns and landscape fragmentation in northern Wisconsin, USA

Treesearch

Charlotte E. Gonzalez-Abraham; Volker C. Radeloff; Roger B. Hammer; Todd J. Hawbaker; Susan I. Stewart; Murray K. Clayton

2007-01-01

Housing growth is prevalent in rural areas in the United States and landscape fragmentation is one of its many effects. Since the 1930s, rural sprawl has been increasing in areas rich in recreational amenities. The question is how housing growth has affected landscape fragmentation. We thus tested three hypotheses relating land cover and land ownership to density and...

Multiplex analysis of DNA

DOEpatents

Church, George M.; Kieffer-Higgins, Stephen

1992-01-01

This invention features vectors and a method for sequencing DNA. The method includes the steps of: a) ligating the DNA into a vector comprising a tag sequence, the tag sequence includes at least 15 bases, wherein the tag sequence will not hybridize to the DNA under stringent hybridization conditions and is unique in the vector, to form a hybrid vector, b) treating the hybrid vector in a plurality of vessels to produce fragments comprising the tag sequence, wherein the fragments differ in length and terminate at a fixed known base or bases, wherein the fixed known base or bases differs in each vessel, c) separating the fragments from each vessel according to their size, d) hybridizing the fragments with an oligonucleotide able to hybridize specifically with the tag sequence, and e) detecting the pattern of hybridization of the tag sequence, wherein the pattern reflects the nucleotide sequence of the DNA.

Multitemporal spatial pattern analysis of Tulum's tropical coastal landscape

NASA Astrophysics Data System (ADS)

Ramírez-Forero, Sandra Carolina; López-Caloca, Alejandra; Silván-Cárdenas, José Luis

2011-11-01

The tropical coastal landscape of Tulum in Quintana Roo, Mexico has a high ecological, economical, social and cultural value, it provides environmental and tourism services at global, national, regional and local levels. The landscape of the area is heterogeneous and presents random fragmentation patterns. In recent years, tourist services of the region has been increased promoting an accelerate expansion of hotels, transportation and recreation infrastructure altering the complex landscape. It is important to understand the environmental dynamics through temporal changes on the spatial patterns and to propose a better management of this ecological area to the authorities. This paper addresses a multi-temporal analysis of land cover changes from 1993 to 2000 in Tulum using Thematic Mapper data acquired by Landsat-5. Two independent methodologies were applied for the analysis of changes in the landscape and for the definition of fragmentation patterns. First, an Iteratively Multivariate Alteration Detection (IR-MAD) algorithm was used to detect and localize land cover change/no-change areas. Second, the post-classification change detection evaluated using the Support Vector Machine (SVM) algorithm. Landscape metrics were calculated from the results of IR-MAD and SVM. The analysis of the metrics indicated, among other things, a higher fragmentation pattern along roadways.

Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.

PubMed

Huschmann, Franziska U; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S; Mueller, Uwe

2016-05-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.

Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library

PubMed Central

Huschmann, Franziska U.; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S.; Mueller, Uwe

2016-01-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin–fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity. PMID:27139825

BBN: Description of the PLUM System as Used for MUC-4

DTIC Science & Technology

1992-01-01

in the MUC-4 corpus’ . Here are the 8 parse fragments generated by FPP for the first sentence of TST2- MUC4 -0048 : ("SALVADORAN PRESIDENT-ELECT ALFREDO...extensive patterns for fragment combination . Figure 2 shows a graphical version of the semantics generated for the first fragment of S1 in TST2- MUC4 ...trigger. Following is the discourse event structure for the first event in TST2- MUC4 -0048 : Event MURDER Trigger fragments: "SALVADORAN PRESIDENT

Contact lens materials, mucin fragmentation and relation to symptoms.

PubMed

Berry, Monica; Purslow, Chris; Murphy, Paul J; Pult, Heiko

2012-07-01

Mucins adhere to contact lenses (CLs), reflecting the renewal of the preocular fluid and enzymatic activity at the ocular surface. In this study, we aimed to analyze mucin fragmentation on materials new to the ocular surface and investigate whether this correlates with wearing comfort. Lenses were obtained from new CL wearers after 2 weeks each of wearing vifilcon A, followed by senofilcon A, and then by vifilcon A lenses. Symptoms were evaluated using the Ocular Surface Disease Index (OSDI). CLs were extracted in a mixture of guanidinium hydrochloride and radioimmunoprecipitation assay buffer. Mucin mobility was analyzed after electrophoresis, Western blotting, and visualization with antibodies against mucin peptide core. Mobilities, normalized to total reactivity in the lane, were compared between visits for each subject and were expressed as shifts. Mucin (MUC)5AC polymers exceeding 260 kDa were observed in agarose gels; NuPAGE resolved polymers from 260 to 3.5 kDa: when large mucins were detected, the smallest fragments were missing. Fragmentation patterns were significantly different between lens types for MUC1 (analysis of variance, P = 0.006) and MUC4 (P < 0.001) but not for MUC5AC or MUC16 (P > 0.293). Mobility shifts of MUC1 and MUC4 were significantly negatively correlated (Pearson, r = -0.908; P = 0.002). For OSDI scores >15, mucin fragmentation was unchanged, whereas for OSDI scores <15, MUC4 and MUC5AC fragments were longer on vifilcon A than on senofilcon lenses (unpaired t test, P = 0.046), irrespective of the direction of change (analysis of variance, P > 0.366). Changes in MUC1 breakdown were significantly negatively correlated to the overall OSDI score (r = -0.891, P = 0.001). In asymptomatic CL wearers, only changes in mucin fragmentation in response to a new material were consistent and fast, irrespective of CL order. Lack of change seems, therefore, to be connected with discomfort during CL wear.

Cancerous 'floater': a lesson learned about tissue identity testing, endometrial cancer and microsatellite instability.

PubMed

Bossuyt, Veerle; Buza, Natalia; Ngo, Nhu T; Much, Melissa A; Asis, Maria C; Schwartz, Peter E; Hui, Pei

2013-09-01

A 46-year-old woman presented with endometrial cells on a pap smear and underwent endometrial curettage. The specimen revealed secretory endometrium and a possible endometrial polyp. In addition, a single 4 mm fragment of well-differentiated adenocarcinoma was found. Tissue identity DNA genotyping was performed and the adenocarcinoma tissue fragment showed a drastically different allelic pattern from that of the background endometrium. To confirm tissue contamination, genotyping of three other tumor specimens-probable sources for a contaminant-was performed but failed to identify a match. Without confirmation of contamination, a second endometrial curettage was obtained from the patient, in which similar adenocarcinoma tissue was once again found. Further workup demonstrated that the patient had a microsatellite unstable (MSI) endometrial adenocarcinoma by immunohistochemistry and molecular testing. The patient subsequently underwent staging surgery, which revealed an early-stage, well-differentiated endometrioid adenocarcinoma. This case study illustrates an uncommon, yet important caveat of tissue identity testing by DNA genotyping, where MSI instability can significantly alter the allelic pattern of DNA polymorphisms in the tumor genome, leading to erroneous conclusion regarding the tissue identity. Awareness of this phenomenon is crucial for a molecular pathologist to avoid interpretation errors of tissue identity testing in a cancer diagnostic workup.

Characterization of major and minor alk(en)ylresorcinols from mango (Mangifera indica L.) peels by high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry.

PubMed

Knödler, Matthias; Berardini, Nicolai; Kammerer, Dietmar R; Carle, Reinhold; Schieber, Andreas

2007-01-01

5-Alkyl- and 5-alkenylresorcinols, as well as their hydroxylated derivatives, were extracted from mango (Mangifera indica L.) peels, purified on polyamide and characterized by high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry (HPLC/APcI-MS) for the first time. Among the 15 compounds analyzed, 3 major and 12 minor C(15)-, C(17)-, and C(19)-substituted resorcinols and related analogues, showing varying degrees of unsaturation, were characterized by their specific fragmentation patterns in collision-induced dissociation experiments. This marks the first report on the occurrence of mono-, di-, and triunsaturated C(15)-homologues, saturated and triunsaturated C(17)-homologues, and mono- and diunsaturated C(19)-homologues in mango peels. Additionally, several hydroxylated C(15)- and C(17)-homologues, also not yet described in mango, and a C(14)-monoene, unique because of its even-numbered side chain, were tentatively identified on the basis of their fragmentation patterns. The results obtained in the present study indicate that HPLC-DAD-APcI-MS(n), combined with the newly developed solid-phase extraction, is a powerful tool for the analysis of alk(en)ylresorcinols and could therefore be used for their determination in various matrices.

Use of Amplified Fragment Length Polymorphisms for Typing Corynebacterium diphtheriae

PubMed Central

De Zoysa, Aruni; Efstratiou, Androulla

2000-01-01

Amplified fragment length polymorphism (AFLP) was investigated for the differentiation of Corynebacterium diphtheriae isolates. Analysis using Taxotron revealed 10 distinct AFLP profiles among 57 isolates. Strains with ribotype patterns D1, D4, and D12 could not be distinguished; however, the technique discriminated isolates of ribotype patterns D3, D6, and D7 further. AFLP was rapid, fairly inexpensive, and reproducible and could be used as an alternative to ribotyping. PMID:11015416

Voronoi cell patterns: Theoretical model and applications

NASA Astrophysics Data System (ADS)

González, Diego Luis; Einstein, T. L.

2011-11-01

We use a simple fragmentation model to describe the statistical behavior of the Voronoi cell patterns generated by a homogeneous and isotropic set of points in 1D and in 2D. In particular, we are interested in the distribution of sizes of these Voronoi cells. Our model is completely defined by two probability distributions in 1D and again in 2D, the probability to add a new point inside an existing cell and the probability that this new point is at a particular position relative to the preexisting point inside this cell. In 1D the first distribution depends on a single parameter while the second distribution is defined through a fragmentation kernel; in 2D both distributions depend on a single parameter. The fragmentation kernel and the control parameters are closely related to the physical properties of the specific system under study. We use our model to describe the Voronoi cell patterns of several systems. Specifically, we study the island nucleation with irreversible attachment, the 1D car-parking problem, the formation of second-level administrative divisions, and the pattern formed by the Paris Métro stations.

A detailed mechanistic fragmentation analysis of methamphetamine and select regioisomers by GC/MS.

PubMed

Sachs, Sandra B; Woo, Francis

2007-03-01

A novel ring-substituted methamphetamine regioisomer, N,alpha,4-trimethyl phenmethylamine, was synthesized in order to study the validity of proposed structures for various mass spectrometry (MS)-derived peaks in a methamphetamine fragmentation pattern. While other research efforts have studied aspects of methamphetamine in detail, a full fragmentation study has not been reported previously. In addition to showing molecular structures represented by fragment peaks, mechanisms for selected processes are detailed. An empirically derived procedure to easily determine by simple spectral peak pattern recognition the geometry of dimethyl- or ethyl-substituted immonium ions (RRC = N+ RR) where m/z = 58 is outlined. These results are platform independent for electron ionization (EI) instruments, but have also proven to be helpful in explaining spectral peaks observed in spectra from ion trap systems. The spectrum for the synthesized methamphetamine regioisomer was accurately predicted using this methodology. While this approach is useful in some casework, the converse may be more useful: when an unexpected or unusual peak pattern arises in a spectrum, being able to analyze it to determine the structure of the molecule. This paper gives an analyst the means to begin such retro-synthetic analyses.

Deforestation and Forest Fragmentation in South Ecuador since the 1970s - Losing a Hotspot of Biodiversity.

PubMed

Tapia-Armijos, María Fernanda; Homeier, Jürgen; Espinosa, Carlos Iván; Leuschner, Christoph; de la Cruz, Marcelino

2015-01-01

Deforestation and fragmentation are major components of global change; both are contributing to the rapid loss of tropical forest area with important implications for ecosystem functioning and biodiversity conservation. The forests of South Ecuador are a biological 'hotspot' due to their high diversity and endemism levels. We examined the deforestation and fragmentation patterns in this area of high conservation value using aerial photographs and Aster satellite scenes. The registered annual deforestation rates of 0.75% (1976-1989) and 2.86% (1989-2008) for two consecutive survey periods, the decreasing mean patch size and the increasing isolation of the forest fragments show that the area is under severe threat. Approximately 46% of South Ecuador's original forest cover had been converted by 2008 into pastures and other anthropogenic land cover types. We found that deforestation is more intense at lower elevations (premontane evergreen forest and shrubland) and that the deforestation front currently moves in upslope direction. Improved awareness of the spatial extent, dynamics and patterns of deforestation and forest fragmentation is urgently needed in biologically diverse areas like South Ecuador.

Strategy to obtain axenic cultures from field-collected samples of the cyanobacterium Phormidium animalis.

PubMed

Vázquez-Martínez, Guadalupe; Rodriguez, Mario H; Hernández-Hernández, Fidel; Ibarra, Jorge E

2004-04-01

An efficient strategy, based on a combination of procedures, was developed to obtain axenic cultures from field-collected samples of the cyanobacterium Phormidium animalis. Samples were initially cultured in solid ASN-10 medium, and a crude separation of major contaminants from P. animalis filaments was achieved by washing in a series of centrifugations and resuspensions in liquid medium. Then, manageable filament fragments were obtained by probe sonication. Fragmentation was followed by forceful washing, using vacuum-driven filtration through an 8-microm pore size membrane and an excess of water. Washed fragments were cultured and treated with a sequential exposure to four different antibiotics. Finally, axenic cultures were obtained from serial dilutions of treated fragments. Monitoring under microscope examination and by inoculation in Luria-Bertani (LB) agar plates indicated either axenicity or the degree of contamination throughout the strategy.

The influence of arbuscular mycorrhizae on root precision nutrient foraging of two pioneer plant species during early reclamation

NASA Astrophysics Data System (ADS)

Boldt-Burisch, Katja; Naeth, M. Anne

2017-04-01

On many post mining sites in the Lusatian Mining District (East Germany) soil heterogeneity consists of sandy soil with embedded clay-silt fragments. Those clays silt fragments might act as nutrient hotspots. Arbuscular mycorrhizal fungi in an infertile ecosystem could enhance a plant's ability to selectively forage for those nutrients and thus to improve plants nutrient supply. In our study we investigated whether silt-clay fragments within a sandy soil matrix induced preferential root growth of Lotus corniculatus and Calamagrostis epigeios, whether arbuscular mycorrhizae influenced root foraging patterns, and to what extent selective rooting in clay silt fragments influenced plant growth were addressed in this research. Soil types were sterile and non-sterile sandy soil and clay-silt fragments. Treatments were with and without arbuscular mycorrhizae, with and without soil solution, and soil solution and mycorrhizal inoculum combined. Root biomass, root density and intraradical fungal alkaline phosphatase activity and frequency were determined in fragments relative to sandy soil. Furthermore, temporal relationship of number of roots in fragments and plant height was assessed. Lotus corniculatus showed strong selective rooting into fragments especially with those plants treated with commercial cultivated arbuscular mycorrhizae; Calamagrostis epigeios did not. Without arbuscular mycorrhizae, L. corniculatus growth was significantly reduced and selective rooting did not occur. Selective rooting induced significant growth spurts of L. corniculatus. Roots in fragments had higher fungal alkaline phosphatase activity suggesting that mycorrhizal efficiency and related plants phosphorus supply is enhanced in roots in fragments. The application of cultivated arbuscular mycorrhizal fungi significantly and quickly influenced root foraging patterns, especially those of L. corniculatus, suggesting mycorrhizae may also enhance the ability of other plants to selectively forage for nutrients and could therefore play an important role in early plant establishment on infertile reclamation sites.

Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.

PubMed

García-Garcerà, Marc; Gigli, Elena; Sanchez-Quinto, Federico; Ramirez, Oscar; Calafell, Francesc; Civit, Sergi; Lalueza-Fox, Carles

2011-01-01

Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.

THE ADVANTAGES OF FEMTOSECOND LASER-ASSISTED CATARACT SURGERY

PubMed Central

Gavris, M Monica; Belicioiu, Roxana; Olteanu, Ioana; Horge, Ioan

2015-01-01

Purpose: To present the advantages of performing femtosecond laser-assisted (Alcon-LenSx Inc.) cataract surgery. Methods: Cataract surgery was performed with the LenSx femtosecond laser (Alcon-LenSx Inc.) in 50 eyes of 50 patients. The laser was programmed to perform a 4,9-4,5 mm capsulorhexis, a 2,3 mm main corneal incision, two 1,3 mm side-port incisions and either a hybrid-pattern or a cylinder-pattern fragmentation of the nucleus. The evaluated parameters were the capsulotomy, the corneal wounds and the nucleus fragmentation. Phacoemulsification of the nucleus and aspiration of the cortex were performed with the Alcon Centurion Vision System and monofocal, toric and multifocal IOLs were successfully implanted. Results: A continuous, central, curvilinear capsulorhexis was performed in 48 cases, 96% (free-floating capsulotomy). In 2 cases, micro-adhesions were reported and detached with the Utrata forceps. Femtolaser capsulotomy resulted in a complete overlap of the anterior capsule over the IOL optics in all cases. Horizontal decentration was found in 2 cases, 4% and vertical decentration in 1 case, 2%. The main corneal incision was self-sealing in 49 cases, 98%. Sutures were used in 1 case, 2%. The hybrid pattern of nucleus fragmentation was used in 42 cases, 84% and the cylindrical pattern in 8 cases, 16%. The fragmentation was incomplete in one case of white cataract and in one case of traumatic cataract. Conclusions: The main advantages of femtolaser cataract surgery are standardized corneal incisions, perfectly centered, round capsulorhexis, and lens nucleus fragmentation even in eyes with hard cataracts. The laser precision is due to the real time OCT software programs, which cover the whole anterior segment, up to the posterior lens capsule. PMID:27373114

Fragmentation cross sections of medium-energy {sup 35}Cl, {sup 40}Ar, and {sup 48}Ti beams on elemental targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeitlin, C.; Guetersloh, S.; Heilbronn, L.

Charge-changing and fragment production cross sections at 0 deg. have been obtained for interactions of 290, 400, and 650 MeV/nucleon {sup 40}Ar beams, 650 and 1000 MeV/nucleon {sup 35}Cl beams, and a 1000 MeV/nucleon {sup 48}Ti beam. Targets of C, CH{sub 2}, Al, Cu, Sn, and Pb were used. Using standard analysis methods, we obtained fragment cross sections for charges as low as 8 for Cl and Ar beams and as low as 10 for the Ti beam. Using data obtained with small-acceptance detectors, we report fragment production cross sections for charges as low as 5, corrected for acceptance usingmore » a simple model of fragment angular distributions. With the lower-charged fragment cross sections, we can compare the data to predictions from several models (including NUCFRG2, EPAX2, and PHITS) in a region largely unexplored in earlier work. As found in earlier work with other beams, NUCFRG2 and PHITS predictions agree reasonably well with the data for charge-changing cross sections, but these models do not accurately predict the fragment production cross sections. The cross sections for the lightest fragments demonstrate the inadequacy of several models in which the cross sections fall monotonically with the charge of the fragment. PHITS, despite its not agreeing particularly well with the fragment production cross sections on average, nonetheless qualitatively reproduces some significant features of the data that are missing from the other models.« less

NMR-Fragment Based Virtual Screening: A Brief Overview.

PubMed

Singh, Meenakshi; Tam, Benjamin; Akabayov, Barak

2018-01-25

Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.

Modeling of biologically motivated self-learning equivalent-convolutional recurrent-multilayer neural structures (BLM_SL_EC_RMNS) for image fragments clustering and recognition

NASA Astrophysics Data System (ADS)

Krasilenko, Vladimir G.; Lazarev, Alexander A.; Nikitovich, Diana V.

2018-03-01

The biologically-motivated self-learning equivalence-convolutional recurrent-multilayer neural structures (BLM_SL_EC_RMNS) for fragments images clustering and recognition will be discussed. We shall consider these neural structures and their spatial-invariant equivalental models (SIEMs) based on proposed equivalent two-dimensional functions of image similarity and the corresponding matrix-matrix (or tensor) procedures using as basic operations of continuous logic and nonlinear processing. These SIEMs can simply describe the signals processing during the all training and recognition stages and they are suitable for unipolar-coding multilevel signals. The clustering efficiency in such models and their implementation depends on the discriminant properties of neural elements of hidden layers. Therefore, the main models and architecture parameters and characteristics depends on the applied types of non-linear processing and function used for image comparison or for adaptive-equivalent weighing of input patterns. We show that these SL_EC_RMNSs have several advantages, such as the self-study and self-identification of features and signs of the similarity of fragments, ability to clustering and recognize of image fragments with best efficiency and strong mutual correlation. The proposed combined with learning-recognition clustering method of fragments with regard to their structural features is suitable not only for binary, but also color images and combines self-learning and the formation of weight clustered matrix-patterns. Its model is constructed and designed on the basis of recursively continuous logic and nonlinear processing algorithms and to k-average method or method the winner takes all (WTA). The experimental results confirmed that fragments with a large numbers of elements may be clustered. For the first time the possibility of generalization of these models for space invariant case is shown. The experiment for an images of different dimensions (a reference array) and fragments with diferent dimensions for clustering is carried out. The experiments, using the software environment Mathcad showed that the proposed method is universal, has a significant convergence, the small number of iterations is easily, displayed on the matrix structure, and confirmed its prospects. Thus, to understand the mechanisms of self-learning equivalence-convolutional clustering, accompanying her to the competitive processes in neurons, and the neural auto-encoding-decoding and recognition principles with the use of self-learning cluster patterns is very important which used the algorithm and the principles of non-linear processing of two-dimensional spatial functions of images comparison. The experimental results show that such models can be successfully used for auto- and hetero-associative recognition. Also they can be used to explain some mechanisms, known as "the reinforcementinhibition concept". Also we demonstrate a real model experiments, which confirm that the nonlinear processing by equivalent function allow to determine the neuron-winners and customize the weight matrix. At the end of the report, we will show how to use the obtained results and to propose new more efficient hardware architecture of SL_EC_RMNS based on matrix-tensor multipliers. Also we estimate the parameters and performance of such architectures.

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

PubMed Central

Skoglund, Pontus; Northoff, Bernd H.; Shunkov, Michael V.; Derevianko, Anatoli P.; Pääbo, Svante; Krause, Johannes; Jakobsson, Mattias

2014-01-01

One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation—summarized in a postmortem degradation score—which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material. PMID:24469802

Typical ultraviolet spectra in combination with diagnostic mass fragmentation analysis for the rapid and comprehensive profiling of chlorogenic acids in the buds of Lonicera macranthoides.

PubMed

Zhang, Shui-Han; Hu, Xin; Shi, Shu-Yun; Huang, Lu-Qi; Chen, Wei; Chen, Lin; Cai, Ping

2016-05-01

A major challenge of profiling chlorogenic acids (CGA) in natural products is to effectively detect unknown or minor isomeric compounds. Here, we developed an effective strategy, typical ultraviolet (UV) spectra in combination with diagnostic mass fragmentation analysis based on HPLC-DAD-QTOF-MS/MS, to comprehensively profile CGA in the buds of Lonicera macranthoides. First, three CGA UV patterns were obtained by UV spectra screening. Second, 13 types of CGA classified by molecular weights were found by thorough analysis of CGA peaks using high-resolution MS. Third, selected ion monitoring (SIM) was carried out for each type of CGA to avoid overlooking of minor ones. Fourth, MS/MS spectra of each CGA were investigated. Then 70 CGA were identified by matching their UV spectra, accurate mass signals and fragmentation patterns with standards or previously reported compounds, including six caffeoylquinic acids (CQA), six diCQA, one triCQA, three caffeoylshikimic acids (CSA), six diCSA, one triCSA, three p-coumaroylquinic acids (pCoQA), four p-coumaroylcaffeoylquinic acids (pCoCQA), four feruloylquinic acids (FQA), five methyl caffeoylquinates (MCQ), three ethyl caffeoylquinates (ECQ), three dimethoxycinnamoylquinic acids (DQA), six caffeoylferuloylquinic acids (CFQA), six methyl dicaffeoylquinates (MdiCQ), four FQA glycosides (FQAG), six MCQ glycosides (MCQG), and three ethyl dicaffeoylquinates (EdiCQ). Forty-five of them were discovered from Lonicera species for the first time, and it is noted that CGA profiles were investigated for the first time in L. macranthoides. Results indicated that the developed method was a useful approach to explore unknown and minor isomeric compounds from complex natural products.

Using a non-spin flip model to rationalize the irregular patterns observed in the activation of the C-H and Si-H bonds of small molecules by CpMCO (M = Co, Rh) complexes.

PubMed

Castro, Guadalupe; Colmenares, Fernando

2017-09-20

The activation of the C-H and Si-H bonds of CH(CH 3 ) 3 and SiH(CH 3 ) 3 molecules by organometallic compounds CpMCO (M = Co, Rh) has been investigated through DFT and CASSCF-MRMP2 calculations. In particular, we have analyzed the pathways joining the lowest-lying triplet and singlet states of the reactants with the products arising from the insertion of the metal atom into the C-H or Si-H bonds of the organic molecules. Channels connecting the reactants with the inserted structure Cp(CO)H-M-C(CH 3 ) 3 through the oxidative addition of the C-H bond of the organic molecule to the metal fragment were found only for the reaction CpRhCO + CH(CH 3 ) 3 . However, inserted structures could also be obtained for the interactions of SiH(CH 3 ) 3 with CpCoCO and CpRhCO by two sequential reactions involving the formation and rebounding of the radical fragments Cp(CO)H-M + Si(CH 3 ) 3 . According to this two-step reaction scheme, the complex CpCoCO is unable to activate the C-H bond of the CH(CH 3 ) 3 molecule due to the high energy at which the radical fragments Cp(CO)H-M + C(CH 3 ) 3 are located. The picture attained for these interactions is consistent with the available experimental data for this kind of reaction and allows rationalization of the differences in the reactivity patterns determined for them without using spin-flip models, as has been proposed in previous studies.

Biogenic volatile organic compound analyses by PTR-TOF-MS: Calibration, humidity effect and reduced electric field dependency.

PubMed

Pang, Xiaobing

2015-06-01

Green leaf volatiles (GLVs) emitted by plants after stress or damage induction are a major part of biogenic volatile organic compounds (BVOCs). Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) is a high-resolution and sensitive technique for in situ GLV analyses, while its performance is dramatically influenced by humidity, electric field, etc. In this study the influence of gas humidity and the effect of reduced field (E/N) were examined in addition to measuring calibration curves for the GLVs. Calibration curves measured for seven of the GLVs in dry air were linear, with sensitivities ranging from 5 to 10 ncps/ppbv (normalized counts per second/parts per billion by volume). The sensitivities for most GLV analyses were found to increase by between 20% and 35% when the humidity of the sample gas was raised from 0% to 70% relative humidity (RH) at 21°C, with the exception of (E)-2-hexenol. Product ion branching ratios were also affected by humidity, with the relative abundance of the protonated molecular ions and higher mass fragment ions increasing with humidity. The effect of reduced field (E/N) on the fragmentation of GLVs was examined in the drift tube of the PTR-TOF-MS. The structurally similar GLVs are acutely susceptible to fragmentation following ionization and the fragmentation patterns are highly dependent on E/N. Overall the measured fragmentation patterns contain sufficient information to permit at least partial separation and identification of the isomeric GLVs by looking at differences in their fragmentation patterns at high and low E/N. Copyright © 2015. Published by Elsevier B.V.

Abundance and fragmentation patterns of the ecosystem engineer Lithophyllum byssoides (Lamarck) Foslie along the Iberian Peninsula Atlantic coast. Conservation and management implications

NASA Astrophysics Data System (ADS)

Veiga, Puri; Rubal, Marcos; Cacabelos, Eva; Moreira, Juan; Sousa-Pinto, Isabel

2013-10-01

The crustose calcareous red macroalgae Lithophyllum byssoides (Lamarck) Foslie is a common ecosystem engineer along the Atlantic and Mediterranean coast of the Iberian Peninsula. This species is threatened by several anthropogenic impacts acting at different spatial scales, such as pollution or global warming. The aim of this study is to identify scales of spatial variation in the abundance and fragmentation patterns of L. byssoides along the Atlantic coast of the Iberian Peninsula. For this aim we used a hierarchical sampling design considering four spatial scales (from metres to 100s of kilometres). Results of the present study indicated no significant variability among regions investigated whereas significant variability was found at the scales of shore and site in spatial patterns of abundance and fragmentation of L. byssoides. Variance components were higher at the spatial scale of shore for abundance and fragmentation of L. byssoides with the only exception of percentage cover and thus, processes acting at the scale of 10s of kilometres seem to be more relevant in shaping the spatial variability both in abundance and fragmentation of L. byssoides. These results provided quantitative estimates of abundance and fragmentation of L. byssoides at the Atlantic coast of the Iberian Peninsula establishing the observational basis for future assessment, monitoring and experimental investigations to identify the processes and anthropogenic impacts affecting L. byssoides populations. Finally we have also identified percentage cover and patch density as the best variables for long-term monitoring programs aimed to detect future anthropogenic impacts on L. byssoides. Therefore, our results have important implications for conservation and management of this valuable ecosystem engineer along the Atlantic coast of the Iberian Peninsula.

Habitat Fragmentation and Species Extirpation in Freshwater Ecosystems; Causes of Range Decline of the Indus River Dolphin (Platanista gangetica minor)

PubMed Central

Braulik, Gill T.; Arshad, Masood; Noureen, Uzma; Northridge, Simon P.

2014-01-01

Habitat fragmentation of freshwater ecosystems is increasing rapidly, however the understanding of extinction debt and species decline in riverine habitat fragments lags behind that in other ecosystems. The mighty rivers that drain the Himalaya - the Ganges, Brahmaputra, Indus, Mekong and Yangtze - are amongst the world’s most biodiverse freshwater ecosystems. Many hundreds of dams have been constructed, are under construction, or are planned on these rivers and large hydrological changes and losses of biodiversity have occurred and are expected to continue. This study examines the causes of range decline of the Indus dolphin, which inhabits one of the world’s most modified rivers, to demonstrate how we may expect other vertebrate populations to respond as planned dams and water developments come into operation. The historical range of the Indus dolphin has been fragmented into 17 river sections by diversion dams; dolphin sighting and interview surveys show that river dolphins have been extirpated from ten river sections, they persist in 6, and are of unknown status in one section. Seven potential factors influencing the temporal and spatial pattern of decline were considered in three regression model sets. Low dry-season river discharge, due to water abstraction at irrigation barrages, was the principal factor that explained the dolphin’s range decline, influencing 1) the spatial pattern of persistence, 2) the temporal pattern of subpopulation extirpation, and 3) the speed of extirpation after habitat fragmentation. Dolphins were more likely to persist in the core of the former range because water diversions are concentrated near the range periphery. Habitat fragmentation and degradation of the habitat were inextricably intertwined and in combination caused the catastrophic decline of the Indus dolphin. PMID:25029270

Habitat fragmentation and species extirpation in freshwater ecosystems; causes of range decline of the Indus river dolphin (Platanista gangetica minor).

PubMed

Braulik, Gill T; Arshad, Masood; Noureen, Uzma; Northridge, Simon P

2014-01-01

Habitat fragmentation of freshwater ecosystems is increasing rapidly, however the understanding of extinction debt and species decline in riverine habitat fragments lags behind that in other ecosystems. The mighty rivers that drain the Himalaya - the Ganges, Brahmaputra, Indus, Mekong and Yangtze - are amongst the world's most biodiverse freshwater ecosystems. Many hundreds of dams have been constructed, are under construction, or are planned on these rivers and large hydrological changes and losses of biodiversity have occurred and are expected to continue. This study examines the causes of range decline of the Indus dolphin, which inhabits one of the world's most modified rivers, to demonstrate how we may expect other vertebrate populations to respond as planned dams and water developments come into operation. The historical range of the Indus dolphin has been fragmented into 17 river sections by diversion dams; dolphin sighting and interview surveys show that river dolphins have been extirpated from ten river sections, they persist in 6, and are of unknown status in one section. Seven potential factors influencing the temporal and spatial pattern of decline were considered in three regression model sets. Low dry-season river discharge, due to water abstraction at irrigation barrages, was the principal factor that explained the dolphin's range decline, influencing 1) the spatial pattern of persistence, 2) the temporal pattern of subpopulation extirpation, and 3) the speed of extirpation after habitat fragmentation. Dolphins were more likely to persist in the core of the former range because water diversions are concentrated near the range periphery. Habitat fragmentation and degradation of the habitat were inextricably intertwined and in combination caused the catastrophic decline of the Indus dolphin.

Evidence for Sequence Scrambling and Divergent H/D Exchange Reactions of Doubly-Charged Isobaric b-Type Fragment Ions

NASA Astrophysics Data System (ADS)

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H.; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10 2+ that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10 2+ and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10 2+, suggesting that b10 2+ may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10 2+; over 30 % of the observed SORI-CID fragment ions from substance P b10 2+ had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10 2+, whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10 2+.

Evidence for sequence scrambling and divergent H/D exchange reactions of doubly-charged isobaric b-type fragment ions.

PubMed

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10(2+) that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10(2+) and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10(2+), suggesting that b10(2+) may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10(2+); over 30% of the observed SORI-CID fragment ions from substance P b10(2+) had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10(2+), whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10(2+).

sc-PDB-Frag: a database of protein-ligand interaction patterns for Bioisosteric replacements.

PubMed

Desaphy, Jérémy; Rognan, Didier

2014-07-28

Bioisosteric replacement plays an important role in medicinal chemistry by keeping the biological activity of a molecule while changing either its core scaffold or substituents, thereby facilitating lead optimization and patenting. Bioisosteres are classically chosen in order to keep the main pharmacophoric moieties of the substructure to replace. However, notably when changing a scaffold, no attention is usually paid as whether all atoms of the reference scaffold are equally important for binding to the desired target. We herewith propose a novel database for bioisosteric replacement (scPDBFrag), capitalizing on our recently published structure-based approach to scaffold hopping, focusing on interaction pattern graphs. Protein-bound ligands are first fragmented and the interaction of the corresponding fragments with their protein environment computed-on-the-fly. Using an in-house developed graph alignment tool, interaction patterns graphs can be compared, aligned, and sorted by decreasing similarity to any reference. In the herein presented sc-PDB-Frag database ( http://bioinfo-pharma.u-strasbg.fr/scPDBFrag ), fragments, interaction patterns, alignments, and pairwise similarity scores have been extracted from the sc-PDB database of 8077 druggable protein-ligand complexes and further stored in a relational database. We herewith present the database, its Web implementation, and procedures for identifying true bioisosteric replacements based on conserved interaction patterns.

Tools for neuroanatomy and neurogenetics in Drosophila

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pfeiffer, Barret D.; Jenett, Arnim; Hammonds, Ann S.

2008-08-11

We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayedmore » for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that >80% drive expression patterns in the brain; the observed patterns were, on average, comprised of <100 cells. Our results suggest that the D. melanogaster genome contains >50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain.« less

Fragmentation of {sup 14}N, {sup 16}O, {sup 20}Ne, and {sup 24}Mg nuclei at 290 to 1000 MeV/nucleon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeitlin, C.; Miller, J.; Guetersloh, S.

We report fragmentation cross sections measured at 0 deg. for beams of {sup 14}N, {sup 16}O, {sup 20}Ne, and {sup 24}Mg ions, at energies ranging from 290 MeV/nucleon to 1000 MeV/nucleon. Beams were incident on targets of C, CH{sub 2}, Al, Cu, Sn, and Pb, with the C and CH{sub 2} target data used to obtain hydrogen-target cross sections. Using methods established in earlier work, cross sections obtained with both large-acceptance and small-acceptance detectors are extracted from the data and, when necessary, corrected for acceptance effects. The large-acceptance data yield cross sections for fragments with charges approximately half of themore » beam charge and above, with minimal corrections. Cross sections for lighter fragments are obtained from small-acceptance spectra, with more significant, model-dependent corrections that account for the fragment angular distributions. Results for both charge-changing and fragment production cross sections are compared to the predictions of the Los Alamos version of the quark gluon string model (LAQGSM) as well as the NASA Nuclear Fragmentation (NUCFRG2) model and the Particle and Heavy Ion Transport System (PHITS) model. For all beams and targets, cross sections for fragments as light as He are compared to the models. Estimates of multiplicity-weighted helium production cross sections are obtained from the data and compared to PHITS and LAQGSM predictions. Summary statistics show that the level of agreement between data and predictions is slightly better for PHITS than for either NUCFRG2 or LAQGSM.« less

Electronic speckle-pattern interferometry (ESPI) applied to the study of mechanical behavior of human jaws

NASA Astrophysics Data System (ADS)

Roman, Juan F.; Moreno de las Cuevas, Vincente; Salgueiro, Jose R.; Suarez, David; Fernandez, Paula; Gallas, Mercedes; Blanchard, Alain

1996-01-01

The study of the mechanical behavior of the human jaw during chewing is helpful in several specific medical fields that cover the maxillo-facial area. In this work, electronic speckle pattern interferometry has been applied to study dead jaw bones under external stress which simulates the deformations induced during chewing. Fringes obtained after subtraction of two images of the jaw, the image of the relaxed jaw and that of the jaw under stress, give us information about the most stressed zones. The interferometric analysis proposed here is attractive as it can be done in real time with the jaw under progressive stress. Image processing can be applied for improving the quality of fringes. This research can be of help in orthognathic surgery, for example in diagnosis and treatment of fractured jaws, in oral surgery, and in orthodontics because it would help us to know the stress dispersion when we insert an osseointegrated implant or place an orthodontic appliance, respectively. Studying fragments of human jaw some results about its elasticity and flexibility were obtained.

Clustering document fragments using background color and texture information

NASA Astrophysics Data System (ADS)

Chanda, Sukalpa; Franke, Katrin; Pal, Umapada

2012-01-01

Forensic analysis of questioned documents sometimes can be extensively data intensive. A forensic expert might need to analyze a heap of document fragments and in such cases to ensure reliability he/she should focus only on relevant evidences hidden in those document fragments. Relevant document retrieval needs finding of similar document fragments. One notion of obtaining such similar documents could be by using document fragment's physical characteristics like color, texture, etc. In this article we propose an automatic scheme to retrieve similar document fragments based on visual appearance of document paper and texture. Multispectral color characteristics using biologically inspired color differentiation techniques are implemented here. This is done by projecting document color characteristics to Lab color space. Gabor filter-based texture analysis is used to identify document texture. It is desired that document fragments from same source will have similar color and texture. For clustering similar document fragments of our test dataset we use a Self Organizing Map (SOM) of dimension 5×5, where the document color and texture information are used as features. We obtained an encouraging accuracy of 97.17% from 1063 test images.

Differentiation of Toxocara canis and Toxocara cati based on PCR-RFLP analyses of rDNA-ITS and mitochondrial cox1 and nad1 regions.

PubMed

Mikaeili, Fattaneh; Mathis, Alexander; Deplazes, Peter; Mirhendi, Hossein; Barazesh, Afshin; Ebrahimi, Sepideh; Kia, Eshrat Beigom

2017-09-26

The definitive genetic identification of Toxocara species is currently based on PCR/sequencing. The objectives of the present study were to design and conduct an in silico polymerase chain reaction-restriction fragment length polymorphism method for identification of Toxocara species. In silico analyses using the DNASIS and NEBcutter softwares were performed with rDNA internal transcribed spacers, and mitochondrial cox1 and nad1 sequences obtained in our previous studies along with relevant sequences deposited in GenBank. Consequently, RFLP profiles were designed and all isolates of T. canis and T. cati collected from dogs and cats in different geographical areas of Iran were investigated with the RFLP method using some of the identified suitable enzymes. The findings of in silico analyses predicted that on the cox1 gene only the MboII enzyme is appropriate for PCR-RFLP to reliably distinguish the two species. No suitable enzyme for PCR-RFLP on the nad1 gene was identified that yields the same pattern for all isolates of a species. DNASIS software showed that there are 241 suitable restriction enzymes for the differentiation of T. canis from T. cati based on ITS sequences. RsaI, MvaI and SalI enzymes were selected to evaluate the reliability of the in silico PCR-RFLP. The sizes of restriction fragments obtained by PCR-RFLP of all samples consistently matched the expected RFLP patterns. The ITS sequences are usually conserved and the PCR-RFLP approach targeting the ITS sequence is recommended for the molecular differentiation of Toxocara species and can provide a reliable tool for identification purposes particularly at the larval and egg stages.

Profiling and Quantifying Differential Gene Transcription Provide Insights into Ganoderic Acid Biosynthesis in Ganoderma lucidum in Response to Methyl Jasmonate

PubMed Central

Shi, Liang; Mu, Da-Shuai; Jiang, Ai-Liang; Han, Qin; Zhao, Ming-Wen

2013-01-01

Ganoderma lucidum is a mushroom with traditional medicinal properties that has been widely used in China and other countries in Eastern Asia. Ganoderic acids (GA) produced by G. lucidum exhibit important pharmacological activities. Previous studies have demonstrated that methyl jasmonate (MeJA) is a potent inducer of GA biosynthesis and the expression of genes involved in the GA biosynthesis pathway in G. lucidum. To further explore the mechanism of GA biosynthesis, cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) was used to identify genes that are differentially expressed in response to MeJA. Using 64 primer combinations, over 3910 transcriptionally derived fragments (TDFs) were obtained. Reliable sequence data were obtained for 390 of 458 selected TDFs. Ninety of these TDFs were annotated with known functions through BLASTX searching the GenBank database, and 12 annotated TDFs were assigned into secondary metabolic pathways by searching the KEGGPATHWAY database. Twenty-five TDFs were selected for qRT-PCR analysis to confirm the expression patterns observed with cDNA-AFLP. The qRT-PCR results were consistent with the altered patterns of gene expression revealed by the cDNA-AFLP technique. Additionally, the transcript levels of 10 genes were measured at the mycelium, primordia, and fruiting body developmental stages of G. lucidum. The greatest expression levels were reached during primordia for all of the genes except cytochrome b2 reached its highest expression level in the mycelium stage. This study not only identifies new candidate genes involved in the regulation of GA biosynthesis but also provides further insight into MeJA-induced gene expression and secondary metabolic response in G. lucidum. PMID:23762280

Missing Fragments: Detecting Cooperative Binding in Fragment-Based Drug Design

PubMed Central

2012-01-01

The aim of fragment-based drug design (FBDD) is to identify molecular fragments that bind to alternate subsites within a given binding pocket leading to cooperative binding when linked. In this study, the binding of fragments to human phenylethanolamine N-methyltransferase is used to illustrate how (a) current protocols may fail to detect fragments that bind cooperatively, (b) theoretical approaches can be used to validate potential hits, and (c) apparent false positives obtained when screening against cocktails of fragments may in fact indicate promising leads. PMID:24900472

Use of Conserved Randomly Amplified Polymorphic DNA (RAPD) Fragments and RAPD Pattern for Characterization of Lactobacillus fermentum in Ghanaian Fermented Maize Dough

PubMed Central

Hayford, Alice E.; Petersen, Anne; Vogensen, Finn K.; Jakobsen, Mogens

1999-01-01

The present work describes the use of randomly amplified polymorphic DNA (RAPD) for the characterization of 172 dominant Lactobacillus isolates from present and previous studies of Ghanaian maize fermentation. Heterofermentative lactobacilli dominate the fermentation flora, since approximately 85% of the isolates belong to this group. Cluster analysis of the RAPD profiles obtained showed the presence of two main clusters. Cluster 1 included Lactobacillus fermentum, whereas cluster 2 comprised the remaining Lactobacillus spp. The two distinct clusters emerged at the similarity level of <50%. All isolates in cluster 1 showed similarity in their RAPD profile to the reference strains of L. fermentum included in the study. These isolates, yielding two distinct bands of approximately 695 and 773 bp with the primers used, were divided into four subclusters, indicating that several strains are involved in the fermentation and remain dominant throughout the process. The two distinct RAPD fragments were cloned, sequenced, and used as probes in Southern hybridization experiments. With one exception, Lactobacillus reuteri LMG 13045, the probes hybridized only to fragments of different sizes in EcoRI-digested chromosomal DNA of L. fermentum strains, thus indicating the specificity of the probes and variation within the L. fermentum isolates. PMID:10388723

Statistical analysis of fragmentation patterns of electron ionization mass spectra of enolized-trimethylsilylated anabolic androgenic steroids

NASA Astrophysics Data System (ADS)

Fragkaki, A. G.; Angelis, Y. S.; Tsantili-Kakoulidou, A.; Koupparis, M.; Georgakopoulos, C.

2009-08-01

Anabolic androgenic steroids (AAS) are included in the List of prohibited substances of the World Anti-Doping Agency (WADA) as substances abused to enhance athletic performance. Gas chromatography coupled to mass spectrometry (GC-MS) plays an important role in doping control analyses identifying AAS as their enolized-trimethylsilyl (TMS)-derivatives using the electron ionization (EI) mode. This paper explores the suitability of complementary GC-MS mass spectra and statistical analysis (principal component analysis, PCA and partial least squares-discriminant analysis, PLS-DA) to differentiate AAS as a function of their structural and conformational features expressed by their fragment ions. The results obtained showed that the application of PCA yielded a classification among the AAS molecules which became more apparent after applying PLS-DA to the dataset. The application of PLS-DA yielded a clear separation among the AAS molecules which were, thus, classified as: 1-ene-3-keto, 3-hydroxyl with saturated A-ring, 1-ene-3-hydroxyl, 4-ene-3-keto, 1,4-diene-3-keto and 3-keto with saturated A-ring anabolic steroids. The study of this paper also presents structurally diagnostic fragment ions and dissociation routes providing evidence for the presence of unknown AAS or chemically modified molecules known as designer steroids.

Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neustetter, M.; Jabbour Al Maalouf, E.; Denifl, S., E-mail: Stephan.Denifl@uibk.ac.at, E-mail: plimaovieira@fct.unl.pt

2016-08-07

Electron ionization of neat tungsten hexacarbonyl (W(CO){sub 6}) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO){sub 6} clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO){sub n}{sup +} (0 ≤ n ≤ 6) and W{sub 2}(CO){sub n}{sup +} (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO){sub n}{sup +} (0 ≤more » n ≤ 3) and W{sub 2}C(CO){sub n}{sup +} (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.« less

The 'fragmented' scintigraphic lung pattern in pulmonary lymphangitic carcinomatosis secondary to breast cancer.

PubMed

Vattimo, A V; Burroni, L; Bertelli, P; Vella, A; Volterrani, D

1998-01-01

Pulmonary lymphangitic carcinomatosis (PLC) is an unusual presentation of diffuse infiltrative lung disease. In this report we present two cases secondary to breast cancer; the diagnosis was made by means of transbronchial lung biopsy or postmortem examination. The goal of this study was to analyze the scintigraphic pattern of pulmonary perfusion performed with technetium-99m macroaggregated albumin (99mTc-MAA) in the hope of achieving improved recognition of PLC and its subsequent diagnosis. Upon admission, both patients underwent routine clinical exams followed by chest X-rays. The second patient also underwent CT examination, and both were ultimately examined using pulmonary perfusion scintigraphy with 99mTc-MAA. In the various exams performed, the most reliable and easily identified diagnostic finding turned out to be a characteristic 'fragmented' lung pattern revealed with the perfusion lung scan. Unfortunately, in both cases the patients' conditions rapidly worsened and death occurred shortly following scintigraphy. We were able to conclude that the recognition of the mentioned fragmented scintigraphic lung pattern may be useful in suspected PLC, whereas the nonspecific clinical presentation of this pathology makes diagnosis extremely difficult, with the most significant results being achieved through a comparison of scintigraphic and high resolution CT data.

Routine use of PCR-restriction fragment length polymorphism analysis for identification of mycobacteria growing in liquid media.

PubMed Central

Taylor, T B; Patterson, C; Hale, Y; Safranek, W W

1997-01-01

A PCR-restriction fragment length polymorphism (PCR-RFLP) procedure capable of rapidly identifying 28 species of clinically encountered mycobacteria was evaluated for use in the routine identification of acid-fast isolates growing in BACTEC 12B and 13A liquid media. PCR-RFLP identified 100 of 103 acid-fast isolates recovered from 610 patient specimens submitted for culture during the study. The three isolates unidentifiable by PCR-RFLP produced restriction patterns not included in the PCR-RFLP algorithm and could therefore not be assigned to a species. These isolates were characterized by their morphologic and biochemical characteristics. Two of the isolates were identified as M. terrae complex and M. gordonae. The third isolate could not be definitively identified and could only be characterized as a Mycobacterium sp. most closely resembling M. chelonae. PCR-RFLP identifications agreed with the conventional identifications for 96 of the 100 isolates identified by PCR-RFLP. Subsequent identification of the four discordant isolates by gas chromatography analysis supported the PCR-RFLP identification of each isolate. Amplification products were also obtained from isolates of Streptococcus albus and Rhodococcus equi recovered from patient specimens; however, the restriction patterns of these nonmycobacterial species did not resemble the patterns of any mycobacterial species included in the PCR-RFLP algorithm. PCR-RFLP seems to be a reliable procedure for the routine identification of mycobacteria and has the potential for providing identifications of mycobacterial isolates which are more accurate than conventional identification techniques based on morphologic and biochemical characteristics. PMID:8968884

Impacts of changes in land use and fragmentation patterns on Atlantic coastal forests in northern Spain.

PubMed

Teixido, Alberto L; Quintanilla, Luis G; Carreño, Francisco; Gutiérrez, David

2010-01-01

Changes in forested landscapes may have important consequences for ecosystem services and biodiversity conservation. In northern Spain, major changes in land use occurred during the second half of the 20th century, but their impacts on forests have not been quantified. We evaluated the dynamics of landscape and forest distribution patterns between 1957 and 2003 in Fragas do Eume Natural Park (northwestern Spain). We used orthoimages and a set of standard landscape metrics to determine transitions between land cover classes and to examine forest distribution patterns. Eucalypt plantations showed the greatest increase in area (197%) over time. Furthermore, transitions to eucalypt plantations were found in all major land cover classes. Forest showed a net decline of 20% in total area and represented 30% of the landscape area in 2003. Forest losses were mainly due to eucalypt plantations and the building of a water reservoir, while forest gains were due to increases in shrubland, meadows and cultivated fields which had been recolonised. Forest patch size and core area decreased, and edge length increased over time. In turn, increases were obtained in mean distance between forest patches, and in adjacency to eucalypt plantations and to a water reservoir. These results suggest an increase in forest fragmentation from 1957 to 2003, as well as a change in the nature of the habitat surrounding forest patches. This study shows that land use changes, mostly from eucalypt plantation intensification, negatively affected forested habitats, although some regeneration was ongoing through ecological succession from land abandonment. Copyright 2009 Elsevier Ltd. All rights reserved.

Velocity distribution of fragments of catastrophic impacts

NASA Technical Reports Server (NTRS)

Takagi, Yasuhiko; Kato, Manabu; Mizutani, Hitoshi

1992-01-01

Three dimensional velocities of fragments produced by laboratory impact experiments were measured for basalts and pyrophyllites. The velocity distribution of fragments obtained shows that the velocity range of the major fragments is rather narrow, at most within a factor of 3 and that no clear dependence of velocity on the fragment mass is observed. The NonDimensional Impact Stress (NDIS) defined by Mizutani et al. (1990) is found to be an appropriate scaling parameter to describe the overall fragment velocity as well as the antipodal velocity.

Deforestation and Forest Fragmentation in South Ecuador since the 1970s – Losing a Hotspot of Biodiversity

PubMed Central

Tapia-Armijos, María Fernanda; Homeier, Jürgen; Espinosa, Carlos Iván; Leuschner, Christoph; de la Cruz, Marcelino

2015-01-01

Deforestation and fragmentation are major components of global change; both are contributing to the rapid loss of tropical forest area with important implications for ecosystem functioning and biodiversity conservation. The forests of South Ecuador are a biological ‘hotspot’ due to their high diversity and endemism levels. We examined the deforestation and fragmentation patterns in this area of high conservation value using aerial photographs and Aster satellite scenes. The registered annual deforestation rates of 0.75% (1976–1989) and 2.86% (1989–2008) for two consecutive survey periods, the decreasing mean patch size and the increasing isolation of the forest fragments show that the area is under severe threat. Approximately 46% of South Ecuador’s original forest cover had been converted by 2008 into pastures and other anthropogenic land cover types. We found that deforestation is more intense at lower elevations (premontane evergreen forest and shrubland) and that the deforestation front currently moves in upslope direction. Improved awareness of the spatial extent, dynamics and patterns of deforestation and forest fragmentation is urgently needed in biologically diverse areas like South Ecuador. PMID:26332681

Deforestation trends of tropical dry forests in central Brazil

USGS Publications Warehouse

Bianchi, Carlos A.; Haig, Susan M.

2013-01-01

Tropical dry forests are the most threatened forest type in the world yet a paucity of research about them stymies development of appropriate conservation actions. The Paranã River Basin has the most significant dry forest formations in the Cerrado biome of central Brazil and is threatened by intense land conversion to pastures and agriculture. We examined changes in Paranã River Basin deforestation rates and fragmentation across three time intervals that covered 31 yr using Landsat imagery. Our results indicated a 66.3 percent decrease in forest extent between 1977 and 2008, with an annual rate of forest cover change of 3.5 percent. Landscape metrics further indicated severe forest loss and fragmentation, resulting in an increase in the number of fragments and reduction in patch sizes. Forest fragments in flatlands have virtually disappeared and the only significant forest remnants are mostly found over limestone outcrops in the eastern part of the basin. If current patterns persist, we project that these forests will likely disappear within 25 yr. These patterns may be reversed with creation of protected areas and involvement of local people to preserve small fragments that can be managed for restoration.

Fragmentation of forest, grassland, and shrubland

Treesearch

Kurt H. Riitters

2013-01-01

As humans introduce competing land uses into natural landscapes, the public concerns regarding landcover patterns are expressed through headline issues such as urban sprawl, forest fragmentation, water quality, and wilderness preservation. The spatial arrangement of an environment affects all human perceptions and ecological processes within that environment, but this...

The Fragment Network: A Chemistry Recommendation Engine Built Using a Graph Database.

PubMed

Hall, Richard J; Murray, Christopher W; Verdonk, Marcel L

2017-07-27

The hit validation stage of a fragment-based drug discovery campaign involves probing the SAR around one or more fragment hits. This often requires a search for similar compounds in a corporate collection or from commercial suppliers. The Fragment Network is a graph database that allows a user to efficiently search chemical space around a compound of interest. The result set is chemically intuitive, naturally grouped by substitution pattern and meaningfully sorted according to the number of observations of each transformation in medicinal chemistry databases. This paper describes the algorithms used to construct and search the Fragment Network and provides examples of how it may be used in a drug discovery context.

Computed tomography of calcaneal fractures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heger, L.; Wulff, K.; Seddiqi, M.S.A.

1985-07-01

Computed tomography (CT) of 25 fractured calcanei was performed to investigate the potential of CT in evaluating the pattern and biomechanics of these fractures. The characteristic findings of typical fractures are presented, including the number and type of principal fragments, size and dislocation of the sustentacular fragment, and involvement of the anterior and posterior facets of the subtalar joint. In 17 cases, the calcaneus consisted of four or more fragments. Furthermore, in 17 cases the sustentacular fragment included all or part of the posterior facet joint. In 18 of the 25 cases, the sustentacular fragment was displaced. It is concludedmore » that well performed CT is an invaluable adjunct in understanding the fracture mechanism and in detecting pain-provoking impingement between the fibular malleolus and the tuberosity fragment.« less

Rb-Sr Isotopic Systematics of Alkali-Rich Fragments in the Yamato-74442 LL-Chondritic Breccia

NASA Technical Reports Server (NTRS)

Yokoyama, T.; Misawa, K.; Okano, O.; Shih, C.-Y.; Nyquist, L. E.; Simo, J. I.; Tappa, M. J.; Yoneda, S.

2012-01-01

Alkali-rich igneous fragments were identified in the brecciated LL-chondrites, Kr henberg (LL5)], Bhola (LL3-6) and Yamato (Y)-74442 (LL4), and show characteristic fractionation patterns of alkaline elements. The K-Rb-Cs-rich fragments in Kr henberg, Bhola, and Y-74442 are very similar in mineralogy and petrography (olivine + pyroxene + glass), suggesting that they could have come from related precursor materials. We have undertaken Rb-Sr isotopic studies on alkali-rich fragments in Y-74442 to precisely determine their crystallization ages and the isotopic signatures of their precursor material(s).

Extreme ultraviolet photoionization of aldoses and ketoses

NASA Astrophysics Data System (ADS)

Shin, Joong-Won; Dong, Feng; Grisham, Michael E.; Rocca, Jorge J.; Bernstein, Elliot R.

2011-04-01

Gas phase monosaccharides (2-deoxyribose, ribose, arabinose, xylose, lyxose, glucose galactose, fructose, and tagatose), generated by laser desorption of solid sample pellets, are ionized with extreme ultraviolet photons (EUV, 46.9 nm, 26.44 eV). The resulting fragment ions are analyzed using a time of flight mass spectrometer. All aldoses yield identical fragment ions regardless of size, and ketoses, while also generating same ions as aldoses, yields additional features. Extensive fragmentation of the monosaccharides is the result the EUV photons ionizing various inner valence orbitals. The observed fragmentation patterns are not dependent upon hydrogen bonding structure or OH group orientation.

Juxta-articular Plate Fixation in Distal Radius Intra-articular Fractures with Accompanying Volar Free Fragments beyond the Watershed Line

PubMed Central

Lee, Jun-Ku; Lee, Soo-Hyun; Sim, Young-Suk; Kim, Tae-Ho; Baek, Eugene

2018-01-01

Background Although distal radius fractures (DRF) are common fractures, intra-articular comminuted DRF with volar free fragments are uncommon. There is considerable difficulty in the fixation of free fragments beyond the watershed line using the existing volar locking plate. We aimed to examine the efficacy and potential complications associated with the use of juxta-articular volar plates in intra-articular DRF accompanied by free fragments beyond the watershed line. Methods The patients were enrolled in a consecutive manner between 2007 and 2016. In cases of DRF with free fragments beyond the watershed line, we employed a 2.4-mm small fragment juxta-articular volar locking compression plate using a volar Henry approach. A total of 32 patients were included in this study. There were 15 males and 17 females with a mean age of 52.3 years (range, 33 to 69 years). The mean follow-up period was 14.5 months (range, 10 to 24 months). Preoperative radiographs and three-dimensional computed tomography images were used to analyze fracture patterns and assess the free fragments beyond the watershed line. The mean number of free fracture fragments beyond the watershed line was 2.33. Plain radiographs of immediate postoperative and last follow-up were used to confirm fracture union, incongruence, radial height, volar tilt, radial inclination, and arthritic changes. For functional assessment, we measured grip strength, range of motion (ROM), modified Mayo wrist score (MMWS) and determined Disabilities of Arm, Shoulder and Hand (DASH) scores at the last follow-up. Postoperative complications were monitored during the follow-up period. Results All patients obtained sound union without significant complications. At the last follow-up, 16 cases presented with an articular step-off of more than 1 mm (mean, 1.10 mm). The mean MMWS was 76.3 (range, 55 to 90), mean DASH score was 15.38 (range, 9 to 22), mean visual analogue scale score for pain was 1.2 and mean grip strength was 75.5% of the opposite side. The mean ROM was 74.3° for volar flexion and 71.5° for dorsiflexion. Conclusions In cases of intra-articular DRF with free fragments beyond the watershed line, a volar approach with use of a juxtaarticular plate provided favorable outcomes without significant complications. PMID:29854335

Does avian species richness in natural patch mosaics follow the forest fragmentation paradigm?

USGS Publications Warehouse

Pavlacky, D.C.; Anderson, S.H.

2007-01-01

As one approaches the north-eastern limit of pinyon (Pinus spp.) juniper (Juniperus spp.) vegetation on the Colorado Plateau, USA, woodland patches become increasingly disjunct, grading into sagebrush (Artemisia spp.)-dominated landscapes. Patterns of avian species richness in naturally heterogeneous forests may or may not respond to patch discontinuity in the same manner as bird assemblages in fragmented agricultural systems. We used observational data from naturally patchy woodlands and predictions derived from studies of human-modified agricultural forests to estimate the effects of patch area, shape, isolation and distance to contiguous woodland on avian species richness. We predicted that patterns of species richness in naturally patchy juniper woodlands would differ from those observed in fragmented agricultural systems. Our objectives were to (1) estimate the effect of naturally occurring patch structure on avian species richness with respect to habitat affinity and migratory strategy and (2) assess the concordance of the effects to predictions from agricultural forest systems. We used the analogy between populations and communities to estimate species richness, where species are treated as individuals in the application of traditional capture-recapture theory. Information-theoretic model selection showed that overall species richness was explained primarily by the species area relationship. There was some support for a model with greater complexity than the equilibrium theory of island biogeography where the isolation of large patches resulted in greater species richness. Species richness of woodland-dwelling birds was best explained by the equilibrium hypothesis with partial landscape complementation by open-country species in isolated patches. Species richness within specific migratory strategies showed concomitant increases and no shifts in species composition along the patch area gradient. Our results indicate that many patterns of species richness considered to be fragmentation effects may be general consequences of patch discontinuity and are ubiquitous in naturally heterogeneous systems. There was no evidence for the effects of patch shape and distance to contiguous woodland in juniper woodland, suggesting edge effects and dependence upon regional species pools are characteristics of fragmented agricultural systems. Natural patch mosaics may provide benchmarks for evaluating fragmentation effects and managing forests by mimicking natural landscape patterns. ?? 2007 The Zoological Society of London.

Fragmentation Cross Sections of Medium-Energy 35Cl, 40Ar, and 48TiBeams on Elemental Targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeitlin, C.; Guetersloh, S.; Heilbronn, L.

Charge-changing and fragment production cross sections at 0degrees have been obtained for interactions of 290, 400, and 650MeV/nucleon 40Ar beams, 650 and 1000 MeV/nucleon 35Cl beams, and a 1000MeV/nucleon 48Ti beam. Targets of C, CH2, Al, Cu, Sn, and Pb were used.Using standard analysis methods, we obtain fragment cross sections forcharges as low as 8 for Cl and Ar beams, and as low as 10 for the Tibeam. Using data obtained with small-acceptance detectors, we reportfragment production cross sections for charges as low as 5, corrected foracceptance using a simple model of fragment angular distributions. Withthe lower-charged fragment cross sections,more » we cancompare the data topredictions from several models (including NUCFRG2, EPAX2, and PHITS) ina region largely unexplored in earlier work. As found in earlier workwith other beams, NUCFRG2 and PHITS predictions agree reasonably wellwith the data for charge-changing cross sections, but do not accuratelypredict the fragment production cross sections. The cross sections forthe lightest fragments demonstrate the inadequacy of several models inwhich the cross sections fall monotonically with the charge of thefragment. PHITS, despite not agreeing particularly well with the fragmentproduction cross sections on average, nonetheless qualitativelyreproduces somesignificant features of the data that are missing from theother models.« less

Chemistry Within Molecular Clusters

DTIC Science & Technology

1992-06-01

reactions, and only occur within van der Waals clusters. 23 They include the generation of (C2H4F2),>4H+ ions from 1,1- difluoroethane clusters, 4 the...of fragment ions, and identification of the molecule must be made by the characteristic fragmentation pattern. The mass spectrum of 1,1- difluoroethane

Chemistry within Molecular Clusters

DTIC Science & Technology

1992-05-29

within van der Waals clusters. 23 They include the generation of (C2H4F 2),,>4H+ ions from 1,1- difluoroethane clusters, 24 the generation of (CH 3...fragment ions, and identification of the molecule must be made by the characteristic fragmentation pattern. The mass spectrum of 1,1- difluoroethane (DFE

Production and genetic analysis of resynthesized Brassica napus from a B. rapa landrace from the Qinghai-Tibet Plateau and B. alboglabra.

PubMed

Liu, H D; Zhao, Z G; Du, D Z; Deng, C R; Fu, G

2016-01-08

This study aimed to reveal the genetic and epigenetic variations involved in a resynthesized Brassica napus (AACC) generated from a hybridization between a B. rapa (AA) landrace and B. alboglabra (CC). Amplified fragment length polymorphism (AFLP), methylation-sensitive amplified polymorphism, and the cDNA-AFLP technique were performed to detect changes between different generations at the genome, methylation, and transcription levels. We obtained 30 lines of resynthesized B. napus with a mean 1000-seed weight of over 7.50 g. All of the lines were self-compatible, probably because both parents were self-compatible. At the genome level, the S0 generation had the lowest frequency of variations (0.18%) and the S3 generation had the highest (6.07%). The main variation pattern was the elimination of amplified restriction fragments on the CC genome from the S0 to the S4 generations. At the methylation level, we found three loci that exhibited altered methylation patterns on the parental A genome; the variance rate was 1.35%. At the transcription level, we detected 43.77% reverse mutations and 37.56% deletion mutations that mainly occurred on the A and C genomes, respectively, in the S3 generation. Our results highlight the genetic variations that occur during the diploidization of resynthesized B. napus.

Evolutionary history and phylogeography of Encelia farinosa (Asteraceae) from the Sonoran, Mojave, and Peninsular Deserts.

PubMed

Fehlberg, Shannon D; Ranker, Tom A

2009-02-01

Pleistocene glaciations have had a profound influence on the genetic structure of plant species throughout the Northern Hemisphere because of range contractions, fragmentations, and expansions. Phylogeographic studies have contributed to our knowledge of this influence in several geographic regions of North America, however, very few phylogeographic studies have examined plant species in the Sonoran, Mojave, and Peninsular deserts. In this study, we used sequence data from the chloroplast DNA psbA-trnH intergenic spacer to obtain information on phylogeographic patterns among 310 individuals from 21 populations of Encelia farinosa ("brittlebush"; Asteraceae) across its range. We applied several population and spatial genetic analyses that allowed us to interpret our data with respect to Pleistocene climate change. These analyses indicate that E. farinosa displays patterns of genetic differentiation and geographic structuring consistent with postglacial range expansion. Populations of E. farinosa are characterized by distinct haplotype lineages significantly associated with geography. Centers of genetic diversity for the species occur in southwestern Arizona, the plains of Sonora, and Baja California Sur, all of which are putative sites of glacial refugia as predicted by analyses of macrofossil and pollen data. Nested clade analysis suggests that genetic structure in E. farinosa has been affected by past fragmentation followed by range expansion. Range expansion in several locations is further supported by significant departures from neutrality for values of Fu's F(S) and Tajima's D, and mismatch analyses.

Identification of fracture zones and its application in automatic bone fracture reduction.

PubMed

Paulano-Godino, Félix; Jiménez-Delgado, Juan J

2017-04-01

The preoperative planning of bone fractures using information from CT scans increases the probability of obtaining satisfactory results, since specialists are provided with additional information before surgery. The reduction of complex bone fractures requires solving a 3D puzzle in order to place each fragment into its correct position. Computer-assisted solutions may aid in this process by identifying the number of fragments and their location, by calculating the fracture zones or even by computing the correct position of each fragment. The main goal of this paper is the development of an automatic method to calculate contact zones between fragments and thus to ease the computation of bone fracture reduction. In this paper, an automatic method to calculate the contact zone between two bone fragments is presented. In a previous step, bone fragments are segmented and labelled from CT images and a point cloud is generated for each bone fragment. The calculated contact zones enable the automatic reduction of complex fractures. To that end, an automatic method to match bone fragments in complex fractures is also presented. The proposed method has been successfully applied in the calculation of the contact zone of 4 different bones from the ankle area. The calculated fracture zones enabled the reduction of all the tested cases using the presented matching algorithm. The performed tests show that the reduction of these fractures using the proposed methods leaded to a small overlapping between fragments. The presented method makes the application of puzzle-solving strategies easier, since it does not obtain the entire fracture zone but the contact area between each pair of fragments. Therefore, it is not necessary to find correspondences between fracture zones and fragments may be aligned two by two. The developed algorithms have been successfully applied in different fracture cases in the ankle area. The small overlapping error obtained in the performed tests demonstrates the absence of visual overlapping in the figures. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Land Use Change and Agricultural Land Fragmentation due to Anthropogenic Activities in an Hot Spot Area: A Case Study for Thrace Region of Turkey

NASA Astrophysics Data System (ADS)

Altürk, Bahadır; Konukcu, Fatih

2017-04-01

Agricultural lands that supply food, energy and ecosystem services for human life have been lost due to anthropogenic activities such as construction of roads, urban and industry areas. The significant reasons for the increase of artificial surfaces were poorly planned economic decisions by the government and internal migration due to this poorly planning. Unplanned urban sprawl also give rise to land fragmentation. Fragmentation of agricultural land affects both the agricultural production capacity and rural sustainable employment. In this study: i) Land use changes between 1990-2014 period were assessed using remotely sensed data and ii) Spatial and temporal agricultural land fragmentation were investigated using landscape pattern indice (effective mesh size), Morphological Spatial Pattern Analysis (MSPA) and Entropy method for 25 years period. The selected"hot spot" study area is located on east Thrace region of Turkey, being the service and industrial development zone where agricultural activities, water resources and natural habitat have been damaged due to rapid urban and industrial development for about 25 years. The results showed that agricultural lands decreased 6.44%, urban areas increased 111.68% and industry areas increased 251.19% during this 25 years period. Additionally, fragmentation analyses demonstrated that core agricultural areas sharply decreased and relative fragmentation (effective mesh size) increased from 50.68% to 56.77% during 1990 and 2014.

Diterpenes and other constituents from Croton draco (Euphorbiaceae).

PubMed

Murillo, R M; Jakupovic, J; Rivera, J; Castro, V H

2001-03-01

Croton draco (Euphorbiaceae) from Guadalupe, San José, Costa Rica was collected in July 1992 and phytochemically studied (leaves, seeds, wood, bark, sap and flowers separately). Commonly known compounds such as 1-hydroxyjunenol, p-hydroxybenzaldehyde, p-methoxybenzoic acid, 3,4,5-trimethoxycinnamyl alcohol, the coumarin scopoletin, the nor-terpenoids 9-dehydrovomifoliol and 2,3-dihydrovomifoliol were obtained. Taspine, two aporphinic alkaloids, the diterpenes 9(11)-dehydrokaurenic acid, hardwikiic acid, the corresponding new 12-oxo derivative as well as five clerodanes and a phorbol ester were also isolated. Three clerodanes were not previously described and their NMR spectroscopical data and MS fragmentation patterns are reported.

NIR detection of pits and pit fragments in fresh cherries (abstract)

USDA-ARS?s Scientific Manuscript database

The feasibility of using near infrared (NIR) diffuse reflectance spectroscopy for the detection of pits and pit fragments in cherries was demonstrated. For detection of whole pits, 300 cherries were obtained locally and pits were removed from half. NIR reflectance spectra were obtained in triplicate...

Tsallis Entropy and the Transition to Scaling in Fragmentation

NASA Astrophysics Data System (ADS)

Sotolongo-Costa, Oscar; Rodriguez, Arezky H.; Rodgers, G. J.

2000-12-01

By using the maximum entropy principle with Tsallis entropy we obtain a fragment size distribution function which undergoes a transition to scaling. This distribution function reduces to those obtained by other authors using Shannon entropy. The treatment is easily generalisable to any process of fractioning with suitable constraints.

Can you escape the beat? Modelling spatiotemporal biodegradation dynamics during periodic disturbances

NASA Astrophysics Data System (ADS)

König, Sara; Worrich, Anja; Wick, Lukas Y.; Miltner, Anja; Kästner, Matthias; Thullner, Martin; Centler, Florian; Banitz, Thomas; Frank, Karin

2016-04-01

Biodegradation of organic compounds in soil is an important microbial ecosystem service. Soil ecosystems are constantly exposed to disturbances of different spatial configurations and frequencies, challenging their ability to recover the biodegradation function. Thus, the response to these disturbances is crucial for the soil systems' biodegradation performance. The influence of spatial aspects of the disturbance regimes on long-term biodegradation dynamics under periodic disturbances has not been examined, yet. We applied a numerical simulation model considering bacterial growth, degradation, and dispersal to analyze the spatiotemporal biodegradation dynamics under disturbances occuring with different frequencies and with different spatial configurations. We found biodegradation performance decreasing in response to periodic disturbances but on average approaching a new quasi steady state. This mean performance of the disturbed systems increases with both, the interval length between disturbance events and the fragmentation of the spatial disturbance patterns. A detailed spatiotemporal analysis of degradation activity reveals that under highly fragmented disturbance patterns, biodegradation still takes place in the entire disturbed area. For moderately fragmented disturbance patterns, parts of the disturbed area become completely inactive. However, areas with high degradation activity emerge at the interface between disturbed and undisturbed areas, allowing the systems to maintain a relatively high degradation performance. Further decreasing the disturbance patterns' fragmentation, fewer interfaces between disturbed and undisturbed area and, thus, fewer active habitats occur, which reduces biodegradation performances. In additional simulations, we found that bacterial dispersal networks, as for example provided by fungal hyphae, usually increase the areas of high degradation activity and, thus, the biodegradation performance in presence of periodic disturbances. However, for some specific regimes with highly fragmented disturbance patterns, dispersal networks can in turn decrease the biodegradation performance. Our results show that spatial aspects of the periodic disturbance regime influence the biodegradation dynamics, indicating the relevance of spatial processes for functional stability. The level of connectivity between disturbed and undisturbed areas is crucial for the local and global dynamics of the ecosystem service biodegradation. Networks enhancing bacterial dispersal may often, but not always, increase the functional stability.

Genomic Diversity of Erwinia carotovora subsp. carotovora and Its Correlation with Virulence

PubMed Central

Yap, Mee-Ngan; Barak, Jeri D.; Charkowski, Amy O.

2004-01-01

We used genetic and biochemical methods to examine the genomic diversity of the enterobacterial plant pathogen Erwinia carotovora subsp. carotovora. The results obtained with each method showed that E. carotovora subsp. carotovora strains isolated from one ecological niche, potato plants, are surprisingly diverse compared to related pathogens. A comparison of 23 partial mdh sequences revealed a maximum pairwise difference of 10.49% and an average pairwise difference of 2.13%, values which are much greater than the maximum variation (1.81%) and average variation (0.75%) previously reported for Escherichia coli. Pulsed-field gel electrophoresis analysis of I-CeuI-digested genomic DNA revealed seven rrn operons in all E. carotovora subsp. carotovora strains examined except strain WPP17, which had only six copies. We identified 26 I-CeuI restriction fragment length polymorphism patterns and observed significant polymorphism in fragment sizes ranging from 100 to 450 kb for all strains. We detected large plasmids in two strains, including the model strain E. carotovora subsp. carotovora 71. The two least virulent strains had an unusual chromosomal structure, suggesting that a particular pulsotype is correlated with virulence. To compare chromosomal organization of multiple enterobacterial genomes, several genes were mapped onto I-CeuI fragments. We identified portions of the genome that appear to be conserved across enterobacteria and portions that have undergone genome rearrangements. We found that the least virulent strain, WPP17, failed to oxidize cellobiose and was missing several hrp and hrc genes. The unexpected variability among isolates obtained from clonal hosts in one region and in one season suggests that factors other than the host plant, potato, drive the evolution of this common environmental bacterium and key plant pathogen. PMID:15128563

Fragmentation study of iridoid glucosides through positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry.

PubMed

Es-Safi, Nour-Eddine; Kerhoas, Lucien; Ducrot, Paul-Henri

2007-01-01

Mass spectrometric methodology based on the combined use of positive and negative electrospray ionization, collision-induced dissociation (CID) and tandem mass spectrometry (MS/MS) has been applied to the mass spectral study of a series of six naturally occurring iridoids through in-source fragmentation of the protonated [M+H]+, deprotonated [M--H]- and sodiated [M+Na]+ ions. This led to the unambiguous determination of the molecular masses of the studied compounds and allowed CID spectra of the molecular ions to be obtained. Valuable structural information regarding the nature of both the glycoside and the aglycone moiety was thus obtained. Glycosidic cleavage and ring cleavages of both aglycone and sugar moieties were the major fragmentation pathways observed during CID, where the losses of small molecules, the cinnamoyl and the cinnamate parts were also observed. The formation of the ionized aglycones, sugars and their product ions was thus obtained giving information on their basic skeleton. The protonated, i.e. [M+H]+ and deprotonated [M--H]-, ions were found to fragment mainly by glycosidic cleavages. MS/MS spectra of the [M+Na]+ ions gave complementary information for the structural characterization of the studied compounds. Unlike the dissociation of protonated molecular ions, that of sodiated molecules also provided sodiated sugar fragments where the C0+ fragment corresponding to the glucose ion was obtained as base peak for all the studied compounds. Copyright (c) 2007 John Wiley & Sons, Ltd.

Comparisons of molecular karyotype and RAPD patterns of anuran trypanosome isolates during long-term in vitro cultivation.

PubMed

Lun, Z R; Desser, S S

1996-01-01

The patterns of random amplified fragments and molecular karyotypes of 12 isolates of anuran trypanosomes continuously cultured in vitro were compared by random amplified polymorphic DNA (RAPD) analysis and pulsed field gradient gel electrophoresis (PFGE). The time interval between preparation of two series of samples was one year. Changes were not observed in the number and size of sharp, amplified fragments of DNA samples from both series examined with the ten primers used. Likewise, changes in the molecular karyotypes were not detected between the two samples of these isolates. These results suggest that the molecular karyotype and the RAPD patterns of the anuran trypanosomes remain stable after being cultured continuously in vitro for one year.

Chloroplast genes as genetic markers for inferring patterns of change, maternal ancestry and phylogenetic relationships among Eleusine species

PubMed Central

Agrawal, Renuka; Agrawal, Nitin; Tandon, Rajesh; Raina, Soom Nath

2013-01-01

Assessment of phylogenetic relationships is an important component of any successful crop improvement programme, as wild relatives of the crop species often carry agronomically beneficial traits. Since its domestication in East Africa, Eleusine coracana (2n = 4x = 36), a species belonging to the genus Eleusine (x = 8, 9, 10), has held a prominent place in the semi-arid regions of India, Nepal and Africa. The patterns of variation between the cultivated and wild species reported so far and the interpretations based upon them have been considered primarily in terms of nuclear events. We analysed, for the first time, the phylogenetic relationship between finger millet (E. coracana) and its wild relatives by species-specific chloroplast deoxyribonucleic acid (cpDNA) polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) and chloroplast simple sequence repeat (cpSSR) markers/sequences. Restriction fragment length polymorphism of the seven amplified chloroplast genes/intergenic spacers (trnK, psbD, psaA, trnH–trnK, trnL–trnF, 16S and trnS–psbC), nucleotide sequencing of the chloroplast trnK gene and chloroplast microsatellite polymorphism were analysed in all nine known species of Eleusine. The RFLP of all seven amplified chloroplast genes/intergenic spacers and trnK gene sequences in the diploid (2n = 16, 18, 20) and allotetraploid (2n = 36, 38) species resulted in well-resolved phylogenetic trees with high bootstrap values. Eleusine coracana, E. africana, E. tristachya, E. indica and E. kigeziensis did not show even a single change in restriction site. Eleusine intermedia and E. floccifolia were also shown to have identical cpDNA fragment patterns. The cpDNA diversity in Eleusine multiflora was found to be more extensive than that of the other eight species. The trnK gene sequence data complemented the results obtained by PCR–RFLP. The maternal lineage of all three allotetraploid species (AABB, AADD) was the same, with E. indica being the maternal diploid progenitor species. The markers specific to certain species were also identified. PMID:24790119

Chloroplast genes as genetic markers for inferring patterns of change, maternal ancestry and phylogenetic relationships among Eleusine species.

PubMed

Agrawal, Renuka; Agrawal, Nitin; Tandon, Rajesh; Raina, Soom Nath

2014-01-01

Assessment of phylogenetic relationships is an important component of any successful crop improvement programme, as wild relatives of the crop species often carry agronomically beneficial traits. Since its domestication in East Africa, Eleusine coracana (2n = 4x = 36), a species belonging to the genus Eleusine (x = 8, 9, 10), has held a prominent place in the semi-arid regions of India, Nepal and Africa. The patterns of variation between the cultivated and wild species reported so far and the interpretations based upon them have been considered primarily in terms of nuclear events. We analysed, for the first time, the phylogenetic relationship between finger millet (E. coracana) and its wild relatives by species-specific chloroplast deoxyribonucleic acid (cpDNA) polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and chloroplast simple sequence repeat (cpSSR) markers/sequences. Restriction fragment length polymorphism of the seven amplified chloroplast genes/intergenic spacers (trnK, psbD, psaA, trnH-trnK, trnL-trnF, 16S and trnS-psbC), nucleotide sequencing of the chloroplast trnK gene and chloroplast microsatellite polymorphism were analysed in all nine known species of Eleusine. The RFLP of all seven amplified chloroplast genes/intergenic spacers and trnK gene sequences in the diploid (2n = 16, 18, 20) and allotetraploid (2n = 36, 38) species resulted in well-resolved phylogenetic trees with high bootstrap values. Eleusine coracana, E. africana, E. tristachya, E. indica and E. kigeziensis did not show even a single change in restriction site. Eleusine intermedia and E. floccifolia were also shown to have identical cpDNA fragment patterns. The cpDNA diversity in Eleusine multiflora was found to be more extensive than that of the other eight species. The trnK gene sequence data complemented the results obtained by PCR-RFLP. The maternal lineage of all three allotetraploid species (AABB, AADD) was the same, with E. indica being the maternal diploid progenitor species. The markers specific to certain species were also identified.

Momentum peak shift and width of longitudinal momentum distribution of projectilelike fragments produced at E =290 MeV /nucleon

NASA Astrophysics Data System (ADS)

Momota, S.; Kanazawa, M.; Kitagawa, A.; Sato, S.

2018-04-01

Longitudinal momentum (PL) distributions of projectilelike fragments produced at E =290 MeV /nucleon are investigated. PL distributions of fragments produced by Ar and Kr beams with a wide variety of targets (C, Al, Nb, Tb, and Au) were measured using the fragment separator at HIMAC. PL distributions observed for fragments with a wide range of mass losses Δ A (1-30 for Ar beam and 1-64 for Kr beam), show a slightly, but definitely asymmetric nature. The peak shift and width were obtained from the observed PL distributions. No significant target dependence was found in either the peak shift or width. For the practical application, the variation in momentum peak shift with fragment mass (AF) was represented by a parabolic function. The width on the high-PL side (σHigh) is well reproduced by the Goldhaber formula, which is obtained from the contribution of the Fermi momentum. The behavior of the reduced width, σ0, obtained from σHigh via the Goldhaber formulation, is consistent with the mass-dependent Fermi momentum of a nucleon. The width on the low-PL side (σLow) is markedly larger than σHigh and exhibits a clear AF dependence.

Voronoi Cell Patterns: theoretical model and application to submonolayer growth

NASA Astrophysics Data System (ADS)

González, Diego Luis; Einstein, T. L.

2012-02-01

We use a simple fragmentation model to describe the statistical behavior of the Voronoi cell patterns generated by a homogeneous and isotropic set of points in 1D and in 2D. In particular, we are interested in the distribution of sizes of these Voronoi cells. Our model is completely defined by two probability distributions in 1D and again in 2D, the probability to add a new point inside an existing cell and the probability that this new point is at a particular position relative to the preexisting point inside this cell. In 1D the first distribution depends on a single parameter while the second distribution is defined through a fragmentation kernel; in 2D both distributions depend on a single parameter. The fragmentation kernel and the control parameters are closely related to the physical properties of the specific system under study. We apply our model to describe the Voronoi cell patterns of island nucleation for critical island sizes i=0,1,2,3. Experimental results for the Voronoi cells of InAs/GaAs quantum dots are also described by our model.

Fragmentation Point Detection of JPEG Images at DHT Using Validator

NASA Astrophysics Data System (ADS)

Mohamad, Kamaruddin Malik; Deris, Mustafa Mat

File carving is an important, practical technique for data recovery in digital forensics investigation and is particularly useful when filesystem metadata is unavailable or damaged. The research on reassembly of JPEG files with RST markers, fragmented within the scan area have been done before. However, fragmentation within Define Huffman Table (DHT) segment is yet to be resolved. This paper analyzes the fragmentation within the DHT area and list out all the fragmentation possibilities. Two main contributions are made in this paper. Firstly, three fragmentation points within DHT area are listed. Secondly, few novel validators are proposed to detect these fragmentations. The result obtained from tests done on manually fragmented JPEG files, showed that all three fragmentation points within DHT are successfully detected using validators.

Tandem mass spectrometry of coprogen and deferoxamine hydroxamic siderophores.

PubMed

Simionato, Ana V C; de Souza, Gezimar D; Rodrigues-Filho, Edson; Glick, James; Vouros, Paul; Carrilho, Emanuel

2006-01-01

Mechanisms of fragmentation of hydroxamic siderophores are proposed comparing deuterated and nondeuterated samples. Standard siderophores (e.g. deferoxamine and coprogen) were directly injected into both ion trap and linear quadrupole mass spectrometers with electrospray ionization (ESI). Four and two fragmentation steps were carried out for deferoxamine and coprogen (analyzed by positive and negative ESI, respectively). Deferoxamine cleavages occurred in both peptide and hydroxamic bonds while the coprogen fragmentation pattern is more elaborate, since it contains Fe(III) in its structure.

A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates

USGS Publications Warehouse

Delaney, Kathleen Semple; Riley, Seth P.D.; Fisher, Robert N.

2010-01-01

Background: Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings: We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance: Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

Batman-cracks. Observations and numerical simulations

NASA Astrophysics Data System (ADS)

Selvadurai, A. P. S.; Busschen, A. Ten; Ernst, L. J.

1991-05-01

To ensure mechanical strength of fiber reinforced plastics (FRP), good adhesion between fibers and the matrix is considered to be an essential requirement. An efficient test of fiber-matrix interface characterization is the fragmentation test which provides information about the interface slip mechanism. This test consists of the longitudinal loading of a single fiber which is embedded in a matrix specimen. At critical loads the fiber experiences fragmentation. This fragmentation will terminate depending upon the shear-slip strength of the fiber-matrix adhesion, which is inversely proportional to average fragment lengths. Depending upon interface strength characteristics either bond or slip matrix fracture can occur at the onset of fiber fracture. Certain particular features of matrix fracture are observed at the locations of fiber fracture in situations where there is sufficient interface bond strength. These refer to the development of fractures with a complex surface topography. The experimental procedure involved in the fragmentation tests is discussed and the boundary element technique to examine the development of multiple matrix fractures at the fiber fracture locations is examined. The mechanics of matrix fracture is examined. When bond integrity is maintained, a fiber fracture results in a matrix fracture. The matrix fracture topography in a fragmentation test is complex; however, simplified conoidal fracture patterns can be used to investigate the crack extension phenomena. Via a mixed-mode fracture criterion, the generation of a conoidal fracture pattern in the matrix is investigated. The numerical results compare favorably with observed experimental data derived from tests conducted on fragmentation test specimens consisting of a single glass fiber which is embedded in a polyester matrix.

Spatio-temporal Genetic Structure of a Tropical Bee Species Suggests High Dispersal Over a Fragmented Landscape.

PubMed

Suni, Sevan S; Bronstein, Judith L; Brosi, Berry J

2014-03-01

Habitat destruction threatens biodiversity by reducing the amount of available resources and connectivity among geographic areas. For organisms living in fragmented habitats, population persistence may depend on dispersal, which maintains gene flow among fragments and can prevent inbreeding within them. It is centrally important to understand patterns of dispersal for bees living in fragmented areas given the importance of pollination systems and recently documented declines in bee populations. We used population and landscape genetic techniques to characterize patterns of dispersal over a large fragmented area in southern Costa Rica for the orchid bee species Euglossa championi . First, we estimated levels of genetic differentiation among forest fragments as φ pt , an analog to the traditional summary statistic F st , as well as two statistics that may more adequately represent levels of differentiation, G ' st and D est . Second, we used a Bayesian approach to determine the number and composition of genetic groups in our sample. Third we investigated how genetic differentiation changes with distance. Fourth, we determined the extent to which deforested areas restrict dispersal. Finally, we estimated the extent to which there were temporal differences in allele frequencies within the same forest fragments. Within years we found low levels of differentiation even over 80 km, and no effect of land use type on level of genetic differentiation. However, we found significant genetic differentiation between years. Taken together our results suggest that there are high levels of gene flow over this geographic area, and that individuals show low site fidelity over time.

A Rapid, Strong, and Convergent Genetic Response to Urban Habitat Fragmentation in Four Divergent and Widespread Vertebrates

PubMed Central

Delaney, Kathleen Semple; Riley, Seth P. D.; Fisher, Robert N.

2010-01-01

Background Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix. PMID:20862274

Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants

PubMed Central

Hehle, Verena K.; Paul, Matthew J.; Roberts, Victoria A.; van Dolleweerd, Craig J.; Ma, Julian K.-C.

2016-01-01

This study examined the degradation pattern of a murine IgG1κ monoclonal antibody expressed in and extracted from transformed Nicotiana tabacum. Gel electrophoresis of leaf extracts revealed a consistent pattern of recombinant immunoglobulin bands, including intact and full-length antibody, as well as smaller antibody fragments. N-terminal sequencing revealed these smaller fragments to be proteolytic cleavage products and identified a limited number of protease-sensitive sites in the antibody light and heavy chain sequences. No strictly conserved target sequence was evident, although the peptide bonds that were susceptible to proteolysis were predominantly and consistently located within or near to the interdomain or solvent-exposed regions in the antibody structure. Amino acids surrounding identified cleavage sites were mutated in an attempt to increase resistance. Different Guy’s 13 antibody heavy and light chain mutant combinations were expressed transiently in N. tabacum and demonstrated intensity shifts in the fragmentation pattern, resulting in alterations to the full-length antibody-to-fragment ratio. The work strengthens the understanding of proteolytic cleavage of antibodies expressed in plants and presents a novel approach to stabilize full-length antibody by site-directed mutagenesis.—Hehle, V. K., Paul, M. J., Roberts, V. A., van Dolleweerd, C. J., Ma, J. K.-C. Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants. PMID:26712217

Light fragments from (C + Be) interactions at 0.6 GeV/nucleon

DOE PAGES

Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; ...

2016-05-01

We measured nuclear fragments emitted at 3.5° in 12C fragmentation at 0.6 GeV/nucleon. We also used the spectra obtained to test the predictions of four ion-ion interaction models: INCL++, BC, LAQGSM03.03 and QMD as well as for the comparison with the analytical parametrization in the framework of thermodynamical picture of fragmentation.

Cellular features of endometrial hyperplasia and well differentiated adenocarcinoma using the Endocyte sampler: Diagnostic criteria based on the cytoarchitecture of tissue fragments.

PubMed

Norimatsu, Yoshiaki; Shimizu, Keiko; Kobayashi, Tadao K; Moriya, Takuya; Tsukayama, Choutatsu; Miyake, Yasuyuki; Ohno, Eiji

2006-04-25

Because cellular atypia is often limited in endometrial hyperplasia and well-differentiated endometrial adenocarcinoma (WHO Grade 1 adenocarcinoma), diagnostic criteria for endometrial cytology have not been fully established. New diagnostic criteria based on the composition and architecture of tissue fragments (cytoarchitecture) in the smears were used in the present study. Cytologic features are of less importance because the distinction between endometrial hyperplasia and Grade 1 adenocarcinoma relies more on architectural features than cellular changes. Cell clumps of various size are usually collected abundantly with cytologic material using a disposable scraping device and it was noticed that those cell clumps reflected the histologic architecture. The purpose of the current study was to determine the form of the cytoarchitecture that reflects the histologic structure and to examine the cellular features in endometrial hyperplasia and Grade 1 adenocarcinoma. The frequency of each type of cell clump (tube or sheet-shaped pattern, dilated or branched pattern, irregular protrusion, and papillotubular pattern) were obtained from 49 cases of normal proliferative endometrium (NPE) (patient age range, 28-51 yrs; average age, 39.9 yrs), 63 cases of endometrial hyperplasia without atypia (EH) (patient age range, 35-65 yrs; average age, 47.7 yrs), 13 cases of endometrial hyperplasia with atypia (AEH) (patient age range 47-65 yrs; average age, 53.8 yrs), and 49 cases of Grade 1 adenocarcinoma (patient age range, 42-73 yrs; average age, 58.9 yrs). Certain characteristics of the cytoarchitecture were observed. In the NPE, cell clumps with a tube or sheet-shaped pattern were found in 97.5% of cases. In the EH, cell clumps with a dilated or branched pattern were found in 34.9% of cases. In the Grade 1 adenocarcinoma, cell clumps with irregular protrusions were found in 61.8% cases, whereas a papillotubular pattern was present in 29.7% of cases. The results of the current study revealed that cytoarchitectural criteria appear to be more useful for the cytologic assessment of endometrial lesions, especially for the diagnosis of endometrial hyperplasia and Grade 1 adenocarcinoma. Copyright 2006 American Cancer Society.

Introducing Human Population Biology through an Easy Laboratory Exercise on Mitochondrial DNA

ERIC Educational Resources Information Center

Pardinas, Antonio F.; Dopico, Eduardo; Roca, Agustin; Garcia-Vazquez, Eva; Lopez, Belen

2010-01-01

This article describes an easy and cheap laboratory exercise for students to discover their own mitochondrial haplogroup. Students use buccal swabs to obtain mucosa cells as noninvasive tissue samples, extract DNA, and with a simple polymerase chain reaction-restriction fragment length polymorphism analysis they can obtain DNA fragments of…

Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals

PubMed Central

Crooks, Kevin R.; Burdett, Christopher L.; Theobald, David M.; King, Sarah R. B.; Rondinini, Carlo; Boitani, Luigi

2017-01-01

Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world’s terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world’s terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation. PMID:28673992

Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals.

PubMed

Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; King, Sarah R B; Di Marco, Moreno; Rondinini, Carlo; Boitani, Luigi

2017-07-18

Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world's terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world's terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation.

Speaking Rate Affects the Perception of Duration as a Suprasegmental Lexical-Stress Cue

ERIC Educational Resources Information Center

Reinisch, Eva; Jesse, Alexandra; McQueen, James M.

2011-01-01

Three categorization experiments investigated whether the speaking rate of a preceding sentence influences durational cues to the perception of suprasegmental lexical-stress patterns. Dutch two-syllable word fragments had to be judged as coming from one of two longer words that matched the fragment segmentally but differed in lexical stress…

Characterizing forest fragments in boreal, temperate, and tropical ecosystems

Treesearch

Arjan J. H. Meddens; Andrew T. Hudak; Jeffrey S. Evans; William A. Gould; Grizelle Gonzalez

2008-01-01

An increased ability to analyze landscapes in a spatial manner through the use of remote sensing leads to improved capabilities for quantifying human-induced forest fragmentation. Developments of spatially explicit methods in landscape analyses are emerging. In this paper, the image delineation software program eCognition and the spatial pattern analysis program...

Distribution of IS900 restriction fragment length polymorphism types among animal Mycobacterium avium subsp. paratuberculosis isolates from Argentina and Europe.

PubMed

Moreira, A R; Paolicchi, F; Morsella, C; Zumarraga, M; Cataldi, A; Fabiana, B; Alicia, A; Piet, O; van Soolingen, D; Isabel, R M

1999-12-01

Sixty-one Mycobacterium avium subsp. paratuberculosis isolates from cattle and deer from the Buenos Aires province, an important livestock region in Argentina, were typed by restriction fragment length polymorphisms (RFLP) analysis based on IS900. Four different RFLP patterns (designated 'A', 'B', 'C' and 'E') were identified in BstEII digests of genomic DNA. The most frequently observed type, pattern 'A', was found in 46 isolates (75%). The second, pattern 'E', included 8 isolates (13%), while the third, pattern 'B', included 6 isolates (10%). Pattern 'C' was found for only one isolate. All of the deer isolates were classified as pattern 'A', while cattle isolates represented all four RFLP patterns. Twenty-one isolates representing the four different BstEII-RFLP patterns were digested with PstI. Twenty isolates showed identical PstI-RFLP pattern. BstEII-RFLP patterns from Argentine cattle and deer were compared with patterns found in cattle, goat, deer, rabbit, and human isolates from Europe. The most common pattern in Argentina, pattern 'A', was identical to a less frequently occurring pattern R9 (C17) from Europe. The other Argentine patterns 'B', 'C' and 'E', were not found in the Europe. These results indicate that the distribution of M. avium subsp. paratuberculosis genotypes in the Buenos Aires province of Argentina is different from that found in Europe.

Construction of a 3D-shaped, natural product like fragment library by fragmentation and diversification of natural products.

PubMed

Prescher, Horst; Koch, Guido; Schuhmann, Tim; Ertl, Peter; Bussenault, Alex; Glick, Meir; Dix, Ina; Petersen, Frank; Lizos, Dimitrios E

2017-02-01

A fragment library consisting of 3D-shaped, natural product-like fragments was assembled. Library construction was mainly performed by natural product degradation and natural product diversification reactions and was complemented by the identification of 3D-shaped, natural product like fragments available from commercial sources. In addition, during the course of these studies, novel rearrangements were discovered for Massarigenin C and Cytochalasin E. The obtained fragment library has an excellent 3D-shape and natural product likeness, covering a novel, unexplored and underrepresented chemical space in fragment based drug discovery (FBDD). Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural comparisons of two allelic variants of human placental alkaline phosphatase.

PubMed

Millán, J L; Stigbrand, T; Jörnvall, H

1985-01-01

A simple immunosorbent purification scheme based on monoclonal antibodies has been devised for human placental alkaline phosphatase. The two most common allelic variants, S and F, have similar amino acid compositions with identical N-terminal amino acid sequences through the first 13 residues. Both variants have identical lectin binding properties towards concanavalin A, lentil-lectin, wheat germ agglutinin, phytohemagglutinin and soybean agglutinin, and identical carbohydrate contents as revealed by methylation analysis. CNBr fragments of the variants demonstrate identical high performance liquid chromatography patterns. The carbohydrate containing fragment is different from the 32P-labeled active site fragment and the N-terminal fragment.

Movement of feeder-using songbirds: the influence of urban features.

PubMed

Cox, Daniel T C; Inger, Richard; Hancock, Steven; Anderson, Karen; Gaston, Kevin J

2016-11-23

Private gardens provide vital opportunities for people to interact with nature. The most popular form of interaction is through garden bird feeding. Understanding how landscape features and seasons determine patterns of movement of feeder-using songbirds is key to maximising the well-being benefits they provide. To determine these patterns we established three networks of automated data loggers along a gradient of greenspace fragmentation. Over a 12-month period we tracked 452 tagged blue tits Cyantistes caeruleus and great tits Parus major moving between feeder pairs 9,848 times, to address two questions: (i) Do urban features within different forms, and season, influence structural (presence-absence of connections between feeders by birds) and functional (frequency of these connections) connectivity? (ii) Are there general patterns of structural and functional connectivity across forms? Vegetation cover increased connectivity in all three networks, whereas the presence of road gaps negatively affected functional but not structural connectivity. Across networks structural connectivity was lowest in the summer when birds maintain breeding territories, however patterns of functional connectivity appeared to vary with habitat fragmentation. Using empirical data this study shows how key urban features and season influence movement of feeder-using songbirds, and we provide evidence that this is related to greenspace fragmentation.

Assessing the drivers shaping global patterns of urban vegetation landscape structure.

PubMed

Dobbs, C; Nitschke, C; Kendal, D

2017-08-15

Vegetation is one of the main resources involve in ecosystem functioning and providing ecosystem services in urban areas. Little is known on the landscape structure patterns of vegetation existing in urban areas at the global scale and the drivers of these patterns. We studied the landscape structure of one hundred cities around the globe, and their relation to demography (population), socioeconomic factors (GDP, Gini Index), climate factors (temperature and rain) and topographic characteristics (altitude, variation in altitude). The data revealed that the best descriptors of landscape structure were amount, fragmentation and spatial distribution of vegetation. Populated cities tend to have less, more fragmented, less connected vegetation with a centre of the city with low vegetation cover. Results also provided insights on the influence of socioeconomics at a global scale, as landscape structure was more fragmented in areas that are economically unequal and coming from emergent economies. This study shows the effects of the social system and climate on urban landscape patterns that gives useful insights for the distribution in the provision of ecosystem services in urban areas and therefore the maintenance of human well-being. This information can support local and global policy and planning which is committing our cities to provide accessible and inclusive green space for all urban inhabitants. Copyright © 2017 Elsevier B.V. All rights reserved.

Bird diversity along a gradient of fragmented habitats of the Cerrado.

PubMed

Jesus, Shayana DE; Pedro, Wagner A; Bispo, Arthur A

2018-01-01

Understanding the factors that affect biodiversity is of central interest to ecology, and essential to species conservation and ecosystems management. We sampled bird communities in 17 forest fragments in the Cerrado biome, the Central-West region of Brazil. We aimed to know the communities structure pattern and the influence of geographical distance and environmental variables on them, along a gradient of fragmented habitats at both local and landscape scales. Eight structural variables of the fragments served as an environmental distance measurement at the local scale while five metrics served as an environmental distance measurement at the landscape scale. Species presence-absence data were used to calculate the dissimilarity index. Beta diversity was calculated using three indices (βsim, βnes and βsor), representing the spatial species turnover, nestedness and total beta diversity, respectively. Spatial species turnover was the predominant pattern in the structure of the communities. Variations in beta diversity were explained only by the environmental variables of the landscape with spatial configuration being more important than the composition. This fact indicates that, in Cerrado of Goiás avian communities structure, deterministic ecological processes associated to differences in species responses to landscape fragmentation are more important than stochastic processes driven by species dispersal.

Dispersal of remnant endangered trees in a fragmented and disturbed forest by frugivorous birds.

PubMed

Li, Ning; Bai, Bing; Li, Xin-Hai; An, Shu-Qing; Lu, Chang-Hu

2017-07-01

Most endangered plant species in a fragmented forest behave as a unique source population, with a high dependence on frugivorous birds for recruitment and persistence. In this study, we combined field data of dispersal behavior of birds and GIS information of patch attributes to estimate how frugivorous birds could affect the effective dispersal pattern of Chinese yew (Taxus chinensis) in a fragmented and disturbed forest. Nine bird species were observed to visit T. chinensis trees, with Urocissa erythrorhyncha, Zoothera dauma and Picus canus being the most common dispersers. After foraging, six disperser species exhibited different perching patterns. Three specialist species, P. canus, Turdus hortulorum, and Z. dauma stayed in the source patch, while three generalist species, U. erythrorhyncha, Hypsipetes mcclellandii, and H. castanonotus, could perch in bamboo patches and varied in movement ability due to body size. As a consequence of perching, dispersers significantly contributed to the seed bank, but indirectly affected seedling recruitment. Moreover, the recruitment of T. chinensis was also affected by patch attributes in a fragmented forest (distances to source patch, patch type, size). Our results highlighted the ability of unique source population regeneration of T. chinensis in a fragmented forest, with high dependence on both frugivorous birds and patch attributes, which should be considered in future planning for forest management and conservation.

Mercury-induced fragmentation of n-decane and n-undecane in positive mode ion mobility spectrometry.

PubMed

Gunzer, F

2015-09-21

Ion mobility spectrometry is a well-known technique for trace gas analysis. Using soft ionization techniques, fragmentation of analytes is normally not observed, with the consequence that analyte spectra of single substances are quite simple, i.e. showing in general only one peak. If the concentration is high enough, an extra cluster peak involving two analyte molecules can often be observed. When investigating n-alkanes, different results regarding the number of peaks in the spectra have been obtained in the past using this spectrometric technique. Here we present results obtained when analyzing n-alkanes (n-hexane to n-undecane) with a pulsed electron source, which show no fragmentation or clustering at all. However, when investigating a mixture of mercury and an n-alkane, a situation quite typical in the oil and gas industry, a strong fragmentation and cluster formation involving these fragments has been observed exclusively for n-decane and n-undecane.

The role of electron transfer in DNA building blocks: Evaluation of strand breaks and their implications

NASA Astrophysics Data System (ADS)

Almeida, Diogo Alexandre Fialho de

Radiation-induced damage to biological systems, both direct and indirect processes, has increasingly come under scrutiny by the international scientific community due to recent findings that electrons are a very effective agent in damaging DNA/RNA. Indeed, much remains to be discovered regarding the exact physico-chemical processes that occur in the nascent stages of DNA/RNA damage by incident radiation. However, it is also known that electrons do not exist freely in the physiological medium, but rather solvated and/or pre-solvated states. This leads to the need for new techniques that can better explore the damaging role of "bound" electrons to DNA/RNA. The work presented in this thesis consists on the study of electron transfer in collisions of atomic species with molecules of biological relevance. In order to study these processes, two experimental setups were used. One setup consists of a crossed beam experiment where a neutral potassium beam is created and made to collide with an effusive molecular target beam. The anionic products that stem from electron transfer in potassium atom to the molecular target collisions are then extracted and time-of-flight (TOF) mass analysed. In the second setup a beam of anionic species is formed and made to collide with a molecular target. Collisions with three different anionic beams were performed (H-, O- and OH-), as well as with different simple organic molecules, by measuring the positive and negative ion fragmentation patterns with a quadrupole mass spectrometer (QMS). A comparison between these two collisional systems can greatly help to understand the underlying mechanisms of the electron transfer processes. Finally, studies of potassium collisions with sugar surrogates D-Ribose and THF were performed. These studies show very different fragmentation patterns from DEA, although in the case of THF, it is suggested that the initially accessed states are the same as in DEA. With these studies was also possible to show for the first time collision induced site and bond selectivity breaking, where the electron is transferred into a given state of the acceptor molecule and the resulting fragmentation pathways are exclusive to the initial anionic state. Furthermore, the role of the potassium cation post collisionwas explored and indeed its presence is suggested to induce at least partial suppression of auto-detachment. The implications that ensue from this degradation are analysed in the light of the obtained fragmentation patterns.

Effects of habitat fragmentation on passerine birds breeding in Intermountain shrubsteppe

USGS Publications Warehouse

Knick, S.T.; Rotenberry, J.T.

2002-01-01

Habitat fragmentation and loss strongly influence the distribution and abundance of passerine birds breeding in Intermountain shrubsteppe. Wildfires, human activities, and change in vegetation communities often are synergistic in these systems and can result in radical conversion from shrubland to grasslands dominated by exotic annuals at large temporal and spatial scales from which recovery to native conditions is unlikely. As a result, populations of 5 of the 12 species in our review of Intermountain shrubsteppe birds are undergoing significant declines; 5 species are listed as at-risk or as candidates for protection in at least one state. The process by which fragmentation affects bird distributions in these habitats remains unknown because most research has emphasized the detection of population trends and patterns of habitat associations at relatively large spatial scales. Our research indicates that the distribution of shrubland-obligate species, such as Brewer's Sparrows (Spizella breweri), Sage Sparrows (Amphispiza belli), and Sage Thrashers (Oreoscoptes montanus), was highly sensitive to fragmentation of shrublands at spatial scales larger than individual home ranges. In contrast, the underlying mechanisms for both habitat change and bird population dynamics may operate independently of habitat boundaries. We propose alternative, but not necessarily exclusive, mechanisms to explain the relationship between habitat fragmentation and bird distribution and abundance. Fragmentation might influence productivity through differences in breeding density, nesting success, or predation. However, local and landscape variables were not significant determinants either of success, number fledged, or probability of predation or parasitism (although our tests had relatively low statistical power). Alternatively, relative absence of natal philopatry and redistribution by individuals among habitats following fledging or post-migration could account for the pattern of distribution and abundance. Thus, boundary dynamics may be important in determining the distribution of shrubland-obligate species but insignificant relative to the mechanisms causing the pattern of habitat and bird distribution. Because of the dichotomy in responses, Intermountain shrubsteppe systems present a unique challenge in understanding how landscape composition, configuration, and change influence bird population dynamics.

Assessment of Landscape Fragmentation Associated With Urban Centers Using ASTER Data

NASA Astrophysics Data System (ADS)

Stefanov, W. L.

2002-12-01

The role of humans as an integral part of the environment and ecosystem processes has only recently been accepted into mainstream ecological thought. The realization that virtually all ecosystems on Earth have experienced some degree of human alteration or impact has highlighted the need to incorporate humans (and their environmental effects) into ecosystem models. A logical starting point for investigation of human ecosystem dynamics is examination of the land cover characteristics of large urban centers. Land cover and land use changes associated with urbanization are important drivers of local geological, hydrological, ecological, and climatic change. Quantification and monitoring of urban land cover/land use change is part of the primary mission of the ASTER instrument on board the NASA Terra satellite, and comprises the fundamental research objective of the Urban Environmental Monitoring (UEM) Program at Arizona State University. The UEM program seeks to acquire day/night, visible through thermal infrared data twice per year for 100 global urban centers (with an emphasis on semi-arid cities) over the nominal six-year life of the Terra mission. Data have been acquired for the majority of the target urban centers and are used to compare landscape fragmentation patterns on the basis of land cover classifications. Land cover classifications of urban centers are obtained using visible through mid-infrared reflectance and emittance spectra together with calculated vegetation index and spatial variance texture information (all derived from raw ASTER data). This information is combined within a classification matrix, using an expert system framework, to obtain final pixel classifications. Landscape fragmentation is calculated using a pixel per unit area metric for comparison between 55 urban centers with varying geographic and climatic settings including North America, South America, Europe, central and eastern Asia, and Australia. Temporal variations in land cover and landscape fragmentation are assessed for 9 urban centers (Albuquerque, New Mexico, USA; Baghdad, Iraq; Las Vegas, Nevada, USA; Lisbon, Portugal; Madrid, Spain; San Francisco, California, USA; Tokyo, Japan; and Vancouver, Canada). These data provide a useful baseline for comparison of human-dominated ecosystem land cover and associated regional landscape fragmentation. Continued collection of ASTER data throughout the duration of the Terra mission will enable further investigation of urban ecosystem trends.

Highly informative multiclass profiling of lipids by ultra-high performance liquid chromatography - Low resolution (quadrupole) mass spectrometry by using electrospray ionization and atmospheric pressure chemical ionization interfaces.

PubMed

Beccaria, Marco; Inferrera, Veronica; Rigano, Francesca; Gorynski, Krzysztof; Purcaro, Giorgia; Pawliszyn, Janusz; Dugo, Paola; Mondello, Luigi

2017-08-04

A simple, fast, and versatile method, using an ultra-high performance liquid chromatography system coupled with a low resolution (single quadrupole) mass spectrometer was optimized to perform multiclass lipid profiling of human plasma. Particular attention was made to develop a method suitable for both electrospray ionization and atmospheric pressure chemical ionization interfaces (sequentially in positive- and negative-ion mode), without any modification of the chromatographic conditions (mobile phase, flow-rate, gradient, etc.). Emphasis was given to the extrapolation of the structural information based on the fragmentation pattern obtained using atmospheric pressure chemical ionization interface, under each different ionization condition, highlighting the complementary information obtained using the electrospray ionization interface, of support for related molecule ions identification. Furthermore, mass spectra of phosphatidylserine and phosphatidylinositol obtained using the atmospheric pressure chemical ionization interface are reported and discussed for the first time. Copyright © 2017 Elsevier B.V. All rights reserved.

Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis.

PubMed Central

Nübel, U; Engelen, B; Felske, A; Snaidr, J; Wieshuber, A; Amann, R I; Ludwig, W; Backhaus, H

1996-01-01

Sequence heterogeneities in 16S rRNA genes from individual strains of Paenibacillus polymyxa were detected by sequence-dependent separation of PCR products by temperature gradient gel electrophoresis (TGGE). A fragment of the 16S rRNA genes, comprising variable regions V6 to V8, was used as a target sequence for amplifications. PCR products from P. polymyxa (type strain) emerged as a well-defined pattern of bands in the gradient gel. Six plasmids with different inserts, individually demonstrating the migration characteristics of single bands of the pattern, were obtained by cloning the PCR products. Their sequences were analyzed as a representative sample of the total heterogeneity. An amount of 10 variant nucleotide positions in the fragment of 347 bp was observed, with all substitutions conserving the relevant secondary structures of the V6 and V8 regions in the RNA molecules. Hybridizations with specifically designed probes demonstrated different chromosomal locations of the respective rRNA genes. Amplifications of reverse-transcribed rRNA from ribosome preparations, as well as whole-cell hybridizations, revealed a predominant representation of particular sequences in ribosomes of exponentially growing laboratory cultures. Different strains of P. polymyxa showed not only remarkably differing patterns of PCR products in TGGE analysis but also discriminative whole-cell labeling with the designed oligonucleotide probes, indicating the different representation of individual sequences in active ribosomes. Our results demonstrate the usefulness of TGGE for the structural analysis of heterogeneous rRNA genes together with their expression, stress problems of the generation of meaningful data for 16S rRNA sequences and probe designs, and might have consequences for evolutionary concepts. PMID:8824607

Phylogenetic sequence analysis, recombinant expression, and tissue distribution of a channel catfish estrogen receptor beta

USGS Publications Warehouse

Xia, Zhenfang; Gale, William L.; Chang, Xiaotian; Langenau, David; Patino, Reynaldo; Maule, Alec G.; Densmore, Llewellyn D.

2000-01-01

An estrogen receptor β (ERβ) cDNA fragment was amplified by RT-PCR of total RNAextracted from liver and ovary of immature channel catfish. This cDNA fragment was used to screen an ovarian cDNA library made from an immature female fish. A clone was obtained that contained an open reading frame encoding a 575-amino-acid protein with a deduced molecular weight of 63.9 kDa. Maximum parsimony and Neighbor Joining analyses were used to generate a phylogenetic classification of channel catfish ERβ on the basis of 25 full-length teleost and tetrapod ER sequences. The consensus tree obtained indicated the existence of two major vertebrate ER subtypes, α and β. Within each subtype, and in accordance with established phylogenetic relationships, teleost and tetrapod ER were monophyletic confirming the results of a previous analysis (Z. Xiaet al., 1999, Gen. Comp. Endocrinol. 113, 360–368). Extracts of COS-7 cells transfectedwith channel catfish ERβ cDNA bound estrogen with high affinity (Kd = 0.21 nM) and specificity. The affinity of channel catfish ERβ for estrogen was higher than previously reported for channel catfish ERα. As determined by qualitative RT-PCR, the tissue distributions of ERα and ERβ were similar but not identical. Both ER subtypes were present in ovary and testis. ERα was found in all other tissues examined from juvenile and mature fish of both sexes. ERβ was also found in most tissues except, in most cases, whole blood and head kidney. Interestingly, the pattern of expression of ER subtypes in head kidney always corresponded to the pattern in whole blood. In conclusion, we isolated a channel catfish ERβ with ligand-binding affinity and tissue expression patterns different from ERα. Also, we confirmed the validity of our previously proposed general classification scheme for vertebrate ER into α and β subtypes and within each subtype, into teleost and tetrapod clades.

Coulomb fission in multiply charged molecular clusters: Experiment and theory

NASA Astrophysics Data System (ADS)

Harris, Christopher; Baptiste, Joshua; Lindgren, Eric B.; Besley, Elena; Stace, Anthony J.

2017-04-01

A series of three multiply charged molecular clusters, (C6H6)nz+ (benzene), (CH3CNnz) + (acetonitrile), and (C4H8O)nz+ (tetrahydrofuran), where the charge z is either 3 or 4, have been studied for the purpose of identifying the patterns of behaviour close to the charge instability limit. Experiments show that on a time scale of ˜10-4 s, ions close to the limit undergo Coulomb fission where the observed pathways exhibit considerable asymmetry in the sizes of the charged fragments and are all associated with kinetic (ejection) energies of between 1.4 and 2.2 eV. Accurate kinetic energies have been determined through a computer simulation of peak profiles recorded in the experiments and the results modelled using a theory formulated to describe how charged particles of dielectric materials interact with one another [E. Bichoutskaia et al., J. Chem. Phys. 133, 024105 (2010)]. The calculated electrostatic interaction energy between separating fragments gives an accurate account for the measured kinetic energies and also supports the conclusion that +4 ions fragment into +3 and +1 products as opposed to the alternative of two +2 fragments. This close match between the theory and experiment reinforces the assumption that a significant fraction of excess charge resides on the surfaces of the fragment ions. It is proposed that the high degree of asymmetry seen in the fragmentation patterns of the multiply charged clusters is due, in part, to limits imposed by the time window during which observations are made.

Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

2014-01-01

To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

Differentiation of regioisomeric aromatic ketocarboxylic acids by atmospheric pressure chemical ionization CAD tandem mass spectrometry in a linear quadrupole ion trap mass spectrometer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amundson, Lucas M.; Owen, Ben C.; Gallardo, Vanessa A.

2011-01-01

Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS n ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at differentmore » collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.« less

Land use/land cover change and their effects on landscape patterns in the Yanqi Basin, Xinjiang (China).

PubMed

Wang, Shuixian; Wang, Shengli

2013-12-01

Human modification of land use and land cover change (LUCC) drives the change of landscape patterns and limits the availability of products and services for human and livestock. LUCC can undermine environmental health. Thus, this study aimed to develop an understanding of LUCC in the Yanqi Basin, Xinjiang, China, an arid area experiencing dramatic water and land resource use. A time series of satellite images (1964, 1973, 1989, 1999, and 2009) were used to calculate the index of landscape patterns to study the processes involved in changes to land uses and landscape patterns and the influence of this changes on landscape patterns. The results show that land uses in the Yanqi Basin have changed dramatically since 1964 with grassland being mainly converted to cropland. Landscape fragmentation and diversity have decreased in the study area, although landscape fragmentation increased from 1964 to 1999 and then decreased by 2009. The index of landscape diversity decreased from 1.64 in 1964 to 0.71 in 2009. The heterogeneity and complexity of the landscape increased during this period. In contrast, the index of dominance decreased from 0.85 in 1964 to 0.83 in 2009. Land use change drives landscape patterns of the development of the watershed toward diversity and a fragmented structure. Population growth, economic development, and industrial policies were the dominant driving forces behind LUCC in the Yanqi Basin. Sustainable use of land resources is a significant factor in maintaining economic development and environmental protection in this arid inland river basin.

Mating system and early viability resistance to habitat fragmentation in a bird-pollinated eucalypt

PubMed Central

Breed, M F; Ottewell, K M; Gardner, M G; Marklund, M H K; Stead, M G; Harris, J B C; Lowe, A J

2015-01-01

Habitat fragmentation has been shown to disrupt ecosystem processes such as plant-pollinator mutualisms. Consequently, mating patterns in remnant tree populations are expected to shift towards increased inbreeding and reduced pollen diversity, with fitness consequences for future generations. However, mating patterns and phenotypic assessments of open-pollinated progeny have rarely been combined in a single study. Here, we collected seeds from 37 Eucalyptus incrassata trees from contrasting stand densities following recent clearance in a single South Australian population (intact woodland=12.6 trees ha−1; isolated pasture=1.7 trees ha−1; population area=10 km2). 649 progeny from these trees were genotyped at eight microsatellite loci. We estimated genetic diversity, spatial genetic structure, indirect contemporary pollen flow and mating patterns for adults older than the clearance events and open-pollinated progeny sired post-clearance. A proxy of early stage progeny viability was assessed in a common garden experiment. Density had no impact on mating patterns, adult and progeny genetic diversity or progeny growth, but was associated with increased mean pollen dispersal. Weak spatial genetic structure among adults suggests high historical gene flow. We observed preliminary evidence for inbreeding depression related to stress caused by fungal infection, but which was not associated with density. Higher observed heterozygosities in adults compared with progeny may relate to weak selection on progeny and lifetime-accumulated mortality of inbred adults. E. incrassata appears to be resistant to the negative mating pattern and fitness changes expected within fragmented landscapes. This pattern is likely explained by strong outcrossing and regular long-distance pollen flow. PMID:23188172

Tandem mass spectrometry approach for the investigation of the steroidal metabolism: structure-fragmentation relationship (SFR) in anabolic steroids and their metabolites by ESI-MS/MS analysis.

PubMed

Musharraf, Syed Ghulam; Ali, Arslan; Khan, Naik Tameem; Yousuf, Maria; Choudhary, Muhammad Iqbal; Atta-ur-Rahman

2013-02-01

Electrospray ionization tandem mass spectrometry (ESI-MS/MS) was used to investigate the effect of different substitutions introduced during metabolism on fragmentation patterns of four anabolic steroids including methyltestosterone, methandrostenolone, cis-androsterone and adrenosterone, along with their metabolites. Collision-induced dissociation (CID) analysis was performed to correlate the major product ions of 19 steroids with structural features. The analysis is done to portray metabolic alteration, such as incorporation or reduction of double bonds, hydroxylations, and/or oxidation of hydroxyl moieties to keto functional group on steroidal skeleton which leads to drastically changed product ion spectra from the respective classes of steroids, therefore, making them difficult to identify. The comparative ESI-MS/MS study also revealed some characteristic peaks to differentiate different steroidal metabolites and can be useful for the unambiguous identification of anabolic steroids in biological fluid. Moreover, LC-ESI-MS/MS analysis of fermented extract of methyltestosterone, obtained by Macrophomina phaseolina was also investigated. Copyright © 2012 Elsevier Inc. All rights reserved.

MHC class II B diversity in blue tits: a preliminary study.

PubMed

Aguilar, Juan Rivero-de; Schut, Elske; Merino, Santiago; Martínez, Javier; Komdeur, Jan; Westerdahl, Helena

2013-07-01

In this study, we partly characterize major histocompatibility complex (MHC) class II B in the blue tit (Cyanistes caeruleus). A total of 22 individuals from three different European locations: Spain, The Netherlands, and Sweden were screened for MHC allelic diversity. The MHC genes were investigated using both PCR-based methods and unamplified genomic DNA with restriction fragment length polymorphism (RFLP) and southern blots. A total of 13 different exon 2 sequences were obtained independently from DNA and/or RNA, thus confirming gene transcription and likely functionality of the genes. Nine out of 13 alleles were found in more than one country, and two alleles appeared in all countries. Positive selection was detected in the region coding for the peptide binding region (PBR). A maximum of three alleles per individual was detected by sequencing and the RFLP pattern consisted of 4-7 fragments, indicating a minimum number of 2-4 loci per individual. A phylogenetic analysis, demonstrated that the blue tit sequences are divergent compared to sequences from other passerines resembling a different MHC lineage than those possessed by most passerines studied to date.

MHC class II B diversity in blue tits: a preliminary study

PubMed Central

Aguilar, Juan Rivero-de; Schut, Elske; Merino, Santiago; Martínez, Javier; Komdeur, Jan; Westerdahl, Helena

2013-01-01

In this study, we partly characterize major histocompatibility complex (MHC) class II B in the blue tit (Cyanistes caeruleus). A total of 22 individuals from three different European locations: Spain, The Netherlands, and Sweden were screened for MHC allelic diversity. The MHC genes were investigated using both PCR-based methods and unamplified genomic DNA with restriction fragment length polymorphism (RFLP) and southern blots. A total of 13 different exon 2 sequences were obtained independently from DNA and/or RNA, thus confirming gene transcription and likely functionality of the genes. Nine out of 13 alleles were found in more than one country, and two alleles appeared in all countries. Positive selection was detected in the region coding for the peptide binding region (PBR). A maximum of three alleles per individual was detected by sequencing and the RFLP pattern consisted of 4–7 fragments, indicating a minimum number of 2–4 loci per individual. A phylogenetic analysis, demonstrated that the blue tit sequences are divergent compared to sequences from other passerines resembling a different MHC lineage than those possessed by most passerines studied to date. PMID:23919136

Arzanol, an anti-inflammatory and anti-HIV-1 phloroglucinol alpha-Pyrone from Helichrysum italicum ssp. microphyllum.

PubMed

Appendino, Giovanni; Ottino, Michela; Marquez, Nieves; Bianchi, Federica; Giana, Anna; Ballero, Mauro; Sterner, Olov; Fiebich, Bernd L; Munoz, Eduardo

2007-04-01

An acetone extract of Helichrysum italicum ssp. microphyllum afforded the phloroglucinol alpha-pyrone arzanol (1a) as a potent NF-kappaB inhibitor. Arzanol is identical with homoarenol (2a), whose structure should be revised. The phloroglucinol-type structure of arzanol and the 1,2,4-trihydroxyphenyl-type structure of the base-induced fragmentation product of homoarenol could be reconciled in light of a retro-Fries-type fragmentation that triggers a change of the hydroxylation pattern of the aromatic moiety. On the basis of these findings, the structure of arenol, the major constituent of the clinically useful antibiotic arenarin, should be revised from 2b to 1b, solving a long-standing puzzle over its biogenetic derivation. An alpha-pyrone (micropyrone, 7), the monoterpene rac-E-omega-oleoyloxylinalol (10), four known tremetones (9a-d), and the dimeric pyrone helipyrone (8) were also obtained. Arzanol inhibited HIV-1 replication in T cells and the release of pro-inflammatory cytokines in LPS-stimulated primary monocytes, qualifying as a novel plant-derived anti-inflammatory and antiviral chemotype worth further investigation.

Divergence, hybridization, and recombination in the mitochondrial genome of the human pathogenic yeast Cryptococcus gattii.

PubMed

Xu, Jianping; Yan, Zhun; Guo, Hong

2009-06-01

The inheritance of mitochondrial genes and genomes are uniparental in most sexual eukaryotes. This pattern of inheritance makes mitochondrial genomes in natural populations effectively clonal. Here, we examined the mitochondrial population genetics of the emerging human pathogenic fungus Cryptococcus gattii. The DNA sequences for five mitochondrial DNA fragments were obtained from each of 50 isolates belonging to two evolutionary divergent lineages, VGI and VGII. Our analyses revealed a greater sequence diversity within VGI than that within VGII, consistent with observations of the nuclear genes. The combined analyses of all five gene fragments indicated significant divergence between VGI and VGII. However, the five individual genealogies showed different relationships among the isolates, consistent with recent hybridization and mitochondrial gene transfer between the two lineages. Population genetic analyses of the multilocus data identified evidence for predominantly clonal mitochondrial population structures within both lineages. Interestingly, there were clear signatures of recombination among mitochondrial genes within the VGII lineage. Our analyses suggest historical mitochondrial genome divergence within C. gattii, but there is evidence for recent hybridization and recombination in the mitochondrial genome of this important human yeast pathogen.

Lyme disease with facial nerve palsy: rapid diagnosis using a nested polymerase chain reaction-restriction fragment length polymorphism analysis.

PubMed

Hashimoto, Y; Takahashi, H; Kishiyama, K; Sato, Y; Nakao, M; Miyamoto, K; Iizuka, H

1998-02-01

A 64-year-old woman with Lyme disease and manifesting facial nerve palsy had been bitten by a tick on the left frontal scalp 4 weeks previously. Erythema migrans appeared on the left forehead, accompanied by left facial paralysis. Nested polymerase chain reaction-restriction fragment length polymorphism analysis (nested PCR-RFLP) was performed on DNA extracted from a skin biopsy of the erythema on the left forehead. Borrelia flagellin gene DNA was detected and its RFLP pattern indicated that the organism was B. garinii, Five weeks later, B. garinii was isolated by conventional culture from the erythematous skin lesion, but not from the cerebrospinal fluid. After treatment with ceftriaxone intravenously for 10 days and oral administration of minocycline for 7 days, both the erythema and facial nerve palsy improved significantly. Nested PCR and culture taken after the lesion subsided, using skin samples obtained from a site adjacent to the original biopsy, were both negative. We suggest that nested PCR-RFLP analysis might be useful for the rapid diagnosis of Lyme disease and for evaluating therapy.

Ultrasound elastography assessment of bone/soft tissue interface

NASA Astrophysics Data System (ADS)

Parmar, Biren J.; Yang, Xu; Chaudhry, Anuj; Shafeeq Shajudeen, Peer; Nair, Sanjay P.; Weiner, Bradley K.; Tasciotti, Ennio; Krouskop, Thomas A.; Righetti, Raffaella

2016-01-01

We report on the use of elastographic imaging techniques to assess the bone/soft tissue interface, a region that has not been previously investigated but may provide important information about fracture and bone healing. The performance of axial strain elastograms and axial shear strain elastograms at the bone/soft tissue interface was studied ex vivo on intact and fractured canine and ovine tibias. Selected ex vivo results were corroborated on intact sheep tibias in vivo. The elastography results were statistically analyzed using elastographic image quality tools. The results of this study demonstrate distinct patterns in the distribution of the normalized local axial strains and axial shear strains at the bone/soft tissue interface with respect to the background soft tissue. They also show that the relative strength and distribution of the elastographic parameters change in the presence of a fracture and depend on the degree of misalignment between the fracture fragments. Thus, elastographic imaging modalities might be used in the future to obtain information regarding the integrity of bones and to assess the severity of fractures, alignment of bone fragments as well as to follow bone healing.

Peptides derivatized with bicyclic quaternary ammonium ionization tags. Sequencing via tandem mass spectrometry.

PubMed

Setner, Bartosz; Rudowska, Magdalena; Klem, Ewelina; Cebrat, Marek; Szewczuk, Zbigniew

2014-10-01

Improving the sensitivity of detection and fragmentation of peptides to provide reliable sequencing of peptides is an important goal of mass spectrometric analysis. Peptides derivatized by bicyclic quaternary ammonium ionization tags: 1-azabicyclo[2.2.2]octane (ABCO) or 1,4-diazabicyclo[2.2.2]octane (DABCO), are characterized by an increased detection sensitivity in electrospray ionization mass spectrometry (ESI-MS) and longer retention times on the reverse-phase (RP) chromatography columns. The improvement of the detection limit was observed even for peptides dissolved in 10 mM NaCl. Collision-induced dissociation tandem mass spectrometry of quaternary ammonium salts derivatives of peptides showed dominant a- and b-type ions, allowing facile sequencing of peptides. The bicyclic ionization tags are stable in collision-induced dissociation experiments, and the resulted fragmentation pattern is not significantly influenced by either acidic or basic amino acid residues in the peptide sequence. Obtained results indicate the general usefulness of the bicyclic quaternary ammonium ionization tags for ESI-MS/MS sequencing of peptides. Copyright © 2014 John Wiley & Sons, Ltd.

Analysis of complex repeat sequences within the spinal muscular atrophy (SMA) candidate region in 5q13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davies, K.E.; Morrison, K.E.; Daniels, R.I.

1994-09-01

We previously reported that the 400 kb interval flanked the polymorphic loci D5S435 and D5S557 contains blocks of a chromosome 5 specific repeat. This interval also defines the SMA candidate region by genetic analysis of recombinant families. A YAC contig of 2-3 Mb encompassing this area has been constructed and a 5.5 kb conserved fragment, isolated from a YAC end clone within the above interval, was used to obtain cDNAs from both fetal and adult brain libraries. We describe the identification of cDNAs with stretches of high DNA sequence homology to exons of {beta} glucuronidase on human chromosome 7. Themore » cDNAs map both to the candidate region and to an area of 5p using FISH and deletion hybrid analysis. Hybridization to bacteriophage and cosmid clones from the YACs localizes the {beta} glucuronidase related sequences within the 400 kb region of the YAC contig. The cDNAs show a polymorphic pattern on hybridization to genomic BamH1 fragments in the size range of 10-250 kb. Further analysis using YAC fragmentation vectors is being used to determine how these {beta} glucuronidase related cDNAs are distributed within 5q13. Dinucleotide repeats within the region are being investigated to determine linkage disequilibrium with the disease locus.« less

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling.

PubMed

Ahmed, Zeeshan; Zeeshan, Saman; Huber, Claudia; Hensel, Michael; Schomburg, Dietmar; Münch, Richard; Eisenreich, Wolfgang; Dandekar, Thomas

2013-07-09

The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution. The open-source software "Least Square Mass Isotopomer Analyzer" (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman's least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed. The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.

Multiprimer PCR system for differential identification of mycobacteria in clinical samples.

PubMed Central

Del Portillo, P; Thomas, M C; Martínez, E; Marañón, C; Valladares, B; Patarroyo, M E; Carlos López, M

1996-01-01

A novel multiprimer PCR method with the potential to identify mycobacteria in clinical samples is presented. The assay relies on the simultaneous amplification of three bacterial DNA genomic fragments by using different sets of oligonucleotide primers. The first set of primers amplifies a 506-bp fragment from the gene for the 32-kDa antigen of Mycobacterium tuberculosis, which is present in most of the species belonging to the genus Mycobacterium. The second set of primers amplifies a 984-bp fragment from the IS6110 insertion sequence of the bacteria belonging to the M. tuberculosis complex. The third set of primers, derived from an M. tuberculosis species-specific sequence named MTP40, amplifies a 396-bp genomic fragment. Thus, while the multiprimer system would render three amplification fragments from the M. tuberculosis genome and two fragments from the Mycobacterium bovis genome, a unique amplification fragment would be obtained from nontuberculous mycobacteria. The results obtained, using reference mycobacterial strains and typed clinical isolates, show that the multiprimer PCR method may be a rapid, sensitive, and specific tool for the differential identification of various mycobacterial strains in a single-step assay. PMID:8789008

Assembly and analysis of fragmentation data for liquid propellant vessels

NASA Technical Reports Server (NTRS)

Baker, W. E.; Parr, V. B.; Bessey, R. L.; Cox, P. A.

1974-01-01

Fragmentation data was assembled and analyzed for exploding liquid propellant vessels. These data were to be retrieved from reports of tests and accidents, including measurements or estimates of blast yield, etc. A significant amount of data was retrieved from a series of tests conducted for measurement of blast and fireball effects of liquid propellant explosions (Project PYRO), a few well-documented accident reports, and a series of tests to determine auto-ignition properties of mixing liquid propellants. The data were reduced and fitted to various statistical functions. Comparisons were made with methods of prediction for blast yield, initial fragment velocities, and fragment range. Reasonably good correlation was achieved. Methods presented in the report allow prediction of fragment patterns, given type and quantity of propellant, type of accident, and time of propellant mixing.

Comparative study of SOS2 and a novel PMP3-1 gene expression in two sunflower (Helianthus annuus L.) lines differing in salt tolerance.

PubMed

Saadia, Mubshara; Jamil, Amer; Ashraf, Muhammad; Akram, Nudrat Aisha

2013-06-01

Gene expression pattern of two important regulatory proteins, salt overly sensitive 2 (SOS2) and plasma membrane protein 3-1 (PMP3-1), involved in ion homeostasis, was analyzed in two salinity-contrasting sunflower (Helianthus annuus L.) lines, Hysun-38 (salt tolerant) and S-278 (moderately salt tolerant). The pattern was studied at selected time intervals (24 h) under 150 mM NaCl treatment. Using reverse transcription PCR, SOS2 gene fragment was obtained from young leaf and root tissues of opposing lines while that for PMP3-1 was obtained only from young root tissues. Both tolerant and moderately tolerant lines showed a gradual increase in SOS2 expression in sunflower root tissues. Leaf tissues showed the gradually increasing pattern of SOS2 expression in tolerant plants as compared to that for moderately tolerant ones that showed a relatively lower level of expression for this gene. We found the highest level of PMP 3-1 expression in the roots of tolerant sunflower line at 6 and 12 h postsalinity treatment. The moderately tolerant line showed higher expression of PMP3-1 at 12 and 24 h after salt treatment. Overall, the expression of genes for both the regulator proteins varied significantly in the two sunflower lines differing in salinity tolerance.

[Landscape pattern change of Dongzhai Harbour mangrove, South China analyzed with a patch-based method and its driving forces].

PubMed

Huang, Xing; Xin, Kun; Li, Xiu-zhen; Wang, Xue-ping; Ren, Lin-jing; Li, Xi-zhi; Yan, Zhong-zheng

2015-05-01

According to the interpreted results of three satellite images of Dongzhai Harbour obtained in 1988, 1998 and 2009, the changes of landscape pattern and the differences of its driving forces of mangrove forest in Dongzhai Harbour were analyzed with a patch-based method on spatial distribution dynamics. The results showed that the areas of mangrove forest in 1988, 1998 and 2009 were 1809.4, 1738.7 and 1608.2 hm2 respectively, which presented a trend of decrease with enhanced degree of landscape fragmentation. The transformations among different landscape types indicated that the mangrove, agricultural land and forest land were mainly changed into built-up land and aquaculture pond. The statistical results obtained from three different methods, i.e., accumulative counting, percentage counting and main transformation route counting, showed that natural factors were the main reason for the changes of patch number, responsible for 58.6%, 72.2% and 72.1% of patch number change, respectively, while the percentages of patch area change induced by human activities were 70.4%, 70.3% and 76.4%, respectively, indicating that human activities were the primary factors of the change of patch areas.

Landscape-level patterns of avian diversity in the Oregon Coast Range

Treesearch

Samuel A. Cushman; Kevin McGarigal

2003-01-01

We used a comparative mensurative landscape-level experiment to quantify the relative importance of mature forest area and fragmentation and differences among watersheds in influencing avian community diversity in the Oregon Coast Range, USA. Our study design included three large hydrological basins, two levels of fragmentation, and six levels of mature forest area. We...

Effects of habitat loss and fragmentation on amphibians: A review and prospectus

Treesearch

Samuel A. Cushman

2006-01-01

Habitat loss and fragmentation are among the largest threats to amphibian populations. However, most studies have not provided clear insights into their population-level implications. There is a critical need to investigate the mechanisms that underlie patterns of distribution and abundance. In order to understand the population- and species-level implications of...

Allowing macroalgae growth forms to emerge: Use of an agent-based model to understand the growth and spread of macroalgae in Florida coral reefs, with emphasis on Halimeda tuna

USGS Publications Warehouse

Yniguez, A.T.; McManus, J.W.; DeAngelis, D.L.

2008-01-01

The growth patterns of macroalgae in three-dimensional space can provide important information regarding the environments in which they live, and insights into changes that may occur when those environments change due to anthropogenic and/or natural causes. To decipher these patterns and their attendant mechanisms and influencing factors, a spatially explicit model has been developed. The model SPREAD (SPatially-explicit Reef Algae Dynamics), which incorporates the key morphogenetic characteristics of clonality and morphological plasticity, is used to investigate the influences of light, temperature, nutrients and disturbance on the growth and spatial occupancy of dominant macroalgae in the Florida Reef Tract. The model species, Halimeda and Dictyota spp., are modular organisms, with an 'individual' being made up of repeating structures. These species can also propagate asexually through clonal fragmentation. These traits lead to potentially indefinite growth and plastic morphology that can respond to environmental conditions in various ways. The growth of an individual is modeled as the iteration of discrete macroalgal modules whose dynamics are affected by the light, temperature, and nutrient regimes. Fragmentation is included as a source of asexual reproduction and/or mortality. Model outputs are the same metrics that are obtained in the field, thus allowing for easy comparison. The performance of SPREAD was tested through sensitivity analysis and comparison with independent field data from four study sites in the Florida Reef Tract. Halimeda tuna was selected for initial model comparisons because the relatively untangled growth form permits detailed characterization in the field. Differences in the growth patterns of H. tuna were observed among these reefs. SPREAD was able to closely reproduce these variations, and indicate the potential importance of light and nutrient variations in producing these patterns. ?? 2008 Elsevier B.V.

Kawasaki Disease-Specific Molecules in the Sera Are Linked to Microbe-Associated Molecular Patterns in the Biofilms

PubMed Central

Murata, Kenji; Kanno, Shunsuke; Nishio, Hisanori; Saito, Mitsumasa; Tanaka, Tamami; Yamamura, Kenichiro; Sakai, Yasunari; Takada, Hidetoshi; Miyamoto, Tomofumi; Mizuno, Yumi; Ouchi, Kazunobu; Waki, Kenji; Hara, Toshiro

2014-01-01

Background Kawasaki disease (KD) is a systemic vasculitis of unknown etiology. The innate immune system is involved in its pathophysiology at the acute phase. We have recently established a novel murine model of KD coronary arteritis by oral administration of a synthetic microbe-associated molecular pattern (MAMP). On the hypothesis that specific MAMPs exist in KD sera, we have searched them to identify KD-specific molecules and to assess the pathogenesis. Methods We performed liquid chromatography-mass spectrometry (LC-MS) analysis of fractionated serum samples from 117 patients with KD and 106 controls. Microbiological and LC-MS evaluation of biofilm samples were also performed. Results KD samples elicited proinflammatory cytokine responses from human coronary artery endothelial cells (HCAECs). By LC-MS analysis of KD serum samples collected at 3 different periods, we detected a variety of KD-specific molecules in the lipophilic fractions that showed distinct m/z and MS/MS fragmentation patterns in each cluster. Serum KD-specific molecules showed m/z and MS/MS fragmentation patterns almost identical to those of MAMPs obtained from the biofilms formed in vitro (common MAMPs from Bacillus cereus, Yersinia pseudotuberculosis and Staphylococcus aureus) at the 1st study period, and from the biofilms formed in vivo (common MAMPs from Bacillus cereus, Bacillus subtilis/Bacillus cereus/Yersinia pseudotuberculosis and Staphylococcus aureus) at the 2nd and 3rd periods. The biofilm extracts from Bacillus cereus, Bacillus subtilis, Yersinia pseudotuberculosis and Staphylococcus aureus also induced proinflammatory cytokines by HCAECs. By the experiments with IgG affinity chromatography, some of these serum KD-specific molecules bound to IgG. Conclusions We herein conclude that serum KD-specific molecules were mostly derived from biofilms and possessed molecular structures common to MAMPs from Bacillus cereus, Bacillus subtilis, Yersinia pseudotuberculosis and Staphylococcus aureus. Discovery of these KD-specific molecules might offer novel insight into the diagnosis and management of KD as well as its pathogenesis. PMID:25411968

Lack of genetic structure among ecologically adapted populations of an Australian rainforest Drosophila species as indicated by microsatellite markers and mitochondrial DNA sequences.

PubMed

Schiffer, Michele; Kennington, W J; Hoffmann, A A; Blacket, M J

2007-04-01

Although fragmented rainforest environments represent hotspots for invertebrate biodiversity, few genetic studies have been conducted on rainforest invertebrates. Thus, it is not known if invertebrate species in rainforests are highly genetically fragmented, with the potential for populations to show divergent selection responses, or if there are low levels of gene flow sufficient to maintain genetic homogeneity among fragmented populations. Here we use microsatellite markers and DNA sequences from the mitochondrial ND5 locus to investigate genetic differences among Drosophila birchii populations from tropical rainforests in Queensland, Australia. As found in a previous study, mitochondrial DNA diversity was low with no evidence for population differentiation among rainforest fragments. The pattern of mitochondrial haplotype variation was consistent with D. birchii having undergone substantial past population growth. Levels of nuclear genetic variation were high in all populations while F(ST) values were very low, even for flies from geographically isolated areas of rainforest. No significant differentiation was observed between populations on either side of the Burdekin Gap (a long-term dry corridor), although there was evidence for higher gene diversity in low-latitude populations. Spatial autocorrelation coefficients were low and did not differ significantly from random, except for one locus which revealed a clinal-like pattern. Comparisons of microsatellite differentiation contrasted with previously established clinal patterns in quantitative traits in D. birchii, and indicate that the patterns in quantitative traits are likely to be due to selection. These results suggest moderate gene flow in D. birchii over large distances. Limited population structure in this species appears to be due to recent range expansions or cycles of local extinctions followed by recolonizations/expansions. Nevertheless, patterns of local adaptation have developed in D. birchii that may result in populations showing different selection responses when faced with environmental change.

Radical Anions of Oxidized vs. Reduced Oxytocin: Influence of Disulfide Bridges on CID and Vacuum UV Photo-Fragmentation

NASA Astrophysics Data System (ADS)

MacAleese, Luke; Girod, Marion; Nahon, Laurent; Giuliani, Alexandre; Antoine, Rodolphe; Dugourd, Philippe

2018-06-01

The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin's internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV + VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are fundamental for protein structure, could also be responsible for an increased resistance to ionizing radiations. [Figure not available: see fulltext.

Test Methodologies for Personal Protective Equipment Against Anti-Personnel Mine Blast (Methodologies d’essais pour le materiel de protection prsonnel contre le souffle produit par les mines antipersonnel)

DTIC Science & Technology

2004-03-01

probabilistic by design. Finally, as the fragments disperse, fragment density decreases, and the probability of a fragment strike drops rapidly. Given the...Any PPE subjected to such testing needs to be exposed repeatedly to several mines in order to obtain a sufficient number of strikes . This will allow...velocity of each fragment, and the location of fragment strikes cannot be controlled precisely. This means that the same test must be repeated a

Hydrogen atom scrambling in selectively labeled anionic peptides upon collisional activation by MALDI tandem time-of-flight mass spectrometry.

PubMed

Bache, Nicolai; Rand, Kasper D; Roepstorff, Peter; Ploug, Michael; Jørgensen, Thomas J D

2008-12-01

We have previously shown that peptide amide hydrogens undergo extensive intramolecular migration (i.e., complete hydrogen scrambling) upon collisional activation of protonated peptides (Jørgensen et al. J. Am. Chem. Soc. 2005, 127, 2785-2793). The occurrence of hydrogen scrambling enforces severe limitations on the application of gas-phase fragmentation as a convenient method to obtain information about the site-specific deuterium uptake for proteins and peptides in solution. To investigate whether deprotonated peptides exhibit a lower level of scrambling relative to their protonated counterparts, we have now measured the level of hydrogen scrambling in a deprotonated, selectively labeled peptide using MALDI tandem time-of-flight mass spectrometry. Our results conclusively show that hydrogen scrambling is prevalent in the deprotonated peptide upon collisional activation. The amide hydrogens ((1)H/(2)H) have migrated extensively in the anionic peptide, thereby erasing the original regioselective deuteration pattern obtained in solution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Jiang; Malmirchegini, G. Reza; Clubb, Robert T.

Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and non-covalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down mass spectrometry using electrospray ionization (ESI) and a 15-Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Native MS preserves the non-covalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of themore » Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore low fragmentation efficiency. Precursor ion activation allows steady increase of N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and 4 z ions on the α chain; 36 c ions and 2 z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer show similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. Finally, it may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.« less

[Species composition and diversity of soil mesofauna in the 'Holy Hills' fragmentary tropical rain forest of Xishuangbanna, China].

PubMed

Yang, X; Sha, L

2001-04-01

The species composition and diversity of soil mesofauna were examined in fragmented dry tropical seasonal rainforest of tow 'Holy Hills' of Dai nationality, compared with the continuous moist tropical seasonal rain forest of Nature Reserve in Xishuangbanna area. 5 sample quadrats were selected along the diagonal of 20 m x 20 m sampling plot, and the samples of litterfall and 0-3 cm soil were collected from each 50 cm x 10 cm sample quadrat. Animals in soil sample were collected by using dry-funnel(Tullgren's), were identified to their groups according to the order. The H' index, D.G index and the pattern of relative abundance of species were used to compare the diversity of soil mesofauna. The results showed that the disturbance of vegetation and soil resulted by tropical rainforest fragmentation was the major factor affecting the diversity of soil mesofauna. Because the fragmented forest was intruded by some pioneer tree species and the "dry and warm" effect operated, this forest had more litterfall on the floor and more humus in the soil than the continuous moist rain forest. The soil condition with more soil organic matter, total N and P, higher pH value and lower soil bulk density became more favorable to the soil mesofauna. Therefore, the species richness, abundance and diversity of soil mesofauna in fragmented forests were higher than those in continuous forest, but the similarity of species composition in fragmented forest to the continuous forest was minimal. Soil mesofauna diversity in fragmented forests did not change with decreasing fragmented area, indicating that there was no species-area effect operation in this forest. The pattern of relative abundance of species in these forest soils was logarithmic series distribution.

Supercritical-fluid extraction and chromatography-mass spectrometry for analysis of mycotoxins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, R.D.; Udseth, H.R.

1982-07-01

The use of direct supercritical-fluid injection-mass spectrometry for the rapid analysis of mycotoxins of the tricothecene group is demonstrated. A solution containing diacetoxyscirpenol or T-2 toxin is injected into a fluid consisting primarily of pentane or carbon dioxide and is rapidly brought to supercritical conditions. Direct injection of the fluid stream into a chemical ionization source allows thermally labile compounds to be analyzed. Under these conditions trichothecene mass spectra showing significant (M + 1)/sup +/ ions and distinctive fragmentation patterns are obtained. Detection limits are in the subnanogram range. Direct analysis from complex substrates using selective supercritical-fluid extraction is proposed.more » 4 figures.« less

Zygosaccharomyces kombuchaensis, a new ascosporogenous yeast from 'Kombucha tea'.

PubMed

Kurtzman, C P; Robnett, C J; Basehoar-Powers, E

2001-07-01

A new ascosporogenous yeast, Zygosaccharomyces kombuchaensis sp. n. (type strain NRRL YB-4811, CBS 8849), is described; it was isolated from Kombucha tea, a popular fermented tea-based beverage. The four known strains of the new species have identical nucleotide sequences in domain D1/D2 of 26S rDNA. Phylogenetic analysis of D1/D2 and 18S rDNA sequences places Z. kombuchaensis near Zygosaccharomyces lentus. The two species are indistinguishable on standard physiological tests used for yeast identification, but can be recognized from differences in restriction fragment length polymorphism patterns obtained by digestion of 18S-ITS1 amplicons with the restriction enzymes DdeI and MboI.

Classification and treatment of periprosthetic supracondylar femur fractures.

PubMed

Ricci, William

2013-02-01

Locked plating and retrograde nailing are two accepted methods for treatment of periprosthetic distal femur fractures. Each has relative benefits and potential pitfalls. Appropriate patient selection and knowledge of the specific femoral component geometry are required to optimally choose between these two methods. Locked plating may be applied to most periprosthetic distal femur fractures. The fracture pattern, simple or comminuted, will dictate the specific plating technique, compression plating or bridge plating. Nailing requires an open intercondylar box and a distal fragment of enough size to allow interlocking. With proper patient selection and proper techniques, good results can be obtained with either method. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

The PCC assay can be used to predict radiosensitivity in biopsy cultures irradiated with different types of radiation.

PubMed

Suzuki, Masao; Tsuruoka, Chizuru; Nakano, Takashi; Ohno, Tatsuya; Furusawa, Yoshiya; Okayasu, Ryuichi

2006-12-01

The aim of this study was to identify potential biomarkers for radiosensitivity using the relationship between cell killing and the yield of excess chromatin fragments detected with the premature chromosome condensation (PCC) technique. This method was applied to primary cultured cells obtained from biopsies from patients. Six primary culture biopsies were obtained from 6 patients with carcinoma of the cervix before starting radiotherapy. The cultures were irradiated with two different LET carbon-ion beams (LET = 13 keV/microm, 77.1+/-2.8 keV/microm) and 200 kV X-rays. The carbon-ion beams were produced by Heavy Ion Medical Accelerator in Chiba (HIMAC). PCC was performed using the polyethylene glycol-mediated cell fusion technique. The yield of excess chromatin fragments were measured by counting the number of unrejoined chromatin fragments detected with the PCC technique after a 24-h post-irradiation incubation period. Obtained results indicated that cultures which were more sensitive to killing were also more susceptible to the induction of excess chromatin fragments. Furthermore there was a good correlation between cell killing and excess chromatin fragments among the 6 cell cultures examined. There is also evidence that the induction of excess chromatin fragments increased with increasing LET as well as cell-killing effect in the same cell culture. The data reported here support the idea that the yield of excess chromatin fragments detected with the PCC technique might be useful for predicting the radiosensitivity of cells contained in tumor tissue, and to predict responses to different radiation types.

Molecular characterization of natural orchid in South slopes of Mount Merapi, Sleman regency, Yogyakarta

NASA Astrophysics Data System (ADS)

Ferdiani, Defika I.; Devi, Fera L.; Koentjana, Johan P.; Milasari, Asri F.; Nur'aini, Indah; Semiarti, Endang

2015-09-01

Natural orchid is one of the most important tropical biodiversity. In Indonesia there are ± 6000 species out of 30000 orchids species in the world, of which there are ± 60 species at Mount Merapi. Repetitive eruption of Merapi have wiped out the biodiversity of orchids, therefore the efforts to conserve the orchids and to establish the database of natural orchids in Mount Merapi are needed. The orchid's database can be created based on DNA analysis, and establish barcoding DNA. DNA-barcodes can be used as molecular markers. The different character of morphology usually shows different pattern in DNA fragments. This research aims to characterize the phenotype and genotype of natural orchids of Mt. Merapi based on morphology and the structure of DNA in trnL-F intergenic region of chloroplasts DNA of orchid. Amplified Fragment Length Polymorphism (AFLP) technique was used to characterize the molecular types of orchids in silico of intergenic space area of orchid chloroplast. In this study, 11 species of orchids were characterized based on morphological and molecular characters. The molecular characters were obtained from trnL-F intergenic region of leaves chloroplasts. The data indicates that there is a conserve DNA pattern in all orchids and the distinctive characters of some orchids. In this study, based on trnL-F intergenic region of chloroplast genome, the phylogenetic tree revealed that 11 species of orchids at Mt. Merapi can be grouped into 2 clades, that matched with morphological characters.

Oligo-dT anchored cDNA-SCoT: a novel differential display method for analyzing differential gene expression in response to several stress treatments in mango (Mangifera indica L.).

PubMed

Luo, Cong; He, Xin-Hua; Hu, Ying; Yu, Hai-xia; Ou, Shi-Jin; Fang, Zhong-Bin

2014-09-15

Differential display is a powerful technique for analyzing differences in gene expression. Oligo-dT cDNAstart codon targeted marker (cDNA-SCoT) technique is a novel, simple, cheap, rapid, and efficient method for differential gene expression research. In the present study, the oligo-dT anchored cDNA-SCoT technique was exploited to identify differentially expressed genes during several stress treatments in mango. A total of 37 primers combined with oligo-dT anchor primers 3side amplified approximately 150 fragments of 150 bp to 1500 bp in length. Up to 100 fragments were differentially expressed among the stress treatments and control samples, among which 92 were obtained and sequenced. Out of the 92 transcript derived fragments (TDFs), 70% were highly homologous to known genes, and 30% encoded unclassified proteins with unknown functions. The expression pattern of nine genes with known functions involved in several abiotic stresses in other species was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) under cold (4 °C), salinity (NaCl), polyethylene glycol (PEG, MW 6000), and heavy metal treatments in leaves and stems at different time points (0, 24, 48, and 72 h). The expression patterns of the genes (TDF4, TDF7, TDF23, TDF45, TDF49, TDF50, TDF57, TDF91 and TDF92) that had direct or indirect relationships with cold, salinity, drought and heavy metal stress response were analyzed through qRT-PCR. The possible roles of these genes are discussed. This study suggests that the oligo-dT anchored cDNA-SCoT differential display method is a useful tool to serve as an initial step for characterizing transcriptional changes induced by abiotic stresses and provide gene information for further study and application in genetic improvement and breeding in mango. Copyright © 2014 Elsevier B.V. All rights reserved.

The E. coli 16S rRNA binding site of ribosomal protein S15: higher-order structure in the absence and in the presence of the protein.

PubMed Central

Mougel, M; Philippe, C; Ebel, J P; Ehresmann, B; Ehresmann, C

1988-01-01

We have investigated in detail the secondary and tertiary structures of E. coli 16S rRNA binding site of protein S15 using a variety of enzymatic and chemical probes. RNase T1 and nuclease S1 were used to probe unpaired nucleotides and RNase V1 to monitor base-paired or stacked nucleotides. Bases were probed with dimethylsulfate (at A(N-1), C(N-3) and G(N-7)), with 1-cyclohexyl-3 (2-(1-methylmorpholino)-ethyl)-carboiimide-p- toluenesulfonate (at U(N-3) and G(N-1)) and with diethylpyrocarbonate (at A(N-7)). The RNA region corresponding to nucleotides 652 to 753 was tested within: (1) the complete 16S rRNA molecule; (2) a 16S rRNA fragment corresponding to nucleotides 578 to 756 obtained by transcription in vitro; (3) the S15-16S rRNA complex; (4) the S15-fragment complex. Cleavage and modification sites were detected by primer extension with reverse transcriptase. Our results show that: (1) The synthetized fragment folds into the same overall secondary structure as in the complete 16S rRNA, with the exception of the large asymmetrical internal loop (nucleotides 673-676/714-733) which is fully accessible in the fragment while it appears conformationally heterogeneous in the 16S rRNA; (2) the reactivity patterns of the S15-16S rRNA and S15-fragment complexes are identical; (3) the protein protects defined RNA regions, located in the large interior loop and in the 3'-end strand of helix [655-672]-[734-751]; (4) the protein also causes enhanced chemical reactivity and enzyme accessibility interpreted as resulting from a local conformational rearrangement, induced by S15 binding. Images PMID:2453025

Random-breakage mapping method applied to human DNA sequences

NASA Technical Reports Server (NTRS)

Lobrich, M.; Rydberg, B.; Cooper, P. K.; Chatterjee, A. (Principal Investigator)

1996-01-01

The random-breakage mapping method [Game et al. (1990) Nucleic Acids Res., 18, 4453-4461] was applied to DNA sequences in human fibroblasts. The methodology involves NotI restriction endonuclease digestion of DNA from irradiated calls, followed by pulsed-field gel electrophoresis, Southern blotting and hybridization with DNA probes recognizing the single copy sequences of interest. The Southern blots show a band for the unbroken restriction fragments and a smear below this band due to radiation induced random breaks. This smear pattern contains two discontinuities in intensity at positions that correspond to the distance of the hybridization site to each end of the restriction fragment. By analyzing the positions of those discontinuities we confirmed the previously mapped position of the probe DXS1327 within a NotI fragment on the X chromosome, thus demonstrating the validity of the technique. We were also able to position the probes D21S1 and D21S15 with respect to the ends of their corresponding NotI fragments on chromosome 21. A third chromosome 21 probe, D21S11, has previously been reported to be close to D21S1, although an uncertainty about a second possible location existed. Since both probes D21S1 and D21S11 hybridized to a single NotI fragment and yielded a similar smear pattern, this uncertainty is removed by the random-breakage mapping method.

Molecular epidemiology of Escherichia coli O157:H7 strains by bacteriophage lambda restriction fragment length polymorphism analysis: application to a multistate foodborne outbreak and a day-care center cluster.

PubMed

Samadpour, M; Grimm, L M; Desai, B; Alfi, D; Ongerth, J E; Tarr, P I

1993-12-01

Genomic DNAs prepared from 168 isolates of Escherichia coli O157:H7 were analyzed for restriction fragment length polymorphisms on Southern blots probed with bacteriophage lambda DNA. The isolates analyzed included strains from a recent large multistate outbreak of E. coli O157:H7 infection associated with consumption of poorly cooked beef in restaurants, a day-care center cluster, and temporally and geographically unrelated isolates. E. coli O157:H7 isolates recovered from the incriminated meat and from 61 (96.8%) of 63 patients from Washington and Nevada possessed identical lambda restriction fragment length patterns. The lambda restriction fragment length polymorphisms observed in 11 (91.7%) of 12 day-care center patients were identical, but they differed from that of the strain associated with the multistate outbreak. E. coli O157:H7 from 42 patients temporally or geographically unrelated to either cluster of infection possessed unique and different lambda restriction fragment length patterns, except for paired isolates from three separate clusters of infection. These data demonstrate that the hybridization of DNA digests of E. coli O157:H7 with radiolabelled bacteriophage lambda DNA can be a useful, stable, and discriminatory epidemiologic tool for analyzing the linkage between strains of E. coli O157:H7.

Critical thresholds in species` responses to landscape structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

With, K.A.; Crist, T.O.

1995-12-01

Critical thresholds are transition ranges across which small changes in spatial pattern produce abrupt shifts in ecological responses. Habitat fragmentation provides a familiar example of a critical threshold. As the landscape becomes dissected into smaller parcels of habitat. landscape connectivity-the functional linkage among habitat patches - may suddenly become disrupted, which may have important consequences for the distribution and persistence of populations. Landscape connectivity depends not only on the abundance and spatial patterning of habitat. but also on the habitat specificity and dispersal abilities of species. Habitat specialists with limited dispersal capabilities presumably have a much lower threshold to habitatmore » fragmentation than highly vagile species, which may perceive the landscape as functionally connected across a greater range of fragmentation severity. To determine where threshold effects in species, responses to landscape structure are likely to occur, a simulation model modified from percolation theory was developed. Our simulations predicted the distributional patterns of populations in different landscape mosaics, which we tested empirically using two grasshopper species (Orthoptera: Acrididae) that occur in the shortgrass prairie of north-central Colorado. The distribution of these two species in this grassland mosaic matched the predictions from our simulations. By providing quantitative predictions of threshold effects, this modelling approach may prove useful in the formulation of conservation strategies and assessment of land-use changes on species` distributional patterns and persistence.« less

Contrasting patterns of nest survival and postfledging survival in ovenbirds and Acadian flycatchers in Missouri forest fragments

Treesearch

Julianna M. A. Jenkins; Frank R. Thompson; John Faaborg

2016-01-01

We can improve our ability to assess population viability and forecast population growth under different scenarios by understanding factors that limit population parameters in each stage of the annual cycle. Postfledging mortality rates may be as variable as nest survival across regions and fragmentation gradients, although factors that negatively impact nest survival...

Efficient clustering aggregation based on data fragments.

PubMed

Wu, Ou; Hu, Weiming; Maybank, Stephen J; Zhu, Mingliang; Li, Bing

2012-06-01

Clustering aggregation, known as clustering ensembles, has emerged as a powerful technique for combining different clustering results to obtain a single better clustering. Existing clustering aggregation algorithms are applied directly to data points, in what is referred to as the point-based approach. The algorithms are inefficient if the number of data points is large. We define an efficient approach for clustering aggregation based on data fragments. In this fragment-based approach, a data fragment is any subset of the data that is not split by any of the clustering results. To establish the theoretical bases of the proposed approach, we prove that clustering aggregation can be performed directly on data fragments under two widely used goodness measures for clustering aggregation taken from the literature. Three new clustering aggregation algorithms are described. The experimental results obtained using several public data sets show that the new algorithms have lower computational complexity than three well-known existing point-based clustering aggregation algorithms (Agglomerative, Furthest, and LocalSearch); nevertheless, the new algorithms do not sacrifice the accuracy.

Mapping Candidate Ecological Restoration Areas Using Morphological Spatial Pattern Analysis (MSPA)

EPA Science Inventory

Morphological Spatial Pattern Analysis (MSPA) has been widely adopted by landscape ecologists over the past decade. A few examples of its many uses include: 1) quantifying landscape indicators and fragmentation in continental forest assessments, 2) explaining interior-exterior p...

Morphological characteristics of the posterior malleolar fragment according to ankle fracture patterns: a computed tomography-based study.

PubMed

Yi, Young; Chun, Dong-Il; Won, Sung Hun; Park, Suyeon; Lee, Sanghyeon; Cho, Jaeho

2018-02-13

The posterior malleolar fragment (PMF) of an ankle fracture can have various shapes depending on the injury mechanism. The purpose of this study was to evaluate the morphological characteristics of the PMF according to the ankle fracture pattern described in the Lauge-Hansen classification by using computed tomography (CT) images. We retrospectively analyzed CT data of 107 patients (107 ankles) who underwent surgery for trimalleolar fracture from January 2012 to December 2014. The patients were divided into two groups: 76 ankles in the supination-external rotation (SER) stage IV group and 31 ankles in the pronation-external rotation (PER) stage IV group. The PMF type of the two groups was assessed using the Haraguchi and Jan Bartonicek classification. The cross angle (α), fragment length ratio (FLR), fragment area ratio (FAR), sagittal angle (θ), and fragment height (FH) were measured to assess the morphological characteristics of the PMF. The PMF in the SER group mainly had a posterolateral shape, whereas that in the PER group mainly had a posteromedial two-part shape or a large posterolateral triangular shape (P = 0.02). The average cross angle was not significantly different between the two groups (SER group = 19.4°, PER group = 17.6°). The mean FLR and FH were significantly larger in the PER group than in the SER group (P = 0.024, P = 0.006). The mean fragment sagittal angle in the PER group was significantly smaller than that in the SER group (P = 0.017). With regard to the articular involvement, volume, and vertical nature, the SER-type fracture tends to have a smaller fragment due to the rotational force, whereas the PER-type fracture tends to have a larger fragment due to the combination of rotational and axial forces.

Landscape fragmentation affects responses of avian communities to climate change.

PubMed

Jarzyna, Marta A; Porter, William F; Maurer, Brian A; Zuckerberg, Benjamin; Finley, Andrew O

2015-08-01

Forecasting the consequences of climate change is contingent upon our understanding of the relationship between biodiversity patterns and climatic variability. While the impacts of climate change on individual species have been well-documented, there is a paucity of studies on climate-mediated changes in community dynamics. Our objectives were to investigate the relationship between temporal turnover in avian biodiversity and changes in climatic conditions and to assess the role of landscape fragmentation in affecting this relationship. We hypothesized that community turnover would be highest in regions experiencing the most pronounced changes in climate and that these patterns would be reduced in human-dominated landscapes. To test this hypothesis, we quantified temporal turnover in avian communities over a 20-year period using data from the New York State Breeding Atlases collected during 1980-1985 and 2000-2005. We applied Bayesian spatially varying intercept models to evaluate the relationship between temporal turnover and temporal trends in climatic conditions and landscape fragmentation. We found that models including interaction terms between climate change and landscape fragmentation were superior to models without the interaction terms, suggesting that the relationship between avian community turnover and changes in climatic conditions was affected by the level of landscape fragmentation. Specifically, we found weaker associations between temporal turnover and climatic change in regions with prevalent habitat fragmentation. We suggest that avian communities in fragmented landscapes are more robust to climate change than communities found in contiguous habitats because they are comprised of species with wider thermal niches and thus are less susceptible to shifts in climatic variability. We conclude that highly fragmented regions are likely to undergo less pronounced changes in composition and structure of faunal communities as a result of climate change, whereas those changes are likely to be greater in contiguous and unfragmented habitats. © 2015 John Wiley & Sons Ltd.

Population Genetic Analyses of the Fungal Pathogen Colletotrichum fructicola on Tea-Oil Trees in China

PubMed Central

Li, He; Zhou, Guo-Ying; Liu, Jun-Ang; Xu, Jianping

2016-01-01

The filamentous fungus Colletotrichum fructicola is found in all five continents and is capable of causing severe diseases in a number of economically important plants such as avocado, fig, cocoa, pear, and tea-oil trees. However, almost nothing is known about its patterns of genetic variation and epidemiology on any of its host plant species. Here we analyzed 167 isolates of C. fructicola obtained from the leaves of tea-oil tree Camellia oleifera at 15 plantations in seven Chinese provinces. Multilocus sequence typing was conducted for all isolates based on DNA sequences at fragments of four genes: the internal transcribed spacers of the nuclear ribosomal RNA gene cluster (539 bp), calmodulin (633 bp), glutamine synthetase (711 bp), and glyceraldehyde-3-phosphate dehydrogenase (190 bp), yielding 3.52%, 0.63%, 8.44%, and 7.89% of single nucleotide polymorphic sites and resulting in 15, 5, 12 and 11 alleles respectively at the four gene fragments in the total sample. The combined allelic information from all four loci identified 53 multilocus genotypes with the most frequent represented by 21 isolates distributed in eight tea-oil plantations in three provinces, consistent with long-distance clonal dispersal. However, despite evidence for clonal dispersal, statistically significant genetic differentiation among geographic populations was detected. In addition, while no evidence of recombination was found within any of the four gene fragments, signatures of recombination were found among the four gene fragments in most geographic populations, consistent with sexual mating of this species in nature. Our study provides the first insights into the population genetics and epidemiology of the important plant fungal pathogen C. fructicola. PMID:27299731

The relative effects of habitat loss and fragmentation on population genetic variation in the red-cockaded woodpecker (Picoides borealis).

PubMed

Bruggeman, Douglas J; Wiegand, Thorsten; Fernández, Néstor

2010-09-01

The relative influence of habitat loss, fragmentation and matrix heterogeneity on the viability of populations is a critical area of conservation research that remains unresolved. Using simulation modelling, we provide an analysis of the influence both patch size and patch isolation have on abundance, effective population size (N(e)) and F(ST). An individual-based, spatially explicit population model based on 15 years of field work on the red-cockaded woodpecker (Picoides borealis) was applied to different landscape configurations. The variation in landscape patterns was summarized using spatial statistics based on O-ring statistics. By regressing demographic and genetics attributes that emerged across the landscape treatments against proportion of total habitat and O-ring statistics, we show that O-ring statistics provide an explicit link between population processes, habitat area, and critical thresholds of fragmentation that affect those processes. Spatial distances among land cover classes that affect biological processes translated into critical scales at which the measures of landscape structure correlated best with genetic indices. Therefore our study infers pattern from process, which contrasts with past studies of landscape genetics. We found that population genetic structure was more strongly affected by fragmentation than population size, which suggests that examining only population size may limit recognition of fragmentation effects that erode genetic variation. If effective population size is used to set recovery goals for endangered species, then habitat fragmentation effects may be sufficiently strong to prevent evaluation of recovery based on the ratio of census:effective population size alone.

Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment.

PubMed

Waleron, Małgorzata; Waleron, Krzysztof; Podhajska, Anna J; Lojkowska, Ewa

2002-02-01

Genotypic characterization, based on the analysis of restriction fragment length polymorphism of the recA gene fragment PCR product (recA PCR-RFLP), was performed on members of the former Erwinia genus. PCR primers deduced from published recA gene sequences of Erwinia carotovora allowed the amplification of an approximately 730 bp DNA fragment from each of the 19 Erwinia species tested. Amplified recA fragments were compared using RFLP analysis with four endonucleases (AluI, HinfI, TasI and Tru1I), allowing the detection of characteristic patterns of RFLP products for most of the Erwinia species. Between one and three specific RFLP groups were identified among most of the species tested (Erwinia amylovora, Erwinia ananas, Erwinia cacticida, Erwinia cypripedii, Erwinia herbicola, Erwinia mallotivora, Erwinia milletiae, Erwinia nigrifluens, Erwinia persicina, Erwinia psidii, Erwinia quercina, Erwinia rhapontici, Erwinia rubrifaciens, Erwinia salicis, Erwinia stewartii, Erwinia tracheiphila, Erwinia uredovora, Erwinia carotovora subsp. atroseptica, Erwinia carotovora subsp. betavasculorum, Erwinia carotovora subsp. odorifera and Erwinia carotovora subsp. wasabiae). However, in two cases, Erwinia chrysanthemi and Erwinia carotovora subsp. carotovora, 15 and 18 specific RFLP groups were detected, respectively. The variability of genetic patterns within these bacteria could be explained in terms of their geographic origin and/or wide host-range. The results indicated that PCR-RFLP analysis of the recA gene fragment is a useful tool for identification of species and subspecies belonging to the former Erwinia genus, as well as for differentiation of strains within E. carotovora subsp. carotovora and E. chrysanthemi.

Experimental and quantum-chemical studies on the three-particle fragmentation of neutral triatomic hydrogen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galster, Ulrich; Baumgartner, Frank; Mueller, Ulrich

2005-12-15

Dissociation of well-defined H{sub 3} Rydberg states into three ground state hydrogen atoms reveals characteristic correlation patterns in the center-of-mass motion of the three fragments. We present an extensive experimental dataset of momentum correlation maps for all lower Rydberg states of H{sub 3} and D{sub 3}. In particular the states with principal quantum number n=2 feature simple correlation patterns with regular occurence of mutual affinities. Energetically higher-lying states typically show more complex patterns which are unique for each state. Quantum-chemical calculations on adiabatic potential energy surfaces of H{sub 3} Rydberg states are presented to illuminate the likely origin of thesemore » differences. We discuss the likely dissociation mechanisms and paths which are responsible for the observed continuum correlation.« less

[Landscape pattern change and its driving forces in Xixi National Wetland Park since 1993].

PubMed

Cheng, Qian; Wu, Xiuju

2006-09-01

Under the support of GIS technology and the TM images of Xixi National Wetland Park, this paper studied the past ten years' landscape pattern change and its driving forces of Xixi Wetland. The results showed that the landscape diversity index increased from 1.7854 in 1993 to 1.8438 in 2001 and 2.2096 in 2003, and the landscape fragmentation index increased from 0.0036 in 1993 to 0.0042 in 2001, and 0.0047 in 2003, suggesting that the landscape fragmentation was increased with time. Human activity was the main driving force, while the exploitation of real estate was the main internal factor of the landscape pattern change of Xixi wetland. In addition, social and economic development level had a strong effect on the overall diversity of the landscape.

Fragmented patterns of flood change across the United States

PubMed Central

Hirsch, R. M.; Viglione, A.; Blöschl, G.

2016-01-01

Abstract Trends in the peak magnitude, frequency, duration, and volume of frequent floods (floods occurring at an average of two events per year relative to a base period) across the United States show large changes; however, few trends are found to be statistically significant. The multidimensional behavior of flood change across the United States can be described by four distinct groups, with streamgages experiencing (1) minimal change, (2) increasing frequency, (3) decreasing frequency, or (4) increases in all flood properties. Yet group membership shows only weak geographic cohesion. Lack of geographic cohesion is further demonstrated by weak correlations between the temporal patterns of flood change and large‐scale climate indices. These findings reveal a complex, fragmented pattern of flood change that, therefore, clouds the ability to make meaningful generalizations about flood change across the United States. PMID:27917010

Fragmented patterns of flood change across the United States

USGS Publications Warehouse

Archfield, Stacey A.; Hirsch, Robert M.; Viglione, A.; Blöschl, G.

2016-01-01

Trends in the peak magnitude, frequency, duration, and volume of frequent floods (floods occurring at an average of two events per year relative to a base period) across the United States show large changes; however, few trends are found to be statistically significant. The multidimensional behavior of flood change across the United States can be described by four distinct groups, with streamgages experiencing (1) minimal change, (2) increasing frequency, (3) decreasing frequency, or (4) increases in all flood properties. Yet group membership shows only weak geographic cohesion. Lack of geographic cohesion is further demonstrated by weak correlations between the temporal patterns of flood change and large-scale climate indices. These findings reveal a complex, fragmented pattern of flood change that, therefore, clouds the ability to make meaningful generalizations about flood change across the United States.

The NH2-terminal and COOH-terminal fragments of dentin matrix protein 1 (DMP1) localize differently in the compartments of dentin and growth plate of bone.

PubMed

Maciejewska, Izabela; Cowan, Cameron; Svoboda, Kathy; Butler, William T; D'Souza, Rena; Qin, Chunlin

2009-02-01

Multiple studies have shown that dentin matrix protein 1 (DMP1) is essential for bone and dentin mineralization. After post-translational proteolytic cleavage, DMP1 exists within the extracellular matrix of bone and dentin as an NH2-terminal fragment, a COOH-terminal fragment, and the proteoglycan form of the NH2-terminal fragment (DMP1-PG). To begin to assess the biological function of each fragment, we evaluated the distribution of both fragments in the rat tooth and bone using antibodies specific to the NH2-terminal and COOH-terminal regions of DMP1 and confocal microscopy. In rat first molar organs, the NH2-terminal fragment localized to predentin, whereas the COOH-terminal fragment was mainly restricted to mineralized dentin. In the growth plate of bone, the NH2-terminal fragment appeared in the proliferation and hypertrophic zones, whereas the COOH-terminal fragment occupied the ossification zone. Forster resonance energy transfer analysis showed colocalization of both fragments of DMP1 in odontoblasts and predentin, as well as hypertrophic chondrocytes within the growth plates of bone. The biochemical analysis of bovine teeth showed that predentin is rich in DMP1-PG, whereas mineralized dentin primarily contains the COOH-terminal fragment. We conclude that the differential patterns of expression of NH2-terminal and COOH-terminal fragments of DMP1 reflect their potentially distinct roles in the biomineralization of dentin and bone matrices.

On the effect of grain burnback on STS-SRM fragment velocity

NASA Astrophysics Data System (ADS)

Eck, Marshall B.; Mukunda, Meera

Concerns raised during the Ulysses Final Safety Analysis Review (FSAR) process called the solid rocket motor (SRM) fragment velocity prediction model into question. The specific area of concern was that there was a section of the SRM casing which was exposed to SRM chamber pressure as the grain (fuel) was consumed. These questions centered on the velocity of fragments which originated from the field joint region given that failure occurred between 37 and 72 seconds mission elapsed time (MET). Two dimensional coupled Eulerian-Lagrangian calculations were performed to assess the hot gas flow field which resulted from SRM casing fragmentation. The fragment to gas interface-pressure time-history obtained from these analyses was reduced to a boundary condition algorithm which was applied to an explicit-time-integration, finite element, three dimensional shell model of the SRM casing and unburned fuel. The results of these calculations showed that the velocity of fragments originating in the field joint was adequately described by the range of velocities given in the Shuttle Data Book (1988). Based on these results, no further analyses were required, and approval was obtained from the Launch Abort Subpanel of the Interagency Nuclear Safety Review Panel to use the SRM fragment velocity environments presented in the Ulysses FSAR (1990).

On the effect of grain burnback on STS-SRM fragment velocity

NASA Astrophysics Data System (ADS)

Eck, Marshall B.; Mukunda, Meera

1991-01-01

Concerns raised during the Ulysses Final Safety Analysis Review (FSAR) process called the solid rocket motor (SRM) fragment velocity prediction model into question. The specific area of concern was that there was a section of the SRM casing which was exposed to SRM chamber pressure as the grain (fuel) was consumed. These questions centered on the velocity of fragments which originated from the field joint region given that failure occurred between 37 and 72 seconds mission elapsed time (MET). Two dimensional coupled Eulerian-Lagrangian calculations were performed to assess the hot gas flow field which resulted from SRM casing fragmentation. The fragment to gas interface-pressure time-history obtained from these analyses was reduced to a boundary condition algorithm which was applied to an explicit-time-integration, finite element, three dimensional shell model of the SRM casing and unburned fuel. The results of these calculations showed that the velocity of fragments originating in the field joint was adequately described by the range of velocities given in the Shuttle Data Book (1988). Based on these results, no further analyses were required, and approval was obtained from the Launch Abort Subpanel of the Interagency Nuclear Safety Review Panel to use the SRM fragment velocity environments presented in the Ulysses FSAR (1990).

The new double energy-velocity spectrometer VERDI

NASA Astrophysics Data System (ADS)

Jansson, Kaj; Frégeau, Marc Olivier; Al-Adili, Ali; Göök, Alf; Gustavsson, Cecilia; Hambsch, Franz-Josef; Oberstedt, Stephan; Pomp, Stephan

2017-09-01

VERDI (VElocity foR Direct particle Identification) is a fission-fragment spectrometer recently put into operation at JRC-Geel. It allows measuring the kinetic energy and velocity of both fission fragments simultaneously. The velocity provides information about the pre-neutron mass of each fission fragment when isotropic prompt-neutron emission from the fragments is assumed. The kinetic energy, in combination with the velocity, provides the post-neutron mass. From the difference between pre- and post-neutron masses, the number of neutrons emitted by each fragment can be determined. Multiplicity as a function of fragment mass and total kinetic energy is one important ingredient, essential for understanding the sharing of excitation energy between fission fragments at scission, and may be used to benchmark nuclear de-excitation models. The VERDI spectrometer design is a compromise between geometrical efficiency and mass resolution. The spectrometer consists of an electron detector located close to the target and two arrays of silicon detectors, each located 50 cm away from the target. In the present configuration pre-neutron and post-neutron mass distributions are in good agreement with reference data were obtained. Our latest measurements performed with spontaneously fissioning 252Cf is presented along with the developed calibration procedure to obtain pulse height defect and plasma delay time corrections.

Genetic Heterogeneity in Mycobacterium tuberculosis Isolates Reflected in IS6110 Restriction Fragment Length Polymorphism Patterns as Low-Intensity Bands

PubMed Central

de Boer, Annette S.; Kremer, Kristin; Borgdorff, Martien W.; de Haas, Petra E. W.; Heersma, Herre F.; van Soolingen, Dick

2000-01-01

Mycobacterium tuberculosis isolates with identical IS6110 restriction fragment length polymorphism (RFLP) patterns are considered to originate from the same ancestral strain and thus to reflect ongoing transmission. In this study, we investigated 1,277 IS6110 RFLP patterns for the presence of multiple low-intensity bands (LIBs), which may indicate infections with multiple M. tuberculosis strains. We did not find any multiple LIBs, suggesting that multiple infections are rare in the Netherlands. However, we did observe a few LIBs in 94 patterns (7.4%) and examined the nature of this phenomenon. With single-colony cultures it was found that LIBs mostly represent mixed bacterial populations with slightly different RFLP patterns. Mixtures were expressed in RFLP patterns as LIBs when 10 to 30% of the DNA analyzed originated from a bacterial population with another RFLP pattern. Presumably, a part of the LIBs did not represent mixed bacterial populations, as in some clusters all strains exhibited LIBs in their RFLP patterns. The occurrence of LIBs was associated with increased age in patients. This may reflect either a gradual change of the bacterial population in the human body over time or IS6110-mediated genetic adaptation of M. tuberculosis to changes in the environmental conditions during the dormant state or reactivation thereafter. PMID:11101583

Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution.

PubMed Central

Torres, J; Padrós, E

1995-01-01

Fourier transform infrared and UV fourth-derivative spectroscopies were used to study the secondary structure of bacteriorhodopsin and its chymotryptic and one of the sodium borohydride fragments dissolved in chloroform-methanol (1:1, v/v), 0.1 M LiClO4. The C1 fragment (helices C, D, E, F, and G) showed an alpha-helical content of about 53%, whereas C2 (helices A and B) had about 60%, and B2 (helices F and G) about 65% alpha-helix. The infrared main band indicated differences in alpha-helical properties between these fragments. These techniques were also used to obtain information on the interactions among helices. According to the results obtained from the hydrogen/deuterium exchange kinetics, about 40% of the amide protons of C2 are particularly protected against exchange, whereas for the C1 fragment this process is unexpectedly fast. UV fourth-derivative spectra of these samples were used to obtain information about the environment of Trp side chains. The results showed that the Trp residues of C2 are more shielded from the solvent than those of C1 or B2. The results of this work indicate that the specific interactions existing between the transmembrane segments induce different types of helical conformations in native bacteriorhodopsin. PMID:7612847

Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed.

PubMed

Wang, Rong; Compton, Stephen G; Shi, Yi-Su; Chen, Xiao-Yong

2012-09-01

Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre- and post-fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind-pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre- and post-fragmentation cohorts. Significant genetic structure was observed in pre-fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post-fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long-term persistence of small remnant populations.

Fragment-based discovery of a potent NAMPT inhibitor.

PubMed

Korepanova, Alla; Longenecker, Kenton L; Pratt, Steve D; Panchal, Sanjay C; Clark, Richard F; Lake, Marc; Gopalakrishnan, Sujatha M; Raich, Diana; Sun, Chaohong; Petros, Andrew M

2017-12-12

NAMPT expression is elevated in many cancers, making this protein a potential target for anticancer therapy. We have carried out both NMR based and TR-FRET based fragment screens against human NAMPT and identified six novel binders with a range of potencies. Co-crystal structures were obtained for two of the fragments bound to NAMPT while for the other four fragments force-field driven docking was employed to generate a bound pose. Based on structural insights arising from comparison of the bound fragment poses to that of bound FK866 we were able to synthetically elaborate one of the fragments into a potent NAMPT inhibitor. Copyright © 2017 Elsevier Ltd. All rights reserved.

A landscape ecology approach to assessing development impacts in the tropics: A geothermal energy example in Hawaii

USGS Publications Warehouse

Griffith, J.A.; Trettin, C.C.; O'Neill, R. V.

2002-01-01

Geographic information systems (GIS) are increasingly being used in environmental impact assessments (EIA) because GIS is useful for analysing spatial impacts of various development scenarios. Spatially representing these impacts provides another tool for landscape ecology in environmental and geographical investigations by facilitating analysis of the effects of landscape patterns on ecological processes and examining change over time. Landscape ecological principles are applied in this study to a hypothetical geothermal development project on the Island of Hawaii. Some common landscape pattern metrics were used to analyse dispersed versus condensed development scenarios and their effect on landscape pattern. Indices of fragmentation and patch shape did not appreciably change with additional development. The amount of forest to open edge, however, greatly increased with the dispersed development scenario. In addition, landscape metrics showed that a human disturbance had a greater simplifying effect on patch shape and also increased fragmentation than a natural disturbance. The use of these landscape pattern metrics can advance the methodology of applying GIS to EIA.

Protein crystallization aboard the Space Shuttle and the Mir space station

NASA Technical Reports Server (NTRS)

Delbaere, Louis T. J.; Vandonselaar, Margaret; Prasad, Lata; Quail, J. W.; Birnbaum, George I.; Delucas, Lawrence J.; Moore, Karen; Bugg, Charles E.

1993-01-01

Two different protein crystallizations, namely ,the free Fab fragment of the Je142 monoclonal antibody and the complex of Fab fragment/HPr with antigen, were performed aboard the Discovery Space Shuttle flights and the Mir space station, respectively. Medium sized crystals of the Je142 Fab fragment were obtained. The Je142 Fab fragment/Hpr complex produced two medium-sized crystals after two months aboard the Mir space station. Microgravity was found to eliminate the tendency of these crystals to form clusters.

Exploration of the fragmentation of laser shock-melted aluminum using x-ray backlighting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Lin, E-mail: zhanglinbox@263.net, E-mail: zhanglinbox@caep.cn; Li, Ying-Hua; Li, Xue-Mei

The fragmentation of shock-melted metal material is an important scientific problem in shock physics and is suitable for experimentally investigating by the laser-driven x-ray backlighting technique. This letter reports on the exploration of laser shock-melted aluminum fragmentation by means of x-ray backlighting at the SGII high energy facility in China. High-quality and high-resolution radiographs with negligible motion blur were obtained and these images enabled analysis of the mass distribution of the fragmentation product.

Subacute Low Dose Nerve Agent Exposure Causes DNA Fragmentation in Guinea Pig Leukocytes

DTIC Science & Technology

2005-10-01

1 SUBACUTE LOW DOSE NERVE AGENT EXPOSURE CAUSES DNA FRAGMENTATION IN GUINEA PIG LEUKOCYTES. Jitendra R. Dave1, John R. Moffett1, Sally M...DNA fragmentation in blood leukocytes from guinea pigs by ‘Comet’ assay after exposure to soman at doses ranging from 0.1LD50 to 0.4 LD50, once per...computer. Data obtained for exposure to soman demonstrated significant increases in DNA fragmentation in circulating leukocytes in CWNA treated guinea pigs as

Screening of Israeli Holstein-Friesian cattle for restriction fragment length polymorphisms using homologous and heterologous deoxyribonucleic acid probes.

PubMed

Hallerman, E M; Nave, A; Soller, M; Beckmann, J S

1988-12-01

Genomic DNA of Israeli Holstein-Friesian dairy cattle were screened with a battery of 17 cloned or subcloned DNA probes in an attempt to document restriction fragment length polymorphisms at a number of genetic loci. Restriction fragment length polymorphisms were observed at the chymosin, oxytocin-neurophysin I, lutropin beta, keratin III, keratin VI, keratin VII, prolactin, and dihydrofolate reductase loci. Use of certain genomic DNA fragments as probes produced hybridization patterns indicative of satellite DNA at the respective loci. Means for distinguishing hybridizations to coding sequences for unique genes from those to satellite DNA were developed. Results of this study are discussed in terms of strategy for the systematic development of large numbers of bovine genomic polymorphisms.

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin

NASA Astrophysics Data System (ADS)

Floris, Federico; Chiron, Lionel; Lynch, Alice M.; Barrow, Mark P.; Delsuc, Marc-André; O'Connor, Peter B.

2018-06-01

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about 23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from 23% to 42%.

Soil erosion and effluent particle size distribution under different initial conditions and rock fragment coverage

NASA Astrophysics Data System (ADS)

Jomaa, S.; Barry, D. A.; Brovelli, A.; Heng, B. C. P.; Sander, G. C.; Parlange, J.-Y.

2012-04-01

It is well known that the presence of rock fragments on the soil surface and the soil's initial characteristics (moisture content, surface roughness, bulk density, etc.) are key factors influencing soil erosion dynamics and sediment delivery. In addition, the interaction of these factors increases the complexity of soil erosion patterns and makes predictions more difficult. The aim of this study was (i) to investigate the effect of soil initial conditions and rock fragment coverage on soil erosion yields and effluent particle size distribution and (ii) to evaluate to what extent the rock fragment coverage controls this relationship. Three laboratory flume experiments with constant precipitation rate of 74 mm/h on a loamy soil parcel with a 2% slope were performed. Experiments with duration of 2 h were conducted using the 6-m × 2-m EPFL erosion flume. During each experiment two conditions were considered, a bare soil and a rock fragment-protected (with 40% coverage) soil. The initial soil surface state was varied between the three experiments, from a freshly re-ploughed and almost dry condition to a compacted soil with a well-developed shield layer and high moisture content. Experiments were designed so that rain splash was the primary driver of soil erosion. Results showed that the amount of eroded mass was highly controlled by the initial soil conditions and whether the steady-state equilibrium was un-, partially- or fully- developed during the previous event. Additionally, results revealed that sediment yields and particle size composition in the initial part of an erosion event are more sensitive to the erosion history than the long-time behaviour. This latter appears to be mainly controlled by rainfall intensity. If steady-state was achieved for a previous event, then the next event consistently produced concentrations for each size class that peaked rapidly, and then declined gradually to steady-state equilibrium. If steady state was not obtained, then different and more complex behaviour was observed in the next event, with large differences found between fine, medium and coarse size classes. The presence of rock fragments on the topsoil reduced the time needed to reach steady state compared with the bare soil. This was attributed to the reduction of rain splash erosion caused by the rapid development of the overland flow, as a result of rock fragments reducing the flow cross-sectional area.

Secondary forest regeneration benefits old-growth specialist bats in a fragmented tropical landscape.

PubMed

Rocha, Ricardo; Ovaskainen, Otso; López-Baucells, Adrià; Farneda, Fábio Z; Sampaio, Erica M; Bobrowiec, Paulo E D; Cabeza, Mar; Palmeirim, Jorge M; Meyer, Christoph F J

2018-02-28

Tropical forest loss and fragmentation are due to increase in coming decades. Understanding how matrix dynamics, especially secondary forest regrowth, can lessen fragmentation impacts is key to understanding species persistence in modified landscapes. Here, we use a whole-ecosystem fragmentation experiment to investigate how bat assemblages are influenced by the regeneration of the secondary forest matrix. We surveyed bats in continuous forest, forest fragments and secondary forest matrix habitats, ~15 and ~30 years after forest clearance, to investigate temporal changes in the occupancy and abundance of old-growth specialist and habitat generalist species. The regeneration of the second growth matrix had overall positive effects on the occupancy and abundance of specialists across all sampled habitats. Conversely, effects on generalist species were negligible for forest fragments and negative for secondary forest. Our results show that the conservation potential of secondary forests for reverting faunal declines in fragmented tropical landscapes increases with secondary forest age and that old-growth specialists, which are often of most conservation concern, are the greatest beneficiaries of secondary forest maturation. Our findings emphasize that the transposition of patterns of biodiversity persistence in island ecosystems to fragmented terrestrial settings can be hampered by the dynamic nature of human-dominated landscapes.

Rural and suburban sprawl in the U.S. midwest from 1940 to 2000 in its relation to forest fragmentation

Treesearch

Volker C. Radeloff; Roger B. Hammer; Susan I. Stewart

2005-01-01

Housing growth and its environmental effects pose major conservation challenges. We sought to (]) quantify spatial and temporal patterns of housing growth across the US. Midwest from 1940-2000, (2) identify ecoregions strongly affected by housing growth, (3) assess the extent to which forests occur near housing, and (4) relate housing to forest fragmentation. We used...

Identification of Organics in Ice Grains from Enceladus

NASA Astrophysics Data System (ADS)

Khawaja, N.; Postberg, F.; Reviol, R.; Nölle, L.; Klenner, F.; Srama, R.

2015-12-01

The Cosmic Dust Analyzer (CDA) aboard the Cassini spacecraft performs in-situ measurements of the chemical composition of icy dust grains impinging onto the target surface. The instrument recorded cationic Time-of-Flight (ToF) mass spectra of organic-bearing ice grains emitted from Enceladus at different impact velocities causing different molecular fragmentation patterns [1,2]. Here we present a detailed analysis of these spectra (Type-2) to identify the composition of organic material embedded in Enceladus ice grains. The organic compounds display a great compositional diversity, which indicates varying contributions of several organic species. The spectra analysis is supported by a large-scale laboratory ground campaign yielding a library of analogue spectra for organic material embedded in a water ice matrix. To mimic the identified pattern of cationic fragments in organic enriched spectra we use a laboratory setup: Infrared Free Liquid MALDI ToF Mass Spectrometer (IR-FL-MALDI-ToF-MS). An infrared laser is used to disperse a liquid micro-beam of a water-solution to get cationic fragments. The laser energy is adjusted to simulate different impact velocities of ice particles on CDA [3]. So far we have identified characteristic fragment patterns of at least three classes of organic molecules: (i) aromatic species, (ii) amines, and (iii) carbonyl group species. (i) ice grains containing aromatic species are identified by a series of characteristic aromatic fragment cations (ii) ice grains containing amines are identified by a pronounced ammonium cation and (iii) ice grains containing carbonyl compounds are specified by a characteristic acylium cation in conjunction with certain others mass lines. Besides aromatic, amine and carbonyl species, Type-2 spectra also show contributions from other, yet un-specified, organic species. Typically, fragment cations of aromatic compounds are stable at impact velocities up-to 15km/s whereas cations of amines and carbonyl species are stable at velocities below 8km/s. Work is in progress to quantify concentrations of the identified species and to assign yet un-specified organic mass lines in Type 2 spectra. Ref: [1]Postberg et al., Icarus-193,2008. [2]Postberg et al., Nature-459,2009. [3]Beinsen, A., University of Göttingen, Dissertation (2011).

Relationship between molecular connectivity and carcinogenic activity: a confirmation with a new software program based on graph theory.

PubMed Central

Malacarne, D; Pesenti, R; Paolucci, M; Parodi, S

1993-01-01

For a database of 826 chemicals tested for carcinogenicity, we fragmented the structural formula of the chemicals into all possible contiguous-atom fragments with size between two and eight (nonhydrogen) atoms. The fragmentation was obtained using a new software program based on graph theory. We used 80% of the chemicals as a training set and 20% as a test set. The two sets were obtained by random sorting. From the training sets, an average (8 computer runs with independently sorted chemicals) of 315 different fragments were significantly (p < 0.125) associated with carcinogenicity or lack thereof. Even using this relatively low level of statistical significance, 23% of the molecules of the test sets lacked significant fragments. For 77% of the molecules of the test sets, we used the presence of significant fragments to predict carcinogenicity. The average level of accuracy of the predictions in the test sets was 67.5%. Chemicals containing only positive fragments were predicted with an accuracy of 78.7%. The level of accuracy was around 60% for chemicals characterized by contradictory fragments or only negative fragments. In a parallel manner, we performed eight paired runs in which carcinogenicity was attributed randomly to the molecules of the training sets. The fragments generated by these pseudo-training sets were devoid of any predictivity in the corresponding test sets. Using an independent software program, we confirmed (for the complex biological endpoint of carcinogenicity) the validity of a structure-activity relationship approach of the type proposed by Klopman and Rosenkranz with their CASE program. Images Figure 1. Figure 2. Figure 3. Figure 4. Figure 5. Figure 6. PMID:8275991

Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences.

PubMed

Defrance, Matthieu; Janky, Rekin's; Sand, Olivier; van Helden, Jacques

2008-01-01

This protocol explains how to discover functional signals in genomic sequences by detecting over- or under-represented oligonucleotides (words) or spaced pairs thereof (dyads) with the Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/). Two typical applications are presented: (i) predicting transcription factor-binding motifs in promoters of coregulated genes and (ii) discovering phylogenetic footprints in promoters of orthologous genes. The steps of this protocol include purging genomic sequences to discard redundant fragments, discovering over-represented patterns and assembling them to obtain degenerate motifs, scanning sequences and drawing feature maps. The main strength of the method is its statistical ground: the binomial significance provides an efficient control on the rate of false positives. In contrast with optimization-based pattern discovery algorithms, the method supports the detection of under- as well as over-represented motifs. Computation times vary from seconds (gene clusters) to minutes (whole genomes). The execution of the whole protocol should take approximately 1 h.

Fabrication of functional fibronectin patterns by nanosecond excimer laser direct write for tissue engineering applications.

PubMed

Grigorescu, S; Hindié, M; Axente, E; Carreiras, F; Anselme, K; Werckmann, J; Mihailescu, I N; Gallet, O

2013-07-01

Laser direct write techniques represent a prospective alternative for engineering a new generation of hybrid biomaterials via the creation of patterns consisting of biological proteins onto practically any type of substrate. In this paper we report on the characterization of fibronectin features obtained onto titanium substrates by UV nanosecond laser transfer. Fourier-transform infrared spectroscopy measurements evidenced no modification in the secondary structure of the post-transferred protein. The molecular weight of the transferred protein was identical to the initial fibronectin, no fragment bands being found in the transferred protein's Western blot migration profile. The presence of the cell-binding domain sequence and the mannose groups within the transferred molecules was revealed by anti-fibronectin monoclonal antibody immunolabelling and FITC-Concanavalin-A staining, respectively. The in vitro tests performed with MC3T3-E1 osteoblast-like cells and Swiss-3T3 fibroblasts showed that the cells' morphology and spreading were strongly influenced by the presence of the fibronectin spots.

Effect of aerated concrete blockwork joints on the heat transfer performance uniformity

NASA Astrophysics Data System (ADS)

Pukhkal, Viktor; Murgul, Vera

2018-03-01

Analysis of data on the effect of joints of the aerated concrete blocks on the heat transfer uniformity of exterior walls was carried out. It was concluded, that the values of the heat transfer performance uniformity factor in the literature sources were obtained for the regular fragment of a wall construction by approximate addition of thermal conductivities. Heat flow patterns for the aerated concrete exterior walls amid different values of the thermal conductivity factors and design ambient air temperature of -26 °C were calculated with the use of "ELCUT" software for modelling of thermal patterns by finite element method. There were defined the values for the heat transfer performance uniformity factor, reduced total thermal resistance and heat-flux density for the exterior walls. The calculated values of the heat transfer performance uniformity factors, as a function of the coefficient of thermal conductivity of aerated concrete blocks, differ from the known data by a more rigorous thermal and physical substantiation.

Morphometric comparison by the ISAS® CASA-DNAf system of two techniques for the evaluation of DNA fragmentation in human spermatozoa

PubMed Central

Sadeghi, Sara; García-Molina, Almudena; Celma, Ferran; Valverde, Anthony; Fereidounfar, Sogol; Soler, Carles

2016-01-01

DNA fragmentation has been shown to be one of the causes of male infertility, particularly related to repeated abortions, and different methods have been developed to analyze it. In the present study, two commercial kits based on the SCD technique (Halosperm® and SDFA) were evaluated by the use of the DNA fragmentation module of the ISAS® v1 CASA system. Seven semen samples from volunteers were analyzed. To compare the results between techniques, the Kruskal–Wallis test was used. Data were used for calculation of Principal Components (two PCs were obtained), and subsequent subpopulations were identified using the Halo, Halo/Core Ratio, and PC data. Results from both kits were significantly different (P < 0.001). In each case, four subpopulations were obtained, independently of the classification method used. The distribution of subpopulations differed depending on the kit used. From the PC data, a discriminant analysis matrix was obtained and a good a posteriori classification was obtained (97.1% for Halosperm and 96.6% for SDFA). The present results are the first approach on morphometric evaluation of DNA fragmentation from the SCD technique. This approach could be used for the future definition of a classification matrix surpassing the current subjective evaluation of this important sperm factor. PMID:27678463

Morphometric comparison by the ISAS® CASA-DNAf system of two techniques for the evaluation of DNA fragmentation in human spermatozoa.

PubMed

Sadeghi, Sara; García-Molina, Almudena; Celma, Ferran; Valverde, Anthony; Fereidounfar, Sogol; Soler, Carles

2016-01-01

DNA fragmentation has been shown to be one of the causes of male infertility, particularly related to repeated abortions, and different methods have been developed to analyze it. In the present study, two commercial kits based on the SCD technique (Halosperm ® and SDFA) were evaluated by the use of the DNA fragmentation module of the ISAS ® v1 CASA system. Seven semen samples from volunteers were analyzed. To compare the results between techniques, the Kruskal-Wallis test was used. Data were used for calculation of Principal Components (two PCs were obtained), and subsequent subpopulations were identified using the Halo, Halo/Core Ratio, and PC data. Results from both kits were significantly different (P < 0.001). In each case, four subpopulations were obtained, independently of the classification method used. The distribution of subpopulations differed depending on the kit used. From the PC data, a discriminant analysis matrix was obtained and a good a posteriori classification was obtained (97.1% for Halosperm and 96.6% for SDFA). The present results are the first approach on morphometric evaluation of DNA fragmentation from the SCD technique. This approach could be used for the future definition of a classification matrix surpassing the current subjective evaluation of this important sperm factor.

Factors Related to Spatial Patterns of Rural Land Fragmentation in Texas

NASA Astrophysics Data System (ADS)

Kjelland, Michael E.; Kreuter, Urs P.; Clendenin, George A.; Wilkins, R. Neal; Wu, X. Ben; Afanador, Edith Gonzalez; Grant, William E.

2007-08-01

Fragmentation of family-owned farms and ranches has been identified as the greatest single threat to wildlife habitat, water supply, and the long-term viability of agriculture in Texas. However, an integrative framework for insights into the pathways of land use change has been lacking. The specific objectives of the study are to test the hypotheses that the nonagricultural value (NAV) of rural land is a reliable indicator of trends in land fragmentation and that NAV in Texas is spatially correlated with population density, and to explore the idea that recent changes in property size patterns are better represented by a categorical model than by one that reflects incremental changes. We propose that the State-and-Transition model, developed to describe the dynamics of semi-arid ecosystems, provides an appropriate conceptual framework for characterizing categorical shifts in rural property patterns. Results suggest that changes in population density are spatially correlated with NAV and farm size, and that rural property size is spatially correlated with changes in NAV. With increasing NAV, the proportion of large properties tends to decrease while the area represented by small properties tends to increase. Although a correlation exists between NAV and population density, it is the trend in NAV that appears to be a stronger predictor of land fragmentation. The empirical relationships established herein, viewed within the conceptual framework of the State-and-Transition model, can provide a useful tool for evaluating land use policies for maintaining critical ecosystem services delivered from privately owned land in private land states, such as Texas.

Home range use and survival of southern flying squirrels in fragmented forest landscapes

USGS Publications Warehouse

Jacques, Christopher N.; Zweep, James S.; Jenkins, Sean E.; Klaver, Robert W.

2017-01-01

We studied home range use, spatial activity patterns, and annual survival of southern flying squirrels (SFS; Glaucomys volans) across fragmented landscapes of west-central Illinois. We calculated seasonal home range sizes and annual survival from 67 animals (36 males, 31 females) captured during 2014–2016. Home range and core area sizes were similar (P ≥ 0.46) among males and females across summer (April–September) and winter (October–March) seasons. Average distance between consecutive animal locations did not vary by sex, season, or year. Similarly, cumulative distance between consecutive locations did not vary by sex, season, or year and ranged from 1,189 to 1,661 m between summer and winter seasons. Mean annual composite home range and core area sizes were 10.39 and 1.25 ha, respectively; estimated home ranges (10.3 ha) of females are the largest documented for this species. We documented 8 deaths, all attributed to predation, the majority (63%) of which occurred during winter; annual survival was 71%. Our results underscore effects of habitat productivity on seasonal home range dynamics and space use patterns of SFS in fragmented landscapes. SFS may compensate for reduced availability of overstory mast-producing trees that characterize unproductive habitats and low-density populations by exhibiting similar movement patterns and use of available habitat by both sexes throughout the year. Winter communal nesting appears to be influenced by availability of cavity trees, thereby confirming the importance of standing snags in contributing essential habitat to flying squirrel populations in fragmented forests.

Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

NASA Astrophysics Data System (ADS)

Rožman, Marko

2016-01-01

Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

Genetic and Epigenetic Alterations of Brassica nigra Introgression Lines from Somatic Hybridization: A Resource for Cauliflower Improvement.

PubMed

Wang, Gui-Xiang; Lv, Jing; Zhang, Jie; Han, Shuo; Zong, Mei; Guo, Ning; Zeng, Xing-Ying; Zhang, Yue-Yun; Wang, You-Ping; Liu, Fan

2016-01-01

Broad phenotypic variations were obtained previously in derivatives from the asymmetric somatic hybridization of cauliflower "Korso" (Brassica oleracea var. botrytis, 2n = 18, CC genome) and black mustard "G1/1" (Brassica nigra, 2n = 16, BB genome). However, the mechanisms underlying these variations were unknown. In this study, 28 putative introgression lines (ILs) were pre-selected according to a series of morphological (leaf shape and color, plant height and branching, curd features, and flower traits) and physiological (black rot/club root resistance) characters. Multi-color fluorescence in situ hybridization revealed that these plants contained 18 chromosomes derived from "Korso." Molecular marker (65 simple sequence repeats and 77 amplified fragment length polymorphisms) analysis identified the presence of "G1/1" DNA segments (average 7.5%). Additionally, DNA profiling revealed many genetic and epigenetic differences among the ILs, including sequence alterations, deletions, and variation in patterns of cytosine methylation. The frequency of fragments lost (5.1%) was higher than presence of novel bands (1.4%), and the presence of fragments specific to Brassica carinata (BBCC 2n = 34) were common (average 15.5%). Methylation-sensitive amplified polymorphism analysis indicated that methylation changes were common and that hypermethylation (12.4%) was more frequent than hypomethylation (4.8%). Our results suggested that asymmetric somatic hybridization and alien DNA introgression induced genetic and epigenetic alterations. Thus, these ILs represent an important, novel germplasm resource for cauliflower improvement that can be mined for diverse traits of interest to breeders and researchers.

Isolation of a Soluble Component of Plasmodium berghei Which Induces Immunity in Rats

PubMed Central

Grothaus, G. D.; Kreier, J. P.

1980-01-01

Soluble material was obtained from sonically freed plasmodiae by three procedures. Two procedures, cryo-impacting and freeze-thawing, were evaluated for their ability to disrupt the parasites and release soluble material. The soluble materials obtained by these procedures were compared to materials washed from the surfaces of sonically freed parasites. Between 35 and 40% of the total parasite protein was solubilized by freeze-thawing or cryo-impacting. One cycle of freeze-thawing released nearly as much protein as could be released by this method, and additional cycles of freeze-thawing had little additional effect. Cryo-impacting solubilized only a small amount of protein in addition to that which was released by the cycle of freeze-thawing inherent in the procedure. Reductions in the packed cell volume of the material remaining after freeze-thawing or cryo-impacting indicate that the insoluble fragments are broken into smaller pieces as treatment is extended. Electron microscopy of 30-s cryo-impacted and three-times freeze-thawed parasites revealed membrane fragments similar in appearance. Patterns obtained by polyacrylamide gel electrophoresis of the soluble material from freeze-thawed and cryo-impacted parasites were also similar, and approximately 13 protein bands were demonstrated. The material washed from the surfaces of the free parasites, on the other hand, resolved into only two to four major bands on the gel columns. In immunization studies, the soluble and insoluble fractions obtained by freeze-thawing or cryo-impacting and the material washed from the surfaces of the parasites all stimulated a protective immune response. On the basis of the amount of protein required to stimulate roughly comparable immunity, the soluble fraction obtained by freeze-thawing or cryo-impacting free parasites was about twice as potent an immunogen as was the insoluble fraction. The material obtained by gentle washing of the freed parasites was approximately 20 times as potent an immunogen as were the freed parasites and about 7 times as potent as the soluble material obtained by freeze-thawing or cryo-impacting. Images Fig. 1 Fig. 2 PMID:6991439

Heavy Ion Fragmentation Experiments at the Bevatron

NASA Technical Reports Server (NTRS)

Heckman, H. H.

1975-01-01

Fragmentation processes of heavy nuclei in matter using the heavy-ion capability of the Bevatron were studied. The purpose was to obtain the single particle inclusive spectra of secondary nuclei produced at 0 deg by the fragmentation of heavy ion beam projectiles. The process being examined is B+T yields F + anything, where B is the beam nucleus, T is the target nucleus, and F is the detected fragment. The fragments F are isotopically identified by experimental procedures involving magnetic analysis, energy loss and time-of-flight measurements. Attempts were also made to: (1) measure the total and partial production cross section for all isotopes, (2) test the applicability of high-energy multi-particle interaction theory to nuclear fragmentation, (3) apply the cross-section data and fragmentation probabilities to cosmic ray transport theory, and (4) search for systematic behavior of fragment production as a means to improve existing semi-empirical theories of cross sections.

Shuttle data book: SRM fragment velocity model. Presented to the SRB Fragment Model Review Panel

NASA Technical Reports Server (NTRS)

1989-01-01

This study was undertaken to determine the velocity of fragments generated by the range safety destruction (RSD) or random failure of a Space Transportation System (STS) Solid Rocket Motor (SRM). The specific requirement was to provide a fragment model for use in those Galileo and Ulysses RTG safety analyses concerned with possible fragment impact on the spacecraft radioisotope thermoelectric generators (RTGS). Good agreement was obtained between predictions and observations for fragment velocity, velocity distributions, azimuths, and rotation rates. Based on this agreement with the entire data base, the model was used to predict the probable fragment environments which would occur in the event of an STS-SRM RSD or randon failure at 10, 74, 84 and 110 seconds. The results of these predictions are the basis of the fragment environments presented in the Shuttle Data Book (NSTS-08116). The information presented here is in viewgraph form.

The 4-dimensional Langevin approach to low energy nuclear fission

NASA Astrophysics Data System (ADS)

Ivanyuk, F. A.; Ishizuka, C.; Usang, M. D.; Chiba, S.

2018-03-01

We applied the four-dimensional Langevin approach to the description of fission of 235U by neutrons and calculated the dependence of the excitation energy of fission fragments on their mass number. For this we have fitted the compact just-before-scission configuration obtained by the Langevin calculations by the two separated fragments and calculated the intrinsic excitation and the deformation energy of each fragment accurately taking into account the shell and pairing effects and their dependence on the temperature and mass of the fragments. For the sharing of energy between the fission fragments we have used the simplest and most reliable assumption - the temperature of each fragment immediately after the neck rupture is the same as the temperature of mother nucleus just before scission. The calculated excitation energy of fission fragments clearly demonstrates the saw-tooth structure in the dependence on fragment mass number.

Study of fission fragment de-excitation by gamma-ray spectrometry with the EXILL experiment

NASA Astrophysics Data System (ADS)

Materna, Thomas; a, Michal Rapał; Letourneau, Alain; Marchix, Anthony; Litaize, Olivier; Sérot, Olivier; Urban, Waldemar; Blanc, Aurélien; Jentschel, Michael; Köster, Ulli; Mutti, Paolo; Soldner, Torsten; Simpson, Gary; Ur, Călin A.; France, Gilles de

2017-09-01

A large array of Ge detectors installed at ILL, around a 235U target irradiated with cold neutrons, (EXILL) allowed measurement of prompt gamma-ray cascades occurring in fission fragments with an unambiguous determination of fragments. Here we present preliminary results of a systematic comparison between experimental γ-ray intensities and those obtained from the Monte-Carlo simulation code FIFRELIN, which is dedicated to the de-excitation of fission fragments. Major γ-ray intensities in the 142Ba and 92Kr fission products, extracted from EXILL data, were compared to FIFRELIN, as well as to reported values (when available) obtained with EUROGAM2 in the spontaneous fission of 248Cm. The evolution of γ-ray intensities in 92Kr versus the complementary partner in fission (i.e. versus the total number of evaporated neutrons by the fission pair) was then extracted and compared to FIFRELIN.

Reduced Genetic Diversity and Increased Dispersal in Guigna (Leopardus guigna) in Chilean Fragmented Landscapes.

PubMed

Napolitano, Constanza; Díaz, Diego; Sanderson, Jim; Johnson, Warren E; Ritland, Kermit; Ritland, Carol E; Poulin, Elie

2015-01-01

Landscape fragmentation is often a major cause of species extinction as it can affect a wide variety of ecological processes. The impact of fragmentation varies among species depending on many factors, including their life-history traits and dispersal abilities. Felids are one of the groups most threatened by fragmented landscapes because of their large home ranges, territorial behavior, and low population densities. Here, we model the impacts of habitat fragmentation on patterns of genetic diversity in the guigna (Leopardus guigna), a small felid that is closely associated with the heavily human-impacted temperate rainforests of southern South America. We assessed genetic variation in 1798 base pairs of mitochondrial DNA sequences, 15 microsatellite loci, and 2 sex chromosome genes and estimated genetic diversity, kinship, inbreeding, and dispersal in 38 individuals from landscapes with differing degrees of fragmentation on Chiloé Island in southern Chile. Increased fragmentation was associated with reduced genetic diversity, but not with increased kinship or inbreeding. However, in fragmented landscapes, there was a weaker negative correlation between pairwise kinship and geographic distance, suggesting increased dispersal distances. These results highlight the importance of biological corridors to maximize connectivity in fragmented landscapes and contribute to our understanding of the broader genetic consequences of habitat fragmentation, especially for forest-specialist carnivores. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Mitochondrial DNA pattern of the fine shrimp Metapenaeus elegans (De Man, 1907) in the lagoon of Segara Anakan, Central Java, using Hind III

NASA Astrophysics Data System (ADS)

Nugraha, Fitra Arya Dwi; Holil, Kholifah; Kurniawan, Nia

2017-05-01

Ecological damages to the Lagoon of Segara Anakan, Central Java, as well as large-scale and continuous exploitation are threatening the sustainability of fine shrimp, Metapenaeus elegans, and resources. Information in regards to genetic resources is crucial to establish long-term conservation programs and to preserve germplasm quality. This study aims to evaluate the number and size of the fragment which is digested with restriction enzyme Hind III. Seven individuals of Metapenaeus elegans from the Lagoon of Segara Anakan were examined using Hind III. Amplification of mitochondrial DNA resulted in 950 bp, and the digestion using Hind III generated four fragments consisting of 114 bp, 200 bp, 250 bp, and 386 bp, which formed a monomorphic pattern. The restriction pattern showed the probability of homozygosity of alleles that restricted using Hind III. Homozygosity indicates no variation of DNA sequence.

Identification of polycomb and trithorax group responsive elements in the regulatory region of the Drosophila homeotic gene Sex combs reduced

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gindhart, J.G. Jr.; Kaufman, T.C.

1995-02-01

The Drosophilia homeotic gene Sex combs reduced (Scr) is necessary for the establishment and maintenance of the morphological identity of the labial and prothoracic segments. In the early embryo, its expression pattern is established through the activity of several gap and segmentation gene products, as well as other transcription factors. Once established, the Polycomb group (Pc-G) and trithorax group (trx-G) gene products maintain the spatial pattern of Scr expression for the remainder of development. We report the identification of DNA fragments in the Scr regulatory region that may be important for its regulation by Polycomb and trithorax group gene products.more » When DNA fragments containing these regulatory sequences are subcloned into P-element vectors containing a white minigene, transformants containing these constructs exhibit mosaic patterns of pigmentation in the adult eye, indicating that white minigene expression is repressed in a clonally heritable manner. The size of pigmented and nonpigmented clones in the adult eye suggests that the event determining whether a cell in the eye anlagen will express white occurs at least as early as the first larval instar. The amount of white minigene repression is reduced in some Polycomb group mutants, whereas repression is enhanced in flies mutant for a subset of trithorax group loci. The repressor activity of one fragment, normally located in Scr Intron 2, is increased when it is able to homologously pair, a property consistent with genetic data suggesting that Scr exhibits transvection. Another Scr regulatory fragment, normally located 40 kb upstream of the Scr promoter, silences ectopic expression of an Scr-lacZ fusion gene in the embryo and does so in a Polycomb-dependent manner. We propose that the regulatory sequences located within these DNA fragments may normally mediate the regulation of Scr by proteins encoded by members of Polycomb and trithorax group loci. 98 refs., 6 figs., 4 tabs.« less

Molecular characterization and evaluation of the emerging antibiotic-resistant Streptococcus pyogenes from eastern India.

PubMed

Ray, Dipanwita; Saha, Somnath; Sinha, Sukanta; Pal, Nishith Kumar; Bhattacharya, Basudev

2016-12-12

Group A Streptococcus strains causing wide variety of diseases, recently became noticeable in eastern India, are not amenable to standard treatment protocol thus enhancing the possibility of disease morbidity by becoming antibiotic resistance. The association of Lancefield group A Streptococcal variation with degree of vir architectural diversity was evaluated using emm typing and restriction fragment length polymorphism analyses. The antibiotic sensitivity patterns were examined by modified Kirby-Bauer method of disk diffusion. Percentage calculations, 95% confidence interval and one-way ANOVA were used to assess differences in proportions. Our observations revealed 20 different emm types and 13 different HaeIII vir typing patterns. A 1.2 kb fragment was found in all HaeIII typing pattern. Fragments of 1.2 kb and 550 bp were conserved in majority of the isolates. HinfI digestion was found proficient in differentiating the strains of same vir typing patterns. Strong predominance of speC (85%) and speF (80%) genes have been observed encoding exotoxins production. 4 isolates were found to be erythromycin resistant and were of genotype emm49. High degree of tetracycline resistance was shown by 53.57% isolates which belonged to 12 different emm genotypes. These findings suggested that in addition to emm typing, sequential application of HaeIII and HinfI restriction enzymes in vir typing analysis is an effective tool for group A streptococcal molecular characterization associated with antibiotic resistance.

Habitat and landscape characteristics underlying anuran community structure along an urban-rural gradient.

PubMed

Pillsbury, Finn C; Miller, James R

2008-07-01

Urbanization has been cited as an important factor in worldwide amphibian declines, and although recent work has illustrated the important influence of broad-scale ecological patterns and processes on amphibian populations, little is known about the factors structuring amphibian communities in urban landscapes. We therefore examined amphibian community responses to wetland habitat availability and landscape characteristics along an urban-rural gradient in central Iowa, USA, a region experiencing rapid suburban growth. We conducted call surveys at 61 wetlands to estimate anuran calling activity, and quantified wetland habitat structure and landscape context. We used canonical correspondence analysis (CCA) to examine patterns in anuran community structure and identify the most important variables associated with those patterns. Urban density at the landscape scale had a significant negative influence on overall anuran abundance and diversity. While every species exhibited a decrease in abundance with increasing urban density, this pattern was especially pronounced for species requiring post-breeding upland habitats. Anurans most affected by urbanization were those associated with short hydroperiods, early breeding activity, and substantial upland habitat use. We suggest that broad-scale landscape fragmentation is an important factor underlying anuran community structure in this region, possibly due to limitations on the accessibility of otherwise suitable habitat in fragmented urban landscapes. This study underscores the importance of a regional approach to amphibian conservation in urban and urbanizing areas; in fragmented landscapes, a network of interconnected wetland and upland habitats may be more likely to support a successful, diverse anuran community than will isolated sites.

GC-MS analysis of amino acid enantiomers as their N(O,S)-perfluoroacyl perfluoroalkyl esters: application to space exploration

NASA Astrophysics Data System (ADS)

Zampolli, M.; Sternberg, R.; Szopa, C.; Pietrogrande, M. C.; Buch, A.; Dondi, F.; Raulin, F.

The search for optical activity in extraterrestrial sample is an important key for the study of the origin of life With this aim detection of chemical biomarkers i e of organic molecules which play an important role in biochemistry will be one of the main goals of future space missions To reach this goal an investigation of a GC-MS method based on the derivatization of amino acids by using a mixture of perfluorinated alcohols and perfluorinated anhydrides has been performed Amino acids are converted in their N O S -perfluoroacyl perfluoroalkyl esters in a single step procedure using different combinations of the derivatization reagents trifluoroacetic anhydride TFAA - 2 2 2-trifluoro-1-ethanol TFE TFAA-2 2 3 3 4 4 4-heptafluoro-1-butanol HFB heptafluorobutyric anhydride HFBA -HFB The obtained derivatives are analyzed using two different chiral columns a Chirasil-L-Val and a gammat cyclodextrin Rt- gamma -DEXsa stationary phases which show different and complementary enantiomeric selectivity The mass spectra of the derivatized compounds are studied and mass fragmentation patterns are proposed significant fragment ions can be identified to detect amino acid derivatives The obtained results are compared in terms of the enantiomeric separation achieved and mass spectrometric response Linearity studies and the measurement of the limit of detection LOD prove that the proposed method is suitable for a quantitative determination of several amino acids enantiomers 1 The use of a PTV Programmed Temperature Vaporiser

Characterization of the organic matter in submicron urban aerosols using a Thermo-Desorption Proton-Transfer-Reaction Time-of-Flight Mass Spectrometer (TD-PTR-TOF-MS)

NASA Astrophysics Data System (ADS)

Salvador, Christian Mark; Ho, T.-T.; Chou, Charles C.-K.; Chen, M.-J.; Huang, W.-R.; Huang, S.-H.

2016-09-01

Organic matter is the most complicated and unresolved major component of atmospheric aerosol particles. Its sources and global budget are still highly uncertain and thereby necessitate further research efforts with state-of-the-art instrument. This study employed a Thermo-Desorption Proton-Transfer-Reaction Time-of-Flight Mass Spectrometer (TD-PTR-TOF-MS) for characterization of ambient organic aerosols. First, five authentic standard substances, which include phthalic acid, levoglucosan, arabitol, cis-pinonic acid and glutaric acid, were utilized to examine the response of the instrument. The results demonstrated the linearity of the TD-PTR-TOF-MS signals against a range of mass loading of specific species on filters. However, it was found that significant fragmentation happened to those challenging compounds, although the proton-transfer-reaction (PTR) was recognized as a soft ionization technique. Consequently, quantitative characterization of aerosols with the TD-PTR-TOF-MS depended on the availability of the fragmentation pattern in mass spectra and the recovery rate with the quantification ion peak(s). The instrument was further deployed to analyze a subset of submicron aerosol samples collected at the TARO (Taipei Aerosol and Radiation Observatory) in Taipei, Taiwan during August 2013. The results were compared with the measurements from a conventional DRI thermo-optical carbon analyzer. The inter-comparison indicated that the TD-PTR-TOF-MS underestimated the mass of total organic matter (TOM) in aerosol samples by 27%. The underestimation was most likely due to the thermo-decomposition during desorption processes and fragmentation in PTR drift tube, where undetectable fragments were formed. Besides, condensation loss of low vapor pressure species in the transfer components was also responsible for the underestimation to a certain degree. Nevertheless, it was showed that the sum of the mass concentrations of the major detected ion peaks correlated strongly with the TOM determined by DRI analyzer (R2 = 0.8578), suggesting that the TD-PTR-TOF-MS measurements explained more than 85% of the variance in the time series of TOM. In addition to identification by comparing with the fragmentation pattern obtained from the mass spectra of the authentic substances, most of the major ions were attributed to protonated or acylium ions of specific parent compounds. Amongst the quantified species with full calibration with authentic standard, phthalic acid was found accounting for 7.0% of the mass loading of TOM. In addition, a high-end estimation of 9.4% was suggested for the mass contribution from glutaric acid, which was made by assuming that the ion with m/z of 73.027 was totally produced from fragmentation of glutaric acid as characterization of authentic standard despite of the formation of protonated methyl-glyoxal ion. Moreover, a substantial contribution from ions corresponding to protonated acetic acid and acetone was measured, which could be produced from fragmentation of larger oxygenated molecules. The TD-PTR-TOF-MS measurements suggested that low molecular weight carboxylic acid (LMWCA), products of photochemical oxidation of gaseous hydrocarbons and fatty acids, constituted a major fraction of secondary organic aerosols in Taipei, Taiwan, a typical subtropical urban area.

Diagnostic fragment-ion-based and extension strategy coupled to DFIs intensity analysis for identification of chlorogenic acids isomers in Flos Lonicerae Japonicae by HPLC-ESI-MS(n).

PubMed

Zhang, Jia-Yu; Zhang, Qian; Li, Ning; Wang, Zi-Jian; Lu, Jian-Qiu; Qiao, Yan-Jiang

2013-01-30

A method of modified diagnostic fragment-ion-based extension strategy (DFIBES) coupled to DFIs (diagnostic fragmentation ions) intensity analysis was successfully established to simultaneously screen and identify the chlorogenic acids (CGAs) in Flos Lonicerae Japonicae (FLJ) by HPLC-ESI-MS(n). DFIs, such as m/z 191 [quinic acid-H](-), m/z 179 [caffeic acid-H](-) and m/z 173 [quinic acid-H-H2O](-) were determined or proposed from the fragmentation patterns analysis of corresponding reference substances for every chemical family of CGAs. A "structure extension" method was then proposed based on the well-demonstrated fragmentation patterns and was successively applied into the rapid screening of CGAs in FLJ. Considering that substitution isomerism is a common phenomenon, a full ESI-MS(n) fragmentation analysis according to the intensity of DFIs has been performed to identify the CGA isomers. Based on the DFIs and intensity analysis, 41 peaks attributed to CGAs including 4 caffeoylquinic acids (CQA), 7 CQA glycosides, 6 dicaffeoylquinic acids (DiCQA), 10 DiCQA glycosides, 1 tricaffeoylquinic acids (TriCQA), 4p-coumaroylquinic acids (pCoQA), 3 feruloylquinic acids (FQA) and 6 caffeoylferuloylquinic acids (CFQA) were identified preliminarily in a 65-min chromatographic run. It was the first time to systematically report the presence of CGAs in FLJ, especially for CQA glycosides, DiCQA glycosides, TriCQA, pCoQA and CFQA. All the results indicated that the method of developed DFIBES coupled to DFIs analysis was feasible, reliable and universal for screening and identifying the constituents with the same carbon skeletons especially the isomeric compounds from the complex extract of TCMs. Copyright © 2012 Elsevier B.V. All rights reserved.

Extrapolation of the dna fragment-size distribution after high-dose irradiation to predict effects at low doses

NASA Technical Reports Server (NTRS)

Ponomarev, A. L.; Cucinotta, F. A.; Sachs, R. K.; Brenner, D. J.; Peterson, L. E.

2001-01-01

The patterns of DSBs induced in the genome are different for sparsely and densely ionizing radiations: In the former case, the patterns are well described by a random-breakage model; in the latter, a more sophisticated tool is needed. We used a Monte Carlo algorithm with a random-walk geometry of chromatin, and a track structure defined by the radial distribution of energy deposition from an incident ion, to fit the PFGE data for fragment-size distribution after high-dose irradiation. These fits determined the unknown parameters of the model, enabling the extrapolation of data for high-dose irradiation to the low doses that are relevant for NASA space radiation research. The randomly-located-clusters formalism was used to speed the simulations. It was shown that only one adjustable parameter, Q, the track efficiency parameter, was necessary to predict DNA fragment sizes for wide ranges of doses. This parameter was determined for a variety of radiations and LETs and was used to predict the DSB patterns at the HPRT locus of the human X chromosome after low-dose irradiation. It was found that high-LET radiation would be more likely than low-LET radiation to induce additional DSBs within the HPRT gene if this gene already contained one DSB.

Landscape genetics in the subterranean rodent Ctenomys "chasiquensis" associated with highly disturbed habitats from the southeastern Pampas region, Argentina.

PubMed

Mora, Matías Sebastián; Mapelli, Fernando J; López, Aldana; Gómez Fernández, María Jimena; Mirol, Patricia M; Kittlein, Marcelo J

2017-12-01

Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys "chasiquensis", a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci. We use landscape genetics approaches to assess the relationship between genetic connectivity among populations and environmental attributes. Our analyses show that populations of C. "chasiquensis" are moderately to highly structured at a regional level. This pattern is most likely the outcome of substantial gene flow on the more homogeneous sand dune habitat of the Northwest of its distributional range, in conjunction with an important degree of isolation of eastern and southwestern populations, where the optimal habitat is surrounded by a highly fragmented landscape. Landscape genetics analysis suggests that habitat quality and longitude were the environmental factors most strongly associated with genetic differentiation/uniqueness of populations. In conclusion, our results indicate an important genetic structure in this species, even at a small spatial scale, suggesting that contemporary habitat fragmentation increases population differentiation.

Liquid chromatography-high resolution mass spectrometry (LC-HRMS) determination of stimulants, anorectic drugs and phosphodiesterase 5 inhibitors (PDE5I) in food supplements.

PubMed

Strano-Rossi, Sabina; Odoardi, Sara; Castrignanò, Erika; Serpelloni, Giovanni; Chiarotti, Marcello

2015-03-15

The paper describes a liquid chromatography/high resolution mass spectrometry LC/HRMS method for the simultaneous identification and quantification of stimulants (ephedrines, caffeine, anorectic drugs such as phentermine, phendimetrazine, phenmetrazine, fenfluramine, benfluorex, mephentermine, fencanfamine, sibutramine) and PDE5I (sildenafil, vardenafil and tadalafil) in food supplements using a benchtop Orbitrap mass spectrometer. The mass detector, with a nominal resolving power of 100,000 (FWHM at m/z 200), operated in full scan mode in ESI positive ionization mode. Analytes were identified by retention times, accurate masses and correspondence of experimental and calculated isotopic patterns. The limits of detection (LOD) obtained varied from 1 to 25 ng g(-1) and limits of quantification (LOQ) were 50 ng g(-1) for all compounds. The method was linear for all the analytes in the ranges from 50 to 2000 ng g(-1), giving correlation coefficients>0.99. Accuracy (intended as %E) and repeatability (% CV) were always lower than 15%. The method was applied to the analysis of 36 dietary supplements, revealing the presence of ephedrine and/or pseudoephedrine in four of them, caffeine in eight of them and sildenafil in four of them. In one case, ephedrine was not reported on the label of the dietary supplement, as well as for caffeine in other two cases. A further confirmation of the analytes identity in positive samples was obtained through in-source fragmentation and comparison of the obtained fragments and their relative abundances with those from certified standards. As the acquisition mode is full scan, it would be also possible to re-process a previously acquired datafile for the investigation of untargeted analytes. Copyright © 2014 Elsevier B.V. All rights reserved.

Genetic variation in parthenogenetic Caucasian rock lizards of the genus Lacerta (L. dahli, L. armeniaca, L. unisexualis) analyzed by DNA fingerprinting.

PubMed

Tokarskaya, O N; Kan, N G; Petrosyan, V G; Martirosyan, I A; Grechko, V V; Danielyan, F D; Darevsky, I S; Ryskov, A P

2001-07-01

Multilocus DNA fingerprinting has been used to study the variability of some mini- and microsatellite sequences in parthenogenetic species of Caucasian rock lizards of the genus Lacerta (L. dahli, L. armeniaca and L. unisexualis). We demonstrate that these clonally reproducing lizards possess species-specific DNA fingerprints with a low degree of intra- and interpopulation variation. Mean indices of similarity obtained using M13 DNA, (GACA)4 and (TCC)50 as probes were 0.962 and 0.966 in L. dahli and L. armeniaca, respectively. The mean index of similarity obtained using M 13 and GATA probes in L. unisexualis was estimated to be 0.95. However, despite the high degree of band-sharing, variable DNA fragments were revealed in all populations with the microsatellite probes. An particularly high level of variability was observed for (TCC)n microsatellites in populations of L. unisexualis. In fact TCC-derived DNA fingerprints were close to being individual-specific, with a mean index of similarity of 0.824. Fingerprint analysis of parthenogenetic families of L. armeniaca showed that all maternal fragments were inherited together by the progeny, and no differences in fingerprint patterns were observed. On the other hand, while identical DNA fingerprints were obtained from L. unisexualis families with M13 and (GATA)4 probes, use of the (TCC)50 probe revealed remarkable intrafamily variation in this species. It is assumed that the genetic heterogeneity observed in parthenogenetic populations may be explained, at least in part, by the existence of genetically unstable microsatellite loci. Our data serve to illustrate processes of spontaneous mutagenesis and the initial stages of clonal differentiation in natural populations of the lizard species studied.

Mass spectrometry analysis of terpene lactones in Ginkgo biloba.

PubMed

Ding, Shujing; Dudley, Ed; Song, Qingbao; Plummer, Sue; Tang, Jiandong; Newton, Russell P; Brenton, A Gareth

2008-01-01

Terpene lactones are a family of compounds with unique chemical structures, first recognised in an extract of Ginkgo biloba. The discovery of terpene lactone derivatives has recently been reported in more and more plant extracts and even food products. In this study, mass spectrometric characteristics of the standard terpene lactones in Ginkgo biloba were comprehensively studied using both an ion trap and a quadrupole time-of-flight (QTOF) mass spectrometer. The mass spectral fragmentation data from both techniques was compared to obtain the mass spectrometric fragmentation pathways of the terpene lactones with high confidence. The data obtained will facilitate the analysis and identification of terpene lactones in future plant research via the fragmentation knowledge reported here.

Lactobacillus strain diversity based on partial hsp60 gene sequences and design of PCR-restriction fragment length polymorphism assays for species identification and differentiation.

PubMed

Blaiotta, Giuseppe; Fusco, Vincenzina; Ercolini, Danilo; Aponte, Maria; Pepe, Olimpia; Villani, Francesco

2008-01-01

A phylogenetic tree showing diversities among 116 partial (499-bp) Lactobacillus hsp60 (groEL, encoding a 60-kDa heat shock protein) nucleotide sequences was obtained and compared to those previously described for 16S rRNA and tuf gene sequences. The topology of the tree produced in this study showed a Lactobacillus species distribution similar, but not identical, to those previously reported. However, according to the most recent systematic studies, a clear differentiation of 43 single-species clusters was detected/identified among the sequences analyzed. The slightly higher variability of the hsp60 nucleotide sequences than of the 16S rRNA sequences offers better opportunities to design or develop molecular assays allowing identification and differentiation of either distant or very closely related Lactobacillus species. Therefore, our results suggest that hsp60 can be considered an excellent molecular marker for inferring the taxonomy and phylogeny of members of the genus Lactobacillus and that the chosen primers can be used in a simple PCR procedure allowing the direct sequencing of the hsp60 fragments. Moreover, in this study we performed a computer-aided restriction endonuclease analysis of all 499-bp hsp60 partial sequences and we showed that the PCR-restriction fragment length polymorphism (RFLP) patterns obtainable by using both endonucleases AluI and TacI (in separate reactions) can allow identification and differentiation of all 43 Lactobacillus species considered, with the exception of the pair L. plantarum/L. pentosus. However, the latter species can be differentiated by further analysis with Sau3AI or MseI. The hsp60 PCR-RFLP approach was efficiently applied to identify and to differentiate a total of 110 wild Lactobacillus strains (including closely related species, such as L. casei and L. rhamnosus or L. plantarum and L. pentosus) isolated from cheese and dry-fermented sausages.

Specificity enhancement by electrospray ionization multistage mass spectrometry--a valuable tool for differentiation and identification of 'V'-type chemical warfare agents.

PubMed

Weissberg, Avi; Tzanani, Nitzan; Dagan, Shai

2013-12-01

The use of chemical warfare agents has become an issue of emerging concern. One of the challenges in analytical monitoring of the extremely toxic 'V'-type chemical weapons [O-alkyl S-(2-dialkylamino)ethyl alkylphosphonothiolates] is to distinguish and identify compounds of similar structure. MS analysis of these compounds reveals mostly fragment/product ions representing the amine-containing residue. Hence, isomers or derivatives with the same amine residue exhibit similar mass spectral patterns in both classical EI/MS and electrospray ionization-MS, leading to unavoidable ambiguity in the identification of the phosphonate moiety. A set of five 'V'-type agents, including O-ethyl S-(2-diisopropylamino)ethyl methylphosphonothiolate (VX), O-isobutyl S-(2-diethylamino)ethyl methylphosphonothiolate (RVX) and O-ethyl S-(2-diethylamino)ethyl methylphosphonothiolate (VM) were studied by liquid chromatography/electrospray ionization/MS, utilizing a QTRAP mass detector. MS/MS enhanced product ion scans and multistage MS(3) experiments were carried out. Based on the results, possible fragmentation pathways were proposed, and a method for the differentiation and identification of structural isomers and derivatives of 'V'-type chemical warfare agents was obtained. MS/MS enhanced product ion scans at various collision energies provided information-rich spectra, although many of the product ions obtained were at low abundance. Employing MS(3) experiments enhanced the selectivity for those low abundance product ions and provided spectra indicative of the different phosphonate groups. Study of the fragmentation pathways, revealing some less expected structures, was carried out and allowed the formulation of mechanistic rules and the determination of sets of ions typical of specific groups, for example, methylphosphonothiolates versus ethylphosphonothiolates. The new group-specific ions elucidated in this work are also useful for screening unknown 'V'-type agents and related compounds, utilizing precursor ion scan experiments. Copyright © 2013 John Wiley & Sons, Ltd.

Lactobacillus Strain Diversity Based on Partial hsp60 Gene Sequences and Design of PCR-Restriction Fragment Length Polymorphism Assays for Species Identification and Differentiation▿ †

PubMed Central

Blaiotta, Giuseppe; Fusco, Vincenzina; Ercolini, Danilo; Aponte, Maria; Pepe, Olimpia; Villani, Francesco

2008-01-01

A phylogenetic tree showing diversities among 116 partial (499-bp) Lactobacillus hsp60 (groEL, encoding a 60-kDa heat shock protein) nucleotide sequences was obtained and compared to those previously described for 16S rRNA and tuf gene sequences. The topology of the tree produced in this study showed a Lactobacillus species distribution similar, but not identical, to those previously reported. However, according to the most recent systematic studies, a clear differentiation of 43 single-species clusters was detected/identified among the sequences analyzed. The slightly higher variability of the hsp60 nucleotide sequences than of the 16S rRNA sequences offers better opportunities to design or develop molecular assays allowing identification and differentiation of either distant or very closely related Lactobacillus species. Therefore, our results suggest that hsp60 can be considered an excellent molecular marker for inferring the taxonomy and phylogeny of members of the genus Lactobacillus and that the chosen primers can be used in a simple PCR procedure allowing the direct sequencing of the hsp60 fragments. Moreover, in this study we performed a computer-aided restriction endonuclease analysis of all 499-bp hsp60 partial sequences and we showed that the PCR-restriction fragment length polymorphism (RFLP) patterns obtainable by using both endonucleases AluI and TacI (in separate reactions) can allow identification and differentiation of all 43 Lactobacillus species considered, with the exception of the pair L. plantarum/L. pentosus. However, the latter species can be differentiated by further analysis with Sau3AI or MseI. The hsp60 PCR-RFLP approach was efficiently applied to identify and to differentiate a total of 110 wild Lactobacillus strains (including closely related species, such as L. casei and L. rhamnosus or L. plantarum and L. pentosus) isolated from cheese and dry-fermented sausages. PMID:17993558

Decoding the spatial signatures of multi-scale climate variability - a climate network perspective

NASA Astrophysics Data System (ADS)

Donner, R. V.; Jajcay, N.; Wiedermann, M.; Ekhtiari, N.; Palus, M.

2017-12-01

During the last years, the application of complex networks as a versatile tool for analyzing complex spatio-temporal data has gained increasing interest. Establishing this approach as a new paradigm in climatology has already provided valuable insights into key spatio-temporal climate variability patterns across scales, including novel perspectives on the dynamics of the El Nino Southern Oscillation or the emergence of extreme precipitation patterns in monsoonal regions. In this work, we report first attempts to employ network analysis for disentangling multi-scale climate variability. Specifically, we introduce the concept of scale-specific climate networks, which comprises a sequence of networks representing the statistical association structure between variations at distinct time scales. For this purpose, we consider global surface air temperature reanalysis data and subject the corresponding time series at each grid point to a complex-valued continuous wavelet transform. From this time-scale decomposition, we obtain three types of signals per grid point and scale - amplitude, phase and reconstructed signal, the statistical similarity of which is then represented by three complex networks associated with each scale. We provide a detailed analysis of the resulting connectivity patterns reflecting the spatial organization of climate variability at each chosen time-scale. Global network characteristics like transitivity or network entropy are shown to provide a new view on the (global average) relevance of different time scales in climate dynamics. Beyond expected trends originating from the increasing smoothness of fluctuations at longer scales, network-based statistics reveal different degrees of fragmentation of spatial co-variability patterns at different scales and zonal shifts among the key players of climate variability from tropically to extra-tropically dominated patterns when moving from inter-annual to decadal scales and beyond. The obtained results demonstrate the potential usefulness of systematically exploiting scale-specific climate networks, whose general patterns are in line with existing climatological knowledge, but provide vast opportunities for further quantifications at local, regional and global scales that are yet to be explored.

Assessment of fragment projection hazard: probability distributions for the initial direction of fragments.

PubMed

Tugnoli, Alessandro; Gubinelli, Gianfilippo; Landucci, Gabriele; Cozzani, Valerio

2014-08-30

The evaluation of the initial direction and velocity of the fragments generated in the fragmentation of a vessel due to internal pressure is an important information in the assessment of damage caused by fragments, in particular within the quantitative risk assessment (QRA) of chemical and process plants. In the present study an approach is proposed to the identification and validation of probability density functions (pdfs) for the initial direction of the fragments. A detailed review of a large number of past accidents provided the background information for the validation procedure. A specific method was developed for the validation of the proposed pdfs. Validated pdfs were obtained for both the vertical and horizontal angles of projection and for the initial velocity of the fragments. Copyright © 2014 Elsevier B.V. All rights reserved.

Neutron Star Mergers and the R process

NASA Astrophysics Data System (ADS)

Joniak, Ronald; Ugalde, Claudio

2017-09-01

About half of the elements of the periodic table that are present today in the Solar System were synthesized before the formation of the Sun via a rapid neutron capture process (r process). However, the astrophysical site of the r process is a longstanding problem that has captivated both experimental and theoretical astrophysicists. Up to date, two possible scenarios for the site of the r process have been suggested: the first involves the high entropy wind of core collapse supernovae, and the second corresponds to the merger of two compact stellar objects such as neutron stars. We will study the robustness of the nucleosynthesis abundance pattern between the second and third r process peaks as produced by neutron star mergers with r process-like neutron exposures. First, we will vary parameters to obtain an understanding of the astrophysical mechanisms that create the r process. Next, we will create a program to obtain the best possible parameters based on a chi-squared test. Once we have the best fits, we will test the effect of fission in the overall isotope abundance pattern distribution. Later on, we will vary the ratio of masses of the two fission fragments and study its effect on elemental abundances. This research was supported by the UIC College of Liberal Arts and Sciences Undergraduate Research Initiative (LASURI).

The vent microbiome: patterns and drivers

NASA Astrophysics Data System (ADS)

Pachiadaki, M.

2015-12-01

Microbial processes within deep-sea hydrothermal vents affect the global biogeochemical cycles. Still, there are significant gaps in our understanding of the microbiology and the biogeochemistry of deep-sea hydrothermal systems. Vents differ in temperature, host rock composition and fluid chemistry; factors that are hypothesized to shape the distribution of the microbial communities, their metabolic capabilities and their activities. Using large-scale single cell genomics, we obtained insights into the genomic content of several linkages of a diffuse flow vent. The genomes show high metabolic versatility. Sulfur oxidation appears to be predominant but there is the potential of using a variety of e- donors and acceptors to obtain energy. To further assess the ecological importance of the vent auto- and heterotrophs, the global biogeography of the analyzed lineages will be investigated by fragment recruitment of metagenomes produced from the same site as well as other hydrothermal systems. Metatranscriptomic and metaproteomic data will be integrated to examine the expression of the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production. The comparative analysis of the key players and associated pathways among various vent sites that differ in physicochemical characteristics is anticipated to decipher the patterns and drivers of the global dispersion and the local diversification of the vent microbiome.

First Monte Carlo analysis of fragmentation functions from single-inclusive e + e - annihilation

DOE PAGES

Sato, Nobuo; Ethier, J. J.; Melnitchouk, W.; ...

2016-12-02

Here, we perform the first iterative Monte Carlo (IMC) analysis of fragmentation functions constrained by all available data from single-inclusive $e^+ e^-$ annihilation into pions and kaons. The IMC method eliminates potential bias in traditional analyses based on single fits introduced by fixing parameters not well contrained by the data, and provides a statistically rigorous determination of uncertainties. Our analysis reveals specific features of fragmentation functions using the new IMC methodology and those obtained from previous analyses, especially for light quarks and for strange quark fragmentation to kaons.

A comment on the validity of fragmentation parameters measured in nuclear emulsions. [cosmic ray nuclei

NASA Technical Reports Server (NTRS)

Waddington, C. J.

1978-01-01

Evidence is reexamined which has been cited as suggesting serious errors in the use of fragmentation parameters appropriate to an airlike medium deduced from measurements made in nuclear emulsions to evaluate corrections for certain effects in balloon-borne observations of cosmic-ray nuclei. Fragmentation parameters for hydrogenlike interactions are calculated and shown to be in overall good agreement with those obtained previously for air. Experimentally measured fragmentation parameters in emulsion are compared with values computed semiempirically, and reasonable agreement is indicated.

Satellite disintegration dynamics

NASA Technical Reports Server (NTRS)

Dasenbrock, R. R.; Kaufman, B.; Heard, W. B.

1975-01-01

The subject of satellite disintegration is examined in detail. Elements of the orbits of individual fragments, determined by DOD space surveillance systems, are used to accurately predict the time and place of fragmentation. Dual time independent and time dependent analyses are performed for simulated and real breakups. Methods of statistical mechanics are used to study the evolution of the fragment clouds. The fragments are treated as an ensemble of non-interacting particles. A solution of Liouville's equation is obtained which enables the spatial density to be calculated as a function of position, time and initial velocity distribution.

Rate equations for nitrogen molecules in ultrashort and intense x-ray pulses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Ji -Cai; Berrah, Nora; Cederbaum, Lorenz S.

Here, we study theoretically the quantum dynamics of nitrogen molecules (N2) exposed to intense and ultrafast x-rays at a wavelength ofmore » $$1.1\\;{\\rm{nm}}$$ ($$1100\\;{\\rm{eV}}$$ photon energy) from the Linac Coherent Light Source (LCLS) free electron laser. Molecular rate equations are derived to describe the intertwined photoionization, decay, and dissociation processes occurring for N2. This model complements our earlier phenomenological approaches, the single-atom, symmetric-sharing, and fragmentation-matrix models of 2012 (J. Chem. Phys. 136 214310). Our rate-equations are used to obtain the effective pulse energy at the sample and the time scale for the dissociation of the metastable dication $${{\\rm{N}}}_{2}^{2+}$$. This leads to a very good agreement between the theoretically and experimentally determined ion yields and, consequently, the average charge states. The effective pulse energy is found to decrease with shortening pulse duration. This variation together with a change in the molecular fragmentation pattern and frustrated absorption—an effect that reduces absorption of x-rays due to (double) core hole formation—are the causes for the drop of the average charge state with shortening LCLS pulse duration discovered previously.« less

Rate equations for nitrogen molecules in ultrashort and intense x-ray pulses

DOE PAGES

Liu, Ji -Cai; Berrah, Nora; Cederbaum, Lorenz S.; ...

2016-03-16

Here, we study theoretically the quantum dynamics of nitrogen molecules (N2) exposed to intense and ultrafast x-rays at a wavelength ofmore » $$1.1\\;{\\rm{nm}}$$ ($$1100\\;{\\rm{eV}}$$ photon energy) from the Linac Coherent Light Source (LCLS) free electron laser. Molecular rate equations are derived to describe the intertwined photoionization, decay, and dissociation processes occurring for N2. This model complements our earlier phenomenological approaches, the single-atom, symmetric-sharing, and fragmentation-matrix models of 2012 (J. Chem. Phys. 136 214310). Our rate-equations are used to obtain the effective pulse energy at the sample and the time scale for the dissociation of the metastable dication $${{\\rm{N}}}_{2}^{2+}$$. This leads to a very good agreement between the theoretically and experimentally determined ion yields and, consequently, the average charge states. The effective pulse energy is found to decrease with shortening pulse duration. This variation together with a change in the molecular fragmentation pattern and frustrated absorption—an effect that reduces absorption of x-rays due to (double) core hole formation—are the causes for the drop of the average charge state with shortening LCLS pulse duration discovered previously.« less

Analysis of 62 synthetic cannabinoids by gas chromatography-mass spectrometry with photoionization.

PubMed

Akutsu, Mamoru; Sugie, Ken-Ichi; Saito, Koichi

2017-01-01

Gas chromatography-mass spectrometry (GC-MS) in electron ionization (EI) mode is one of the most commonly used techniques for analysis of synthetic cannabinoids, because the GC-EI-MS spectra contain characteristic fragment ions for identification of a compound; however, the information on its molecular ions is frequently lacking. To obtain such molecular ion information, GC-MS in chemical ionization (CI) mode is frequently used. However, GC-CI-MS requires a relatively tedious process using reagent gas such as methane or isobutane. In this study, we show that GC-MS in photoionization (PI) mode provided molecular ions in all spectra of 62 synthetic cannabinoids, and 35 of the 62 compounds showed only the molecular radical cations. Except for the 35 compounds, the PI spectra showed very simple patterns with the molecular peak plus only a few fragment peak(s). An advantage is that the ion source for GC-PI-MS can easily be used for GC-EI-MS as well. Therefore, GC-EI/PI-MS will be a useful tool for the identification of synthetic cannabinoids contained in a dubious product. To the best of our knowledge, this is the first report to use GC-PI-MS for analysis of synthetic cannabinoids.

Electronic structure of the benzene dimer cation

NASA Astrophysics Data System (ADS)

Pieniazek, Piotr A.; Krylov, Anna I.; Bradforth, Stephen E.

2007-07-01

The benzene and benzene dimer cations are studied using the equation-of-motion coupled-cluster model with single and double substitutions for ionized systems. The ten lowest electronic states of the dimer at t-shaped, sandwich, and displaced sandwich configurations are described and cataloged based on the character of the constituent fragment molecular orbitals. The character of the states, bonding patterns, and important features of the electronic spectrum are explained using qualitative dimer molecular orbital linear combination of fragment molecular orbital framework. Relaxed ground state geometries are obtained for all isomers. Calculations reveal that the lowest energy structure of the cation has a displaced sandwich structure and a binding energy of 20kcal/mol, while the t-shaped isomer is 6kcal/mol higher. The calculated electronic spectra agree well with experimental gas phase action spectra and femtosecond transient absorption in liquid benzene. Both sandwich and t-shaped structures feature intense charge resonance bands, whose location is very sensitive to the interfragment distance. Change in the electronic state ordering was observed between σ and πu states, which correlate to the B˜ and C˜ bands of the monomer, suggesting a reassignment of the local excitation peaks in the gas phase experimental spectrum.

Distinct compartmentalization of dentin matrix protein 1 fragments in mineralized tissues and cells.

PubMed

Maciejewska, Izabela; Qin, Disheng; Huang, Bingzhen; Sun, Yao; Mues, Gabrielle; Svoboda, Kathy; Bonewald, Lynda; Butler, William T; Feng, Jerry Q; Qin, Chunlin

2009-01-01

Dentin matrix protein 1 (DMP1) has been shown to be critical for the formation of dentin and bone. However, the precise pathway by which DMP1 participates in dentinogenesis and osteogenesis remains to be clarified. DMP1 is present in the extracellular matrix of dentin and bone as processed NH(2)- and COOH-terminal fragments. The NH(2)-terminal fragment occurs as a proteoglycan, whereas the COOH-terminal fragment is highly phosphorylated. The differences in biochemical properties suggest that these fragments may have different tissue and cell distribution in association with distinct functions. In this study, we analyzed the distribution of the NH(2)- and COOH-terminal fragments of DMP1 in tooth, bone, osteocytes as well as MC3T3-E1 and HEK-293 cells. Immunohistochemical analyses were performed using antibodies specific to the NH(2)- or COOH-terminal region of DMP1. Clear differences in the distribution of these fragments were observed. In the teeth and bone, the NH(2)-terminal fragment was primarily located in the nonmineralized predentin and cartilage of the growth plate, while the COOH-terminal fragment accumulated in the mineralized zones. In osteocytes, the NH(2)-terminal fragment appeared more abundant along cell membrane and processes of osteocytes, while the COOH-terminal fragment was often found in the nuclei. This pattern of distribution in cellular compartments was further confirmed by analyses on MC3T3-E1 and HEK-293 cells transfected with a construct containing DMP1 cDNA. In these cell lines, the COOH-terminal fragment accumulated in cell nuclei, while the NH(2)-terminal fragment was in the cytosol. The different distribution of DMP1 fragments indicates that these DMP1 variants must perform distinct functions. Copyright 2008 S. Karger AG, Basel.

Analysis of mexicanolide- and phragmalin-type limonoids from Heynea trijuga using high-performance liquid chromatography/electrospray tandem mass spectrometry.

PubMed

Yang, Wei; Fang, Dong-Mei; He, Hong-Ping; Hao, Xiao-Jiang; Wu, Zhi-Jun; Zhang, Guo-Lin

2013-06-15

Limonoids, a class of tetranortriterpenoids, exhibit various biological effects, including acting as potent antifeedants and insect growth-regulators against various pests. The analysis of phragmalin- and mexicanolide-type limonoids by collision-induced dissociation tandem mass spectrometry (CID-MS/MS) has not been reported. A high-performance liquid chromatography/electrospray ionization (HPLC/ESI)-MS/MS method was developed to investigate the fragmentation patterns of [M+NH4 ](+) ions for nine reference phragmalin- and mexicanolide-type limonoids. The method was also used in the identification of limonoid compounds in botanic extracts of Heynea trijuga. The losses of side chains and the furan part were the major fragmentation patterns. However, there was variation in the relative abundances of product ions resulting from the same fragmentation pathways. A total of 89 phragmalin- and mexicanolide-type limonoids in botanic extracts of Heynea trijuga were detected and 50 of these compounds were identified or tentatively characterized based on elemental constituents, fragmentation pathways, and the profile of the major product ions of reference compounds. In addition, the isomers could be tentatively distinguished. An HPLC/ESI-MS/MS method was developed and could be used to simultaneously identify and screen phragmalin- and mexicanolide-type limonoids in botanic extracts of Heynea trijuga. Copyright © 2013 John Wiley & Sons, Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Yingying; Triscari, Joseph M.; Tseng, George C.

Data mining was performed on 28 330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pairwise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly charged Arg- and Lys-ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides,more » a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton. When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions, y ions, or both depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion intensities.« less

Sleeping Sites and Latrines of Spider Monkeys in Continuous and Fragmented Rainforests: Implications for Seed Dispersal and Forest Regeneration

PubMed Central

González-Zamora, Arturo; Arroyo-Rodríguez, Víctor; Oyama, Ken; Sork, Victoria; Chapman, Colin A.; Stoner, Kathryn E.

2012-01-01

Spider monkeys (Ateles geoffroyi) use sites composed of one or more trees for sleeping (sleeping sites and sleeping trees, respectively). Beneath these sites/trees they deposit copious amounts of dung in latrines. This behavior results in a clumped deposition pattern of seeds and nutrients that directly impacts the regeneration of tropical forests. Therefore, information on the density and spatial distribution of sleeping sites and latrines, and the characteristics (i.e., composition and structure) of sleeping trees are needed to improve our understanding of the ecological significance of spider monkeys in influencing forest composition. Moreover, since primate populations are increasingly forced to inhabit fragmented landscapes, it is important to assess if these characteristics differ between continuous and fragmented forests. We assessed this novel information from eight independent spider monkey communities in the Lacandona rainforest, Mexico: four continuous forest sites and four forest fragments. Both the density of sleeping sites and latrines did not differ between forest conditions. Latrines were uniformly distributed across sleeping sites, but the spatial distribution of sleeping sites within the areas was highly variable, being particularly clumped in forest fragments. In fact, the average inter-latrine distances were almost double in continuous forest than in fragments. Latrines were located beneath only a few tree species, and these trees were larger in diameter in continuous than fragmented forests. Because latrines may represent hotspots of seedling recruitment, our results have important ecological and conservation implications. The variation in the spatial distribution of sleeping sites across the forest indicates that spider monkeys likely create a complex seed deposition pattern in space and time. However, the use of a very few tree species for sleeping could contribute to the establishment of specific vegetation associations typical of the southeastern Mexican rainforest, such as Terminalia-Dialium, and Brosimum-Dialium. PMID:23056486

Native top-down mass spectrometry for the structural characterization of human hemoglobin

DOE PAGES

Zhang, Jiang; Malmirchegini, G. Reza; Clubb, Robert T.; ...

2015-06-09

Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and non-covalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down mass spectrometry using electrospray ionization (ESI) and a 15-Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Native MS preserves the non-covalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of themore » Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore low fragmentation efficiency. Precursor ion activation allows steady increase of N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and 4 z ions on the α chain; 36 c ions and 2 z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer show similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. Finally, it may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.« less

Sleeping sites and latrines of spider monkeys in continuous and fragmented rainforests: implications for seed dispersal and forest regeneration.

PubMed

González-Zamora, Arturo; Arroyo-Rodríguez, Víctor; Oyama, Ken; Sork, Victoria; Chapman, Colin A; Stoner, Kathryn E

2012-01-01

Spider monkeys (Ateles geoffroyi) use sites composed of one or more trees for sleeping (sleeping sites and sleeping trees, respectively). Beneath these sites/trees they deposit copious amounts of dung in latrines. This behavior results in a clumped deposition pattern of seeds and nutrients that directly impacts the regeneration of tropical forests. Therefore, information on the density and spatial distribution of sleeping sites and latrines, and the characteristics (i.e., composition and structure) of sleeping trees are needed to improve our understanding of the ecological significance of spider monkeys in influencing forest composition. Moreover, since primate populations are increasingly forced to inhabit fragmented landscapes, it is important to assess if these characteristics differ between continuous and fragmented forests. We assessed this novel information from eight independent spider monkey communities in the Lacandona rainforest, Mexico: four continuous forest sites and four forest fragments. Both the density of sleeping sites and latrines did not differ between forest conditions. Latrines were uniformly distributed across sleeping sites, but the spatial distribution of sleeping sites within the areas was highly variable, being particularly clumped in forest fragments. In fact, the average inter-latrine distances were almost double in continuous forest than in fragments. Latrines were located beneath only a few tree species, and these trees were larger in diameter in continuous than fragmented forests. Because latrines may represent hotspots of seedling recruitment, our results have important ecological and conservation implications. The variation in the spatial distribution of sleeping sites across the forest indicates that spider monkeys likely create a complex seed deposition pattern in space and time. However, the use of a very few tree species for sleeping could contribute to the establishment of specific vegetation associations typical of the southeastern Mexican rainforest, such as Terminalia-Dialium, and Brosimum-Dialium.

Central cardiovascular and behavioral effects of carboxy- and amino-terminal fragments of substance P in conscious rats.

PubMed

Tschöpe, C; Jost, N; Unger, T; Culman, J

1995-08-28

The central cardiovascular and behavioral effects of carboxy- (SP 5-11, SP 6-11, SP 7-11, SP 8-11) and amino- (SP 1-7, SP 1-9) terminal substance P (SP) fragments were compared with those of SP 1-11 in conscious rats. In addition, the ability of these SP-fragments to induce desensitization of the central NK1 receptor was investigated. SP 1-11 (50 pmol) injected i.c.v. induced an increase in mean arterial blood pressure (MAP), heart rate (HR) and a typical behavioral response consisting of face washing (FW), hindquarter grooming (HQG) and wet-dog shakes (WDS). The cardiovascular and behavioral responses to equimolar doses of SP 5-11 and SP 6-11 were similar to those of SP 1-11, however, only SP 5-11 induced exactly the same behavioral pattern as SP 1-11. SP 6-11 was more potent in inducing FW and WDS than SP 1-11 or SP 5-11. The carboxy-terminal SP-fragments, SP 7-11 and SP 8-11, and the amino-terminal SP-fragments, SP 1-7, SP 1-9, did not elicit any significant cardiovascular or behavioral responses. Pretreatment with SP 1-11 reduced the cardiovascular and behavioral responses to subsequent injections of SP 1-11. Of all SP-fragments tested, only SP 5-11 was able to attenuate the cardiovascular and behavioral responses to SP 1-11. Our results demonstrate that SP 6-11 represents the shortest carboxy-terminal amino acid sequence, that after i.c.v. injection, elicits the same cardiovascular response as SP 1-11, but fails to desensitize the NK1 receptor. The carboxy-terminal fragment, SP 5-11, is the shortest amino acid sequence which produces the same pattern of central cardiovascular and behavioral responses as SP 1-11 and also retains the ability to desensitize the NK1 receptor like SP 1-11.

Fluidized bed combustion of pelletized biomass and waste-derived fuels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chirone, R.; Scala, F.; Solimene, R.

2008-10-15

The fluidized bed combustion of three pelletized biogenic fuels (sewage sludge, wood, and straw) has been investigated with a combination of experimental techniques. The fuels have been characterized from the standpoints of patterns and rates of fuel devolatilization and char burnout, extent of attrition and fragmentation, and their relevance to the fuel particle size distribution and the amount and size distribution of primary ash particles. Results highlight differences and similarities among the three fuels tested. The fuels were all characterized by limited primary fragmentation and relatively long devolatilization times, as compared with the time scale of particle dispersion away frommore » the fuel feeding ports in practical FBC. Both features are favorable to effective lateral distribution of volatile matter across the combustor cross section. The three fuels exhibited distinctively different char conversion patterns. The high-ash pelletized sludge burned according to the shrinking core conversion pattern with negligible occurrence of secondary fragmentation. The low-ash pelletized wood burned according to the shrinking particle conversion pattern with extensive occurrence of secondary fragmentation. The medium-ash pelletized straw yielded char particles with a hollow structure, resembling big cenospheres, characterized by a coherent inorganic outer layer strong enough to prevent particle fragmentation. Inert bed particles were permanently attached to the hollow pellets as they were incorporated into ash melts. Carbon elutriation rates were very small for all the fuels tested. For pelletized sludge and straw, this was mostly due to the shielding effect of the coherent ash skeleton. For the wood pellet, carbon attrition was extensive, but was largely counterbalanced by effective afterburning due to the large intrinsic reactivity of attrited char fines. The impact of carbon attrition on combustion efficiency was negligible for all the fuels tested. The size distribution of primary ash particles liberated upon complete carbon burnoff largely reflected the combustion pattern of each fuel. Primary ash particles of size nearly equal to that of the parent fuel were generated upon complete burnoff of the pelletized sludge. Nonetheless, secondary attrition of primary ash from pelletized sludge is large, to the point where generation of fine ash would be extensive over the typical residence time of bed ash in fluidized bed combustors. Very few and relatively fine primary ash particles were released after complete burnoff of wood pellets. Primary ash particles remaining after complete burnoff of pelletized straw had sizes and shapes that were largely controlled by the occurrence of ash agglomeration phenomena. (author)« less

Spinopelvic dissociation: multidetector computed tomographic evaluation of fracture patterns and associated injuries at a single level 1 trauma center.

PubMed

Gupta, Pushpender; Barnwell, Jonathan C; Lenchik, Leon; Wuertzer, Scott D; Miller, Anna N

2016-06-01

The objective of the present study is to evaluate multidetector computed tomographic (MDCT) fracture patterns and associated injuries in patients with spinopelvic dissociation (SPD). Our institutional trauma registry database was reviewed from Jan. 1, 2006, to Sept. 30, 2012, specifically evaluating patients with sacral fractures. MDCT scans of patients with sacral fractures were reviewed to determine the presence of SPD. SPD cases were characterized into the following fracture patterns: U-shaped, Y-shaped, T-shaped, H-shaped, and burst. The following MDCT features were recorded: level of the horizontal fracture, location of vertical fracture, kyphosis between major fracture fragments, displacement of fracture fragment, narrowing of central spinal canal, narrowing of neural foramina, and extension into sacroiliac joints. Quantitative evaluation of the sacral fractures was performed in accordance with the consensus statement by the Spine Trauma Study Group. Medical records were reviewed to determine associated pelvic and non-pelvic fractures, bladder and bowel injuries, nerve injuries, and type of surgical intervention. Twenty-one patients had SPD, of whom 13 were men and eight were women. Mean age was 41.8 years (range 18.8 to 87.7). Five fractures (24 %) were U-shaped, six (29 %) H-shaped, four (19 %) Y-shaped, and six (29 %) burst. Nine patients (43 %) had central canal narrowing, and 19 (90 %) had neural foramina narrowing. Eleven patients (52 %) had kyphotic angulation between major fracture fragments, and seven patients (33 %) had either anterior (24 %) or posterior (10 %) displacement of the proximal fracture fragment. Fourteen patients (67 %) had associated pelvic fractures, and 20 (95 %) had associated non-pelvic fractures. Two patients (10 %) had associated urethral injuries, and one (5 %) had an associated colon injury. Seven patients (33 %) had associated nerve injuries. Six patients (29 %) had surgical fixation while 15 (71 %) were managed non-operatively. On trauma MDCT examinations, patients with SPD have characteristic fracture patterns. It is important to differentiate SPD from other pelvic ring injuries due to high rate of associated injuries. Although all SPD injuries are unstable and need fixation, the decision for operative management in an individual patient depends on the systemic injury pattern, specific fracture pattern, and the ability to attain stable screw fixation.

A test of the Feynman scaling in the fragmentation region

NASA Technical Reports Server (NTRS)

Doke, T.; Innocente, V.; Kasahara, K.; Kikuchi, J.; Kashiwagi, T.; Lanzano, S.; Masuda, K.; Murakami, H.; Muraki, Y.; Nakada, T.

1985-01-01

The result of the direct measurement of the fragmentation region will be presented. The result will be obtained at the CERN proton-antiproton collider, being exposured the Silicon calorimeters inside beam pipe. This experiment clarifies a long riddle of cosmic ray physics, whether the Feynman scaling does villate at the fragmentation region or the Iron component is increasing at 10 to the 15th power eV.

Fragmentation Cross Sections of 290 and 400 MeV/nucleon 12C Beamson Elemental Targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeitlin, C.; Guetersloh, S.; Heilbronn, L.

Charge-changing and fragment production cross sections at 0circ have been obtained for interactions of 290 MeV/nucleon and 400MeV/nucleon carbon beams with C, CH2, Al, Cu, Sn, and Pb targets. Thesebeams are relevant to cancer therapy, space radiation, and the productionof radioactive beams. We compare to previously published results using Cand CH2 targets at similar beam energies. Due to ambiguities arising fromthe presence of multiple fragments on many events, previous publicationshave reported only cross sections for B and Be fragments. In this work wehave extracted cross sections for all fragment species, using dataobtained at three distinct values of angular acceptance, supplementedmore » bydata taken with the detector stack placed off the beam axis. A simulationof the experiment with the PHITS Monte Carlo code shows fair agreementwith the data obtained with the large acceptance detectors, but agreementis poor at small acceptance. The measured cross sections are alsocompared to the predictions of the one-dimensional cross section modelsEPAX2 and NUCFRG2; the latter is presently used in NASA's space radiationtransport calculations. Though PHITS and NUCFRG2 reproduce thecharge-changing cross sections with reasonable accuracy, none of themodels is able to accurately predict the fragment cross sections for allfragment species and target materials.« less

Mass Extinction and the Disappearance of Unknown Mammal Species: Scenario and Perspectives of a Biodiversity Hotspot’s Hotspot

PubMed Central

Mendes Pontes, Antonio Rossano; Beltrão, Antonio Carlos Mariz; Normande, Iran Campello; Malta, Alexandre de Jesus Rodrigues; da Silva Júnior, Antonio Paulo; Santos, André Maurício Melo

2016-01-01

We aimed to determine the conservation status of medium- and large-sized mammals and evaluate the impact of 500 years of forest fragmentation on this group of animals in the Pernambuco Endemism Center, in the biogeographical zone of the Atlantic forest north of the São Francisco River in northeastern Brazil. Line transect surveys were performed in 21 forest fragments, resulting in a checklist of the mammals of the entire Pernambuco Endemism Center area. We ran a generalized linear model (Factorial ANCOVA) to analyze to what extent the vegetation type, fragment area, isolation, sampling effort (as total kilometers walked), or higher-order interactions predicted (a) richness and (b) sighting rates. To determine if the distribution of the species within the forest fragments exhibited a nested pattern, we used the NODF metric. Subsequently, we performed a Binomial Logistic Regression to predict the probability of encountering each species according to fragment size. Out of 38 medium- and large-sized mammal species formerly occurring in the study area, only 53.8% (n = 21) were sighted. No fragment hosted the entire remaining mammal community, and only four species (19%) occurred in very small fragments (73.3% of the remaining forest fragments, with a mean size of 2.8 ha). The mammalian community was highly simplified, with all large mammals being regionally extinct. Neither the species richness nor sighting rate was controlled by the vegetation type, the area of the forest fragments, isolation or any higher-order interaction. Although a highly significant nested subset pattern was detected, it was not related to the ranking of the area of forest fragments or isolation. The probability of the occurrence of a mammal species in a given forest patch varied unpredictably, and the probability of detecting larger species was even observed to decrease with increasing patch size. In an ongoing process of mass extinction, half of the studied mammals have gone extinct. The remaining medium-sized mammal community is highly simplified and homogenized. The persistence of these species in a forest patch is determined by their ability to adapt to a novel simplified diet, the efficient use of the surrounding matrix without being engulfed by the sink effect, and escaping hunting. Our results suggest that the 21st century medium-sized mammalian fauna of this region will comprise only four species unless strict conservation measures are implemented immediately and every forest fragment is effectively protected. PMID:27191719

Mass Extinction and the Disappearance of Unknown Mammal Species: Scenario and Perspectives of a Biodiversity Hotspot's Hotspot.

PubMed

Mendes Pontes, Antonio Rossano; Beltrão, Antonio Carlos Mariz; Normande, Iran Campello; Malta, Alexandre de Jesus Rodrigues; Silva Júnior, Antonio Paulo da; Santos, André Maurício Melo

2016-01-01

We aimed to determine the conservation status of medium- and large-sized mammals and evaluate the impact of 500 years of forest fragmentation on this group of animals in the Pernambuco Endemism Center, in the biogeographical zone of the Atlantic forest north of the São Francisco River in northeastern Brazil. Line transect surveys were performed in 21 forest fragments, resulting in a checklist of the mammals of the entire Pernambuco Endemism Center area. We ran a generalized linear model (Factorial ANCOVA) to analyze to what extent the vegetation type, fragment area, isolation, sampling effort (as total kilometers walked), or higher-order interactions predicted (a) richness and (b) sighting rates. To determine if the distribution of the species within the forest fragments exhibited a nested pattern, we used the NODF metric. Subsequently, we performed a Binomial Logistic Regression to predict the probability of encountering each species according to fragment size. Out of 38 medium- and large-sized mammal species formerly occurring in the study area, only 53.8% (n = 21) were sighted. No fragment hosted the entire remaining mammal community, and only four species (19%) occurred in very small fragments (73.3% of the remaining forest fragments, with a mean size of 2.8 ha). The mammalian community was highly simplified, with all large mammals being regionally extinct. Neither the species richness nor sighting rate was controlled by the vegetation type, the area of the forest fragments, isolation or any higher-order interaction. Although a highly significant nested subset pattern was detected, it was not related to the ranking of the area of forest fragments or isolation. The probability of the occurrence of a mammal species in a given forest patch varied unpredictably, and the probability of detecting larger species was even observed to decrease with increasing patch size. In an ongoing process of mass extinction, half of the studied mammals have gone extinct. The remaining medium-sized mammal community is highly simplified and homogenized. The persistence of these species in a forest patch is determined by their ability to adapt to a novel simplified diet, the efficient use of the surrounding matrix without being engulfed by the sink effect, and escaping hunting. Our results suggest that the 21st century medium-sized mammalian fauna of this region will comprise only four species unless strict conservation measures are implemented immediately and every forest fragment is effectively protected.

Communication: Identification of daughter ions through their electronic spectroscopy at low temperature

NASA Astrophysics Data System (ADS)

Dedonder, Claude; Féraud, Géraldine; Jouvet, Christophe

2014-10-01

We present experimental results on photofragmentation of cooled fragments issued from the photofragmentation of cold parent ions. The cooling of the daughter ions at a few K allows its characterization not only through its fragmentation pattern but also through its well resolved electronic spectroscopy. The proof of principle of the method is demonstrated on the photofragment resulting from Cα-Cβ bond rupture in protonated tyrosine (TyrH+). The analysis of the daughter ion (m/z 108) photofragmentation spectrum is in agreement with the proposed mechanism implying a proton transfer to the phenyl ring as the first step of the fragmentation mechanism of TyrH+.

Intermediate mass fragment emission and iso-scaling in dissipative Ca+Sn reactions at 45 AMeV

NASA Astrophysics Data System (ADS)

Singh, H.; Quinlan, M. J.; Tõke, J.; Pawelczak, I.; Henry, E.; Schröder, W. U.; Amorini, F.; Anzalone, A.; Maiolino, C.; Auditore, L.; Loria, D.; Trifiro, A.; Trimarchi, M.; Cardella, G.; De Filippo, E.; Pagano, A.; Chatterjee, M. B.; Cavallaro, S.; Geraci, E.; Papa, M.; Pirrone, S.; Verde, G.; Grzeszczuk, A.; Guazzoni, P.; Zetta, L.; La Guidara, E.; Lanzalone, G.; Lo Nigro, S.; Politi, G.; Loria, D.; Porto, F.; Rizzo, F.; Russotto, P.; Vigilante, M.

2013-04-01

The production mechanism of intermediate-mass fragments (IMFs) with atomic numbers Z = 3 - 7 is explored in the intermediate energy regime, studying dissipative 48Ca+112Sn and 48Ca+124Sn reactions at E/A = 45MeV. Various aspects of IMF emission patterns point to an inelastic break-up type production mechanism involving excited projectile-like fragment from dissipative interactions. Isotopic yield ratios of identical IMFs from the above two dissipative reactions have been analysed using the "isoscaling" method. Observed trends are correlated with ground-state binding energy systematics and their relevance for an evaluation of the symmetry energy is discussed.

Antimicrobial susceptibility and genetic relatedness of respiratory tract pathogens in weaner pigs over a 12-month period.

PubMed

Niemann, Lisa; Müller, Petra; Brauns, Jasmin; Nathaus, Rolf; Schäkel, Franziska; Kipschull, Kerstin; Höltig, Doris; Wendt, Michael; Schwarz, Stefan; Kadlec, Kristina

2018-06-01

The collaboration project VASIB aims at reducing the antibiotic consumption in pig production by integrating information from consulting expertise in clinical inspection, hygiene, epidemiology, microbiology and pharmacology. In this VASIB subproject, we investigated the antimicrobial susceptibility and relatedness of porcine respiratory tract pathogens. Bordetella bronchiseptica (n = 47), Pasteurella multocida (n = 18) and Streptococcus suis (n = 58) were obtained from weaner pigs at two farms. Antimicrobial susceptibility testing was performed by broth microdilution according to CLSI standards. Resistance genes were detected via specific PCR assays. Macrorestriction analysis was conducted to determine the relatedness of the isolates and to identify clones. The B. bronchiseptica isolates showed indistinguishable (farm 1) or two closely related XbaI-patterns (farm 2). Different SmaI-PFGE patterns of P. multocida isolates were obtained at three different time points. In contrast, PFGE analysis of S. suis indicated more than one fragment pattern per pig and time point. Isolates exhibiting indistinguishable PFGE patterns were considered to represent the same clone. This study showed that only two closely related B. bronchiseptica clones were present in both farms, which had low MICs to all antimicrobials, except to β-lactams. Different P. multocida clones were present at the three time points. They showed overall low MIC values, with two clones being resistant and one intermediate to tetracycline. S. suis clones were resistant to tetracycline (n = 19) and/or erythromycin/clindamycin (n = 16). They harboured the tetracycline resistance genes tet(O), tet(M) or tet(L) and/or the macrolide/lincosamide/streptogramin B resistance gene erm(B). Five penicillin-resistant S. suis clones were also detected. Copyright © 2018 Elsevier B.V. All rights reserved.

Temporal bird community dynamics are strongly affected by landscape fragmentation in a Central American tropical forest region

USGS Publications Warehouse

Blandón, A.C.; Perelman, S.B.; Ramírez, M.; López, A.; Javier, O.; Robbins, Chandler S.

2016-01-01

Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.

Biophysical modeling of fragment length distributions of DNA plasmids after X and heavy-ion irradiation analyzed by atomic force microscopy.

PubMed

Elsässer, Thilo; Brons, Stephan; Psonka, Katarzyna; Scholz, Michael; Gudowska-Nowak, Ewa; Taucher-Scholz, Gisela

2008-06-01

The investigation of fragment length distributions of plasmid DNA gives insight into the influence of localized energy distribution on the induction of DNA damage, particularly the clustering of double-strand breaks. We present an approach that determines the fragment length distributions of plasmid DNA after heavy-ion irradiation by using the Local Effect Model. We find a good agreement of our simulations with experimental fragment distributions derived from atomic force microscopy (AFM) studies by including experimental constraints typical for AFM. Our calculations reveal that by comparing the fragmentation in terms of fluence, we can uniquely distinguish the effect of different radiation qualities. For very high-LET irradiation using nickel or uranium ions, no difference between their fragment distributions can be expected for the same dose level. However, for carbon ions with an intermediate LET, the fragmentation pattern differs from the distribution for very high-LET particles. The results of the model calculations can be used to determine the optimal experimental parameters for a demonstration of the influence of track structure on primary radiation damage. Additionally, we compare the results of our model for two different plasmid geometries.

An extended patch-dynamic framework for food chains in fragmented landscapes

PubMed Central

Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E.; Nijs, Ivan

2016-01-01

Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

Ion-polycyclic aromatic hydrocarbon collisions: kinetic energy releases for specific fragmentation channels

NASA Astrophysics Data System (ADS)

Reitsma, G.; Zettergren, H.; Boschman, L.; Bodewits, E.; Hoekstra, R.; Schlathölter, T.

2013-12-01

We report on 30 keV He2 + collisions with naphthalene (C10H8) molecules, which leads to very extensive fragmentation. To unravel such complex fragmentation patterns, we designed and constructed an experimental setup, which allows for the determination of the full momentum vector by measuring charged collision products in coincidence in a recoil ion momentum spectrometer type of detection scheme. The determination of fragment kinetic energies is found to be considerably more accurate than for the case of mere coincidence time-of-flight spectrometers. In fission reactions involving two cationic fragments, typically kinetic energy releases of 2-3 eV are observed. The results are interpreted by means of density functional theory calculations of the reverse barriers. It is concluded that naphthalene fragmentation by collisions with keV ions clearly is much more violent than the corresponding photofragmentation with energetic photons. The ion-induced naphthalene fragmentation provides a feedstock of various small hydrocarbonic species of different charge states and kinetic energy, which could influence several molecule formation processes in the cold interstellar medium and facilitates growth of small hydrocarbon species on pre-existing polycyclic aromatic hydrocarbons.

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin.

PubMed

Floris, Federico; Chiron, Lionel; Lynch, Alice M; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

2018-06-04

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.

Fragmentation of negative ions from N-linked carbohydrates, part 4. Fragmentation of complex glycans lacking substitution on the 6-antenna.

PubMed

Harvey, David J; Jaeken, Jaak; Butler, Mike; Armitage, Alison J; Rudd, Pauline M; Dwek, Raymond A

2010-05-01

Negative ion CID spectra of N-linked glycans released from glycoproteins contain many ions that are diagnostic for specific structural features such as the detailed arrangement of antennae and the location of fucose residues. Identification of such ions requires reference glycans that are often difficult to acquire in a pure state. The recent acquisition of a sample of N-glycans from a patient lacking the enzyme N-acetylglucosaminyltransferase-2 provided an opportunity to investigate fragmentation of glycans lacking a 6-antenna. These glycans contained one or two galactose-N-acetylglucosamine-chains attached to the 3-linked mannose residue of the trimannosyl-chitobiose core with and without fucose substitution. The spectra from the patient sample clearly defined the antenna distribution and showed striking differences from the spectra of isomeric compounds obtained from normal subjects. Furthermore, they provided additional information on previously identified antenna-specific fragment ions and indicated the presence of additional ions that were diagnostic of fucose substitution. Glycans obtained from such enzyme-deficient patients can, thus, be a valuable way of obtaining spectra of specific isomers in a relatively pure state for interpretation of mass spectra. 2010 John Wiley & Sons, Ltd.

Natural age dispersion arising from the analysis of broken crystals. Part I: Theoretical basis and implications for the apatite (U-Th)/He thermochronometer

NASA Astrophysics Data System (ADS)

Brown, Roderick W.; Beucher, Romain; Roper, Steven; Persano, Cristina; Stuart, Fin; Fitzgerald, Paul

2013-12-01

Over the last decade major progress has been made in developing both the theoretical and practical aspects of apatite (U-Th)/He thermochronometry and it is now standard practice, and generally seen as best practice, to analyse single grain aliquots. These individual prismatic crystals are often broken and are fragments of larger crystals that have broken during mineral separation along the weak basal cleavage in apatite. This is clearly indicated by the common occurrence of only 1 or no clear crystal terminations present on separated apatite grains, and evidence of freshly broken ends when grains are viewed using a scanning electron microscope. This matters because if the 4He distribution within the whole grain is not homogeneous, because of partial loss due to thermal diffusion for example, then the fragments will all yield ages different from each other and from the whole grain age. Here we use a numerical model with a finite cylinder geometry to approximate 4He ingrowth and thermal diffusion within hexagonal prismatic apatite crystals. This is used to quantify the amount and patterns of inherent, natural age dispersion that arises from analysing broken crystals. A series of systematic numerical experiments were conducted to explore and quantify the pattern and behaviour of this source of dispersion using a set of 5 simple thermal histories that represent a range of plausible geological scenarios. In addition some more complex numerical experiments were run to investigate the pattern and behaviour of grain dispersion seen in several real data sets. The results indicate that natural dispersion of a set of single fragment ages (defined as the range divided by the mean) arising from fragmentation alone varies from c. 7% even for rapid (c. 10 °C/Ma), monotonic cooling to over 50% for protracted, complex histories that cause significant diffusional loss of 4He. The magnitude of dispersion arising from fragmentation scales with the grain cylindrical radius, and is of a similar magnitude to dispersion expected from differences in absolute grain size alone (spherical equivalent radii of 40-150 μm). This source of dispersion is significant compared with typical analytical uncertainties on individual grain analyses (c. 6%) and standard deviations on multiple grain analyses from a single sample (c. 10-20%). Where there is a significant difference in the U and Th concentration of individual grains (eU), the effect of radiation damage accumulation on 4He diffusivity (assessed using the RDAAM model of Flowers et al. (2009)) is the primary cause of dispersion for samples that have experienced a protracted thermal history, and can cause dispersion in excess of 100% for realistic ranges of eU concentration (i.e. 5-100 ppm). Expected natural dispersion arising from the combined effects of reasonable variations in grain size (radii 40-125 μm), eU concentration (5-150 ppm) and fragmentation would typically exceed 100% for complex thermal histories. In addition to adding a significant component of natural dispersion to analyses, the effect of fragmentation also acts to decouple and corrupt expected correlations between grain ages and absolute grain size and to a lesser extent between grain age and effective uranium concentration (eU). Considering fragmentation explicitly as a source of dispersion and analysing how the different sources of natural dispersion all interact with each other provides a quantitative framework for understanding patterns of dispersion that otherwise appear chaotic. An important outcome of these numerical experiments is that they demonstrate that the pattern of age dispersion arising from fragmentation mimics the pattern of 4He distribution within the whole grains, thus providing an important source of information about the thermal history of the sample. We suggest that if the primary focus of a study is to extract the thermal history information from (U-Th)/He analyses then sampling and analytical strategies should aim to maximise the natural dispersion of grain ages, not minimise it, and should aim to analyse circa 20-30 grains from each sample. The key observations and conclusions drawn here are directly applicable to other thermochronometers, such as the apatite, rutile and titanite U-Pb systems, where the diffusion domain is approximated by the physical grain size.

Fragmentation scaling of percolation clusters in two and three dimensions: Large-cell Monte Carlo RG approach

NASA Astrophysics Data System (ADS)

Cheon, M.; Chang, I.

1999-04-01

The scaling behavior for a binary fragmentation of critical percolation clusters is investigated by a large-cell Monte Carlo real-space renormalization group method in two and three dimensions. We obtain accurate values of critical exponents λ and phi describing the scaling of fragmentation rate and the distribution of fragments' masses produced by a binary fragmentation. Our results for λ and phi show that the fragmentation rate is proportional to the size of mother cluster, and the scaling relation σ = 1 + λ - phi conjectured by Edwards et al. to be valid for all dimensions is satisfied in two and three dimensions, where σ is the crossover exponent of the average cluster number in percolation theory, which excludes the other scaling relations.

The Impact of Phosphorylation on Electron Capture Dissociation of Proteins: A Top-Down Perspective

NASA Astrophysics Data System (ADS)

Chen, Bifan; Guo, Xiao; Tucholski, Trisha; Lin, Ziqing; McIlwain, Sean; Ge, Ying

2017-09-01

Electron capture dissociation (ECD) is well suited for the characterization of phosphoproteins, with which labile phosphate groups are generally preserved during the fragmentation process. However, the impact of phosphorylation on ECD fragmentation of intact proteins remains unclear. Here, we have performed a systematic investigation of the phosphorylation effect on ECD of intact proteins by comparing the ECD cleavages of mono-phosphorylated α-casein, multi-phosphorylated β-casein, and immunoaffinity-purified phosphorylated cardiac troponin I with those of their unphosphorylated counterparts, respectively. In contrast to phosphopeptides, phosphorylation has significantly reduced deleterious effects on the fragmentation of intact proteins during ECD. On a global scale, the fragmentation patterns are highly comparable between unphosphorylated and phosphorylated precursors under the same ECD conditions, despite a slight decrease in the number of fragment ions observed for the phosphorylated forms. On a local scale, single phosphorylation of intact proteins imposes minimal effects on fragmentation near the phosphorylation sites, but multiple phosphorylations in close proximity result in a significant reduction of ECD bond cleavages. [Figure not available: see fulltext.

Seed-dispersal distributions by trumpeter hornbills in fragmented landscapes

PubMed Central

Lenz, Johanna; Fiedler, Wolfgang; Caprano, Tanja; Friedrichs, Wolfgang; Gaese, Bernhard H.; Wikelski, Martin; Böhning-Gaese, Katrin

2011-01-01

Frugivorous birds provide important ecosystem services by transporting seeds of fleshy fruited plants. It has been assumed that seed-dispersal kernels generated by these animals are generally leptokurtic, resulting in little dispersal among habitat fragments. However, little is known about the seed-dispersal distribution generated by large frugivorous birds in fragmented landscapes. We investigated movement and seed-dispersal patterns of trumpeter hornbills (Bycanistes bucinator) in a fragmented landscape in South Africa. Novel GPS loggers provide high-quality location data without bias against recording long-distance movements. We found a very weakly bimodal seed-dispersal distribution with potential dispersal distances up to 14.5 km. Within forest, the seed-dispersal distribution was unimodal with an expected dispersal distance of 86 m. In the fragmented agricultural landscape, the distribution was strongly bimodal with peaks at 18 and 512 m. Our results demonstrate that seed-dispersal distributions differed when birds moved in different habitat types. Seed-dispersal distances in fragmented landscapes show that transport among habitat patches is more frequent than previously assumed, allowing plants to disperse among habitat patches and to track the changing climatic conditions. PMID:21177686

rRNA gene restriction patterns as an epidemiological marker in nosocomial outbreaks of Staphylococcus aureus infections.

PubMed

Meugnier, H; Fernandez, M P; Bes, M; Brun, Y; Bornstein, N; Freney, J; Fleurette, J

1993-01-01

rRNA gene restriction patterns (ribotyping) were compared with phage typing, serotyping, enterotoxins and exfoliatin production in the analysis of 26 Staphylococcus aureus strains isolated from two different nosocomial outbreaks. Total DNA was cleaved by EcoRI restriction endonuclease. After agarose gel electrophoresis and Southern transfer, the hybridization of the membranes was done with radiolabelled 16S rRNA gene from Bacillus subtilis inserted into a plasmid vector. Six to 13 fragments were visualized. A core of common fragments was discerned for all strains tested. A full correlation between ribotyping and conventional markers was observed in only one of the outbreaks studied. In both outbreaks, ribotyping proved helpful in characterizing otherwise untypable strains.

Angular distribution of scission neutrons studied with time-dependent Schrödinger equation

NASA Astrophysics Data System (ADS)

Wada, Takahiro; Asano, Tomomasa; Carjan, Nicolae

2018-03-01

We investigate the angular distribution of scission neutrons taking account of the effects of fission fragments. The time evolution of the wave function of the scission neutron is obtained by integrating the time-dependent Schrodinger equation numerically. The effects of the fission fragments are taken into account by means of the optical potentials. The angular distribution is strongly modified by the presence of the fragments. In the case of asymmetric fission, it is found that the heavy fragment has stronger effects. Dependence on the initial distribution and on the properties of fission fragments is discussed. We also discuss on the treatment of the boundary to avoid artificial reflections

Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions.

PubMed

Li, Hui; Li, Wei; Li, Shuhua; Ma, Jing

2008-06-12

Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.

Universality of fragment shapes.

PubMed

Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

2015-03-16

The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism.

Universality of fragment shapes

PubMed Central

Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

2015-01-01

The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism. PMID:25772300

Crystallization of DNA fragments from water-salt solutions, containing 2-methylpentane-2,3-diol.

PubMed

Osica, V D; Sukharevsky, B Y; Vasilchenko, V N; Verkin, B I; Polyvtsev, O F

1976-09-01

Fragments of calf thymus DNA have been crystallized by precipitation from water-salt solutions, containing 2-methylpentane-2,3-diol (MPD). DNA crystals usually take the form either of spherulites up to 100 mu in diameter or of needles with the length up to 50 mu. No irreversible denaturation of DNA occurs during the crystallization process. X-ray diffraction from dense slurries of DNA crystals yields crystalline powder patterns.

Effects of food availability and climate on activity patterns of western black-crested gibbons in an isolated forest fragment in southern Yunnan, China.

PubMed

Ni, Qingyong; Xie, Meng; Grueter, Cyril C; Jiang, Xuelong; Xu, Huailiang; Yao, Yongfang; Zhang, Mingwang; Li, Yan; Yang, Jiandong

2015-10-01

The critically endangered western black-crested gibbon (Nomascus concolor) is distributed in isolated habitat fragments in northern Vietnam, northwestern Laos, and southwestern China. To assess the behavioral adaptation of this species to forest fragments and its response to seasonal variation in food availability and climate, we present activity patterns of a group inhabiting an isolated forest based on two year-long studies in southern Yunnan, China. Annually, the gibbons spent nearly half of their active time resting, followed by moving and feeding. In both study periods, the time allocated to activities varied significantly between months, and was affected by food availability and climate factors. The group delayed retirement when tree fruit was abundant, and they decreased time spent moving and playing during periods of low fruit availability. In the cold months, the gibbons decreased time spent moving, and they decreased active time and resting time when rainfall was high. The results suggest that the group may seek to maximize net energy intake like energy maximizers when high quality food is most available, and adopt an energy-conserving strategy during periods of lower food availability and temperature. The gibbons showed similar diurnal variation in activity patterns to a group inhabiting a continuous forest at Dazhaizi, Mt. Wuliang, central Yunnan. However, they had a longer active period, and devoted more time to resting but less time to feeding. The individuals also spent lower percentages of time engaged in social behavior than those at Dazhaizi. These differences may be due to their smaller home range and unusual group composition caused by habitat fragmentation.

Patterns of bird functional diversity on land-bridge island fragments.

PubMed

Ding, Zhifeng; Feeley, Kenneth J; Wang, Yanping; Pakeman, Robin J; Ding, Ping

2013-07-01

The loss of species diversity due to habitat fragmentation has been extensively studied. In contrast, the impacts of habitat fragmentation on functional diversity remains relatively poorly understood. We conducted bird functional diversity studies on a set of 41 recently isolated land-bridge islands in the Thousand Island Lake, China. We analysed differences in bird species richness and a recently developed suite of complementary functional diversity indices (FRic, volume of functional space occupied; FEve, evenness of abundance distribution in the functional trait space; FDiv, divergence in the distribution of abundance in the trait volume) across different gradients (island area and isolation). We found no correlations between FRic and FEve or FEve and FDiv, but negative correlations between FRic and FDiv. As predicted, island area accounted for most of the variation in bird species richness, whereas isolation explained most of the variation in species evenness (decreasing species evenness with increasing isolation). Functional diversity appears to be more strongly influenced by habitat filtering as opposed to limiting similarity. More specifically, across all islands, both FRic and FEve were significantly lower than expected for randomly assembled communities, but FDiv showed no clear patterns. FRic increased with island area, FEve decreased with island area and FDiv showed no clear patterns. Our finding that FEve decreases with island area at TIL may indicate low functional stability on such islands, and as such large islands and habitat patches may deserve extra attention and/or protection. These results help to demonstrate the importance of considering the effects of fragmentation on functional diversity in habitat management and reserve design plans. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Scanning force microscopy and fluorescence microscopy of microcontact printed antibodies and antibody fragments.

PubMed

LaGraff, John R; Chu-LaGraff, Quynh

2006-05-09

Unlabeled primary immunoglobulin G (IgG) antibodies and its F(ab')2 and Fc fragments were attached to oxygen-plasma-cleaned glass substrates using either microcontact printing (MCP) or physical adsorption during bath application from dilute solutions. Fluorescently labeled secondary IgGs were then bound to surface-immobilized IgG, and the relative surface coverage was determined by measuring the fluorescence intensity. Results indicated that the surface coverage of IgG increased with increasing protein solution concentration for both MCP and bath-applied IgG and that a greater concentration of IgG was transferred to a glass substrate using MCP than during physisorption during bath applications. Scanning force microscopy (SFM) showed that patterned MCP IgG monolayers were 5 nm in height, indicating that IgG molecules lie flat on the substrate. After incubation with a secondary IgG, the overall line thickness increased to around 15 nm, indicating that the secondary IgG was in a more vertical orientation with respect to the substrate. The surface roughness of these MCP patterned IgG bilayers as measured by SFM was observed to increase with increasing surface coverage. Physisorption of IgG to both unmodified patterned polydimethylsiloxane (PDMS) stamps and plasma-cleaned glass substrates was modeled by Langmuir adsorption kinetics yielding IgG binding constants of K(MCP) = 1.7(2) x 10(7) M(-1) and K(bath) = 7.8(7) x 10(5) M(-1), respectively. MCP experiments involving primary F(ab')2 and Fc fragments incubated in fluorescently labeled fragment-specific secondary IgGs were carried out to test for the function and orientation of IgG. Finally, possible origins of MCP stamping defects such as pits, pull outs, droplets, and reverse protein transfer are discussed.

Superasymmetric fission of heavy nuclei induced by intermediate-energy protons

NASA Astrophysics Data System (ADS)

Deppman, A.; Andrade-II, E.; Guimarães, V.; Karapetyan, G. S.; Tavares, O. A. P.; Balabekyan, A. R.; Demekhina, N. A.; Adam, J.; Garcia, F.; Katovsky, K.

2013-12-01

In this work we present the results for the investigation of intermediate-mass fragment (IMF) production with the proton-induced reaction at 660 MeV on 238U and 237Np target. The data were obtained with the LNR Phasotron U-400M Cyclotron at Joint Institute for Nuclear Research (JINR), Dubna, Russia. A total of 93 isotopes, in the mass range of 30

Testing independence of fragment lengths within VNTR loci

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geisser, S.; Johnson, W.

1993-11-01

Methods that were devised to test independence of the bivariate fragment lengths obtained from VNTR loci are applied to several population databases. It is shown that for many of the probes independence (Hardy-Weinberg equilibrium) cannot be sustained. 3 refs., 3 tabs.

Heavy ion fragmentation experiments at the bevatron

NASA Technical Reports Server (NTRS)

Heckman, H. H.

1976-01-01

Collaborative research efforts to study the fragmentation processes of heavy nuclei in matter using heavy ion beams of the Bevatron/Bevalac are described. The goal of the program is to obtain the single particle inclusive spectra of secondary nuclei produced at 0 deg by the fragmentation of heavy ion beam projectiles. The process being examined is B+T yields F + anything, where B is the beam nucleus, T is the target nucleus, and F is the detected fragment. The fragments F are isotopically identified by experimental procedures involving magnetic analysis, energy loss and time-of-flight measurements. Effects were also made to: (a) study processes of heavy nuclei in matter, (b) measure the total and partial production cross section for all isotopes, (c) test the applicability of high energy multiparticle interaction theory to nuclear fragmentation, (d) apply the cross section data and fragmentation probabilities to cosmic ray transport theory, and (e) search for systematic behavior of fragment production as a means to improve existing semi-empirical theories of cross-sections.

In silico development of new acetylcholinesterase inhibitors.

PubMed

Pascoini, A L; Federico, L B; Arêas, A L F; Verde, B A; Freitas, P G; Camps, I

2018-04-19

In this work, we made use of fragment-based drug design (FBDD) and de novo design to obtain more powerful acetylcholinesterase (AChE) inhibitors. AChE is associated with Alzheimer's disease (AD). It was found that the cholinergic pathways in the cerebral cortex are compromised in AD and the accompanying cholinergic deficiency contributes to the cognitive deterioration of AD patients. In the FBDD approach, fragments are docked into the active site of the protein. As fragments are molecular groups with a low number of atoms, it is possible to study their interaction with localized amino acids. Once the interactions are measured, the fragments are organized by affinity and then linked together to form new molecules with a high degree of interaction with the active site. In the other approach, we used the de novo design technique starting from reference drugs used in the AD treatment. These drugs were broken into fragments (seeds). In the growing strategy, fragments were added to each seed, growing new molecules. In the linking strategy, two or more separated seeds were linked with different fragments. Both strategies combined produced a library of more than 2 million compounds. This library was filtered using absorption, distribution, metabolism, and excretion properties. The resulting library with around six thousand compounds was filtered again. In this case, structures with Tanimoto coefficients >.85 were discarded. The final library with 1500 compounds was submitted to docking studies. As a result, 10 compounds with better interaction energy than the reference drugs were obtained.

Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides

NASA Astrophysics Data System (ADS)

McMillen, Chelsea L.; Wright, Patience M.; Cassady, Carolyn J.

2016-05-01

Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides.

PubMed

McMillen, Chelsea L; Wright, Patience M; Cassady, Carolyn J

2016-05-01

Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

Fragmentation of relativistic nuclei in peripheral interactions in nuclear track emulsion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Artemenkov, D. A., E-mail: artemenkov@lhe.jinr.ru; Bradnova, V.; Chernyavsky, M. M.

2008-09-15

The technique of nuclear track emulsions is used to explore the fragmentation of light relativistic nuclei down to the most peripheral interactions: nuclear 'white' stars. A complete pattern of the relativistic dissociation of a 8B nucleus with target fragment accompaniment is presented. Relativistic dissociation {sup 9}Be {yields} 2{alpha} is explored using significant statistics, and a relative contribution of {sup 8}Be decays from 0+ and 2+ states is established. Target fragment accompaniments are shown for relativistic fragmentation {sup 14}N {yields} 3He +H and {sup 22}Ne {yields} 5He. The leading role of the electromagnetic dissociation on heavy nuclei with respect to breakupsmore » on target protons is demonstrated in all these cases. It is possible to conclude that the peripheral dissociation of relativistic nuclei in nuclear track emulsion is a unique tool to study many-body systems composed of the lightest nuclei and nucleons in the energy scale relevant for nuclear astrophysics.« less

Fragmentation studies of fulvic acids using collision induced dissociation fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Witt, Matthias; Fuchser, Jens; Koch, Boris P

2009-04-01

The complex natural organic matter standard Suwannee river fulvic acid (SRFA) was analyzed by negative ion mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS) using on-resonance collision induced dissociation (CID) of single ultrahigh resolved mass peaks in the ICR cell. Molecular formula assignment of precursor masses resulted in exactly one molecular formula for each of the peaks. Analyses of the corresponding fragment spectra and comparison to different standard substances revealed specific neutral losses and fragmentation patterns which result in structures consisting of a high degree of carboxyl- and fewer hydroxyl groups. The comparison of fragmented mass peaks within different pseudohomologous series (CH(2)-series, and CH(4) vs O exchange) suggested structurally based differences between these series. CID FTICR MS allowed isolating single mass peaks in a very complex natural organic matter spectrum. Subsequently, fragmentation gave structural insights into this material. Our results suggest that the structural diversity in complex humic substances is not as high as expected.

Halogeno-substituted 2-aminobenzoic acid derivatives for negative ion fragmentation studies of N-linked carbohydrates.

PubMed

Harvey, David J

2005-01-01

Negative ion electrospray mass spectra of high-mannose N-linked glycans derivatised with 2-aminobenzoic acids and ionised from solutions containing ammonium hydroxide gave prominent [M-H](-) ions accompanied by weaker [M-2H](2-) ions. Fragmentation of both types of ions gave prominent singly charged glycosidic cleavage ions containing the derivatised reducing terminus and ions from the non-reducing terminus that appeared to be products of cross-ring cleavages. Differentiation of these two groups of ions was conveniently achieved in a single spectrum by use of chloro- or bromo-substituted benzoic acids in order to label ions containing the derivative with an atom with a distinctive isotope pattern. Fragmentation of the doubly charged ions gave more abundant fragments, both singly and doubly charged, than did fragmentation of the singly charged ions, but information of chain branching was masked by the appearance of prominent ions produced by internal cleavages. Copyright (c) 2005 John Wiley & Sons, Ltd.

Dimensional crossover in fragmentation

NASA Astrophysics Data System (ADS)

Sotolongo-Costa, Oscar; Rodriguez, Arezky H.; Rodgers, G. J.

2000-11-01

Experiments in which thick clay plates and glass rods are fractured have revealed different behavior of fragment mass distribution function in the small and large fragment regions. In this paper we explain this behavior using non-extensive Tsallis statistics and show how the crossover between the two regions is caused by the change in the fragments’ dimensionality during the fracture process. We obtain a physical criterion for the position of this crossover and an expression for the change in the power-law exponent between the small and large fragment regions. These predictions are in good agreement with the experiments on thick clay plates.

Assessing rates of forest change and fragmentation in Alabama, USA, using the vegetation change tracker model

USGS Publications Warehouse

Li, Mingshi; Huang, Chengquan; Zhu, Zhiliang; Shi, Hua; Lu, Heng; Peng, Shikui

2009-01-01

Forest change is of great concern for land use decision makers and conservation communities. Quantitative and spatial forest change information is critical for addressing many pressing issues, including global climate change, carbon budgets, and sustainability. In this study, our analysis focuses on the differences in geospatial patterns and their changes between federal forests and nonfederal forests in Alabama over the time period 1987–2005, by interpreting 163 Landsat Thematic Mapper (TM) scenes using a vegetation change tracker (VCT) model. Our analysis revealed that for the most part of 1990 s and between 2000 and 2005, Alabama lost about 2% of its forest on an annual basis due to disturbances, but much of the losses were balanced by forest regeneration from previous disturbances. The disturbance maps revealed that federal forests were reasonably well protected, with the fragmentation remaining relatively stable over time. In contrast, nonfederal forests, which are predominant in area share (about 95%), were heavily disturbed, clearly demonstrating decreasing levels of fragmentation during the time period 1987–1993 giving way to a subsequent accelerating fragmentation during the time period 1994–2005. Additionally, the identification of the statistical relationships between forest fragmentation status and forest loss rate and forest net change rate in relation to land ownership implied the distinct differences in forest cutting rate and cutting patterns between federal forests and nonfederal forests. The forest spatial change information derived from the model has provided valuable insights regarding regional forest management practices and disturbance regimes, which are closely associated with regional economics and environmental concerns.

Synergistic interactions between edge and area effects in a heavily fragmented landscape.

PubMed

Ewers, Robert M; Thorpe, Stephen; Didham, Raphael K

2007-01-01

Both area and edge effects have a strong influence on ecological processes in fragmented landscapes, but there is little understanding of how these two factors might interact to exacerbate local species declines. To test for synergistic interactions between area and edge effects, we sampled a diverse beetle community in a heavily fragmented landscape in New Zealand. More than 35,000 beetles of approximately 900 species were sampled over large gradients in habitat area (10(-2) 10(6) ha) and distance from patch edge (2(0)-2(10) m from the forest edge into both the forest and adjacent matrix). Using a new approach to partition variance following an ordination analysis, we found that a synergistic interaction between habitat area and distance to edge was a more important determinant of patterns in beetle community composition than direct edge or area effects alone. The strength of edge effects in beetle-species composition increased nonlinearly with increasing fragment area. One important consequence of the synergy is that the slopes of species area (SA) curves constructed from habitat islands depend sensitively on the distance from edge at which sampling is conducted. Surprisingly, we found negative SA curves for communities sampled at intermediate distances from habitat edges, caused by differential edge responses of matrix- vs. forest-specialist species in fragments of increasing area. Our data indicate that distance to habitat edge has a consistently greater impact on beetle community composition than habitat area and that variation in the strength of edge effects may underlie many patterns that are superficially related to habitat area.

Characterization of epoxy carotenoids by fast atom bombardment collision-induced dissociation MS/MS.

PubMed

Maoka, Takashi; Fujiwara, Yasuhiro; Hashimoto, Keiji; Akimoto, Naoshige

2004-02-01

The characterization and structure of epoxy carotenoids possessing 5,6-epoxy, 5,8-epoxy and 3,6-epoxy end groups conjugated to the polyene chain were investigated using high-energy fast atom bombardment collision-induced dissociation MS/MS methods. In addition to [M - 80](+*), a characteristic fragment ion of an epoxy carotenoid, product ions resulting from the cleavage of C-C bonds in the polyene chain from the epoxy end group, such as m/z 181 (b ion) and 121 (c ion), were detected. On the other hand, diagnostic ions of m/z 286 (e-H ion) and 312 (f-H ion) were observed, not in the 5,6-epoxy or 5,8-epoxy carotenoid but in the 3,6-epoxy carotenoid. These fragmentation patterns can be used to distinguish 3,6-epoxy carotenoids from 5,6-epoxy or 5,8-epoxy carotenoids. The structure of an epoxy carotenoid, 3,6-epoxy-5,6-dihydro-7',8'-didehydro-beta,beta-carotene-5,3'-diol (8), isolated from oyster, was characterized using FAB CID-MS/MS by comparing fragmentation patterns with those of related known compounds.

Urban sprawl and fragmentation in Latin America: a dynamic quantification and characterization of spatial patterns.

PubMed

Inostroza, Luis; Baur, Rolf; Csaplovics, Elmar

2013-01-30

South America is one of the most urbanized continents in the world, where almost 84% of the total population lives in cities, more urbanized than North America (82%) and Europe (73%). Spatial dynamics, their structure, main features, land consumption rates, spatial arrangement, fragmentation degrees and comparability, remain mostly unknown for most Latin American cities. Using satellite imagery the main parameters of sprawl are quantified for 10 Latin American cities over a period of 20 years by monitoring growth patterns and identifying spatial metrics to characterize urban development and sprawling features measured with GIS tools. This quantification contributes to a better understanding of urban form in Latin America. A pervasive spatial expansion has been observed, where most of the studied cities are expanding at fast rates with falling densities trend. Although important differences in the rates of land consumption and densities exist, there is an underlying fragmentation trend towards increasing sprawl. These trends of spatial discontinuity may eventually be intensified by further economic development. Urban Sprawl/Latin America/GIS metrics/spatial development. Copyright © 2012 Elsevier Ltd. All rights reserved.

Peculiarities of RFLP of highly repetitive DNA in crow genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chelomina, G.N.; Kryukov, A.P.; Ivanov, S.V.

1995-02-01

We present a study of the structural organization of highly repetitive DNA in genomes of hooded crow Corvus cornix L., carrion crow C. corone L., and jungle crow C. macrorhynchos Wagl. RFLP and blot-hybridization with {sup 32}P-labeled Msp I fragment from hooded crow nDNA suggest the interspecific structural conservatism of the most repetitive DNA. The family of repeats we studied had tandem organization and the same (210 bp) period of reiteration for a set of restriction enzymes. However, in parallel to the general similarity of restriction patterns, there are species-specific peculiarities. The repetitive family revealed (Alu I, BsuR I, andmore » Msp I fragments) has quantitative RFLP of nDNA and interspecific differences in the extent of the multimer {open_quotes}ladder{close_quotes} pattern of Msp I fragments. The latter is more pronounced in nDNA of carrion crow than in that of phylogenetically distant jungle crow and closely related hooded crow. This suggests a recent amplification event for highly organized homological repeats in crow genomes. 10 refs., 2 figs.« less

Experimental modelling of fragmentation applied to volcanic explosions

NASA Astrophysics Data System (ADS)

Haug, Øystein Thordén; Galland, Olivier; Gisler, Galen R.

2013-12-01

Explosions during volcanic eruptions cause fragmentation of magma and host rock, resulting in fragments with sizes ranging from boulders to fine ash. The products can be described by fragment size distributions (FSD), which commonly follow power laws with exponent D. The processes that lead to power-law distributions and the physical parameters that control D remain unknown. We developed a quantitative experimental procedure to study the physics of the fragmentation process through time. The apparatus consists of a Hele-Shaw cell containing a layer of cohesive silica flour that is fragmented by a rapid injection of pressurized air. The evolving fragmentation of the flour is monitored with a high-speed camera, and the images are analysed to obtain the evolution of the number of fragments (N), their average size (A), and the FSD. Using the results from our image-analysis procedure, we find transient empirical laws for N, A and the exponent D of the power-law FSD as functions of the initial air pressure. We show that our experimental procedure is a promising tool for unravelling the complex physics of fragmentation during phreatomagmatic and phreatic eruptions.

Phylogeography of the dark fruit-eating bat Artibeus obscurus in the Brazilian Amazon.

PubMed

Ferreira, Wallax Augusto Silva; Borges, Bárbara do Nascimento; Rodrigues-Antunes, Symara; de Andrade, Fernanda Atanaena Gonçalves; Aguiar, Gilberto Ferreira de Souza; de Sousa e Silva-Junior, José; Marques-Aguiar, Suely Aparecida; Harada, Maria Lúcia

2014-01-01

Artibeus obscurus (Mammalia: Chiroptera) is endemic to South America, being found in at least 18 Brazilian states. Recent studies revealed that different populations of this genus present distinct phylogeographic patterns; however, very little is known on the population genetics structure of A. obscurus in the Amazon rainforest. Here, using a fragment (1010bp) of the mitochondrial gene cytochrome b from 87 samples, we investigated patterns of genetic divergence among populations of A. obscurus from different locations in the Brazilian Amazon rainforest and compared them with other Brazilian and South American regions. Analysis of molecular variance (AMOVA), fixation index (Fst) analysis, and phylogeographic patterns showed divergence between two major monophyletic groups, each one corresponding to a geographic region associated with the Atlantic and Amazon forest biomes. The Atlantic forest clusters formed a monophyletic group with a high bootstrap support and a fragmented distribution that follows the pattern predicted by the Refuge Theory. On the other hand, a different scenario was observed for the Amazon forest, where no fragmentation was identified. The AMOVA results revealed a significant geographic heterogeneity in the distribution of genetic variation, with 70% found within populations across the studied populations (Fst values ranging from 0.05864 to 0.09673; φST = 0.55). The intrapopulational analysis revealed that one population (Bragança) showed significant evidence of population expansion, with the formation of 2 distinct phylogroups, suggesting the occurrence of a subspecies or at least a different population in this region. These results also suggest considerable heterogeneity for A. obscurus in the Amazon region.

Generating Customized Verifiers for Automatically Generated Code

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2008-01-01

Program verification using Hoare-style techniques requires many logical annotations. We have previously developed a generic annotation inference algorithm that weaves in all annotations required to certify safety properties for automatically generated code. It uses patterns to capture generator- and property-specific code idioms and property-specific meta-program fragments to construct the annotations. The algorithm is customized by specifying the code patterns and integrating them with the meta-program fragments for annotation construction. However, this is difficult since it involves tedious and error-prone low-level term manipulations. Here, we describe an annotation schema compiler that largely automates this customization task using generative techniques. It takes a collection of high-level declarative annotation schemas tailored towards a specific code generator and safety property, and generates all customized analysis functions and glue code required for interfacing with the generic algorithm core, thus effectively creating a customized annotation inference algorithm. The compiler raises the level of abstraction and simplifies schema development and maintenance. It also takes care of some more routine aspects of formulating patterns and schemas, in particular handling of irrelevant program fragments and irrelevant variance in the program structure, which reduces the size, complexity, and number of different patterns and annotation schemas that are required. The improvements described here make it easier and faster to customize the system to a new safety property or a new generator, and we demonstrate this by customizing it to certify frame safety of space flight navigation code that was automatically generated from Simulink models by MathWorks' Real-Time Workshop.

A polymer, random walk model for the size-distribution of large DNA fragments after high linear energy transfer radiation

NASA Technical Reports Server (NTRS)

Ponomarev, A. L.; Brenner, D.; Hlatky, L. R.; Sachs, R. K.

2000-01-01

DNA double-strand breaks (DSBs) produced by densely ionizing radiation are not located randomly in the genome: recent data indicate DSB clustering along chromosomes. Stochastic DSB clustering at large scales, from > 100 Mbp down to < 0.01 Mbp, is modeled using computer simulations and analytic equations. A random-walk, coarse-grained polymer model for chromatin is combined with a simple track structure model in Monte Carlo software called DNAbreak and is applied to data on alpha-particle irradiation of V-79 cells. The chromatin model neglects molecular details but systematically incorporates an increase in average spatial separation between two DNA loci as the number of base-pairs between the loci increases. Fragment-size distributions obtained using DNAbreak match data on large fragments about as well as distributions previously obtained with a less mechanistic approach. Dose-response relations, linear at small doses of high linear energy transfer (LET) radiation, are obtained. They are found to be non-linear when the dose becomes so large that there is a significant probability of overlapping or close juxtaposition, along one chromosome, for different DSB clusters from different tracks. The non-linearity is more evident for large fragments than for small. The DNAbreak results furnish an example of the RLC (randomly located clusters) analytic formalism, which generalizes the broken-stick fragment-size distribution of the random-breakage model that is often applied to low-LET data.

DebriSat - A Planned Laboratory-Based Satellite Impact Experiment for Breakup Fragment Characterizations

NASA Technical Reports Server (NTRS)

Liou, Jer-Chyi; Clark, S.; Fitz-Coy, N.; Huynh, T.; Opiela, J.; Polk, M.; Roebuck, B.; Rushing, R.; Sorge, M.; Werremeyer, M.

2013-01-01

The goal of the DebriSat project is to characterize fragments generated by a hypervelocity collision involving a modern satellite in low Earth orbit (LEO). The DebriSat project will update and expand upon the information obtained in the 1992 Satellite Orbital Debris Characterization Impact Test (SOCIT), which characterized the breakup of a 1960 s US Navy Transit satellite. There are three phases to this project: the design and fabrication of DebriSat - an engineering model representing a modern, 60-cm/50-kg class LEO satellite; conduction of a laboratory-based hypervelocity impact to catastrophically break up the satellite; and characterization of the properties of breakup fragments down to 2 mm in size. The data obtained, including fragment size, area-to-mass ratio, density, shape, material composition, optical properties, and radar cross-section distributions, will be used to supplement the DoD s and NASA s satellite breakup models to better describe the breakup outcome of a modern satellite.

Glioma tissue obtained by modern ultrasonic aspiration with a simple sterile suction trap for primary cell culture and pathological evaluation.

PubMed

Schroeteler, Juliane; Reeker, Ralf; Suero Molina, Eric; Brokinkel, Benjamin; Holling, Markus; Grauer, Oliver M; Senner, Volker; Stummer, Walter; Ewelt, Christian

2014-01-01

Ultrasonic aspiration is widely used in the resection of brain tumors. Nevertheless, tumor tissue fragments obtained by ultrasonic aspiration are usually discarded. In this study, we demonstrate that these fragments are possible sources of material for histopathological study and tissue culture and compare their microscopic features and viability in tissue culture of cavitron ultrasonic surgical aspirator tissue fragments. Brain tumor tissue collected by ultrasonic aspiration (CUSA EXcel®; Integra Radionics Inc.) in a simple sterile suction trap during resection was processed for primary cell culture. Cell viability and immunohistological markers were measured by the WST-1 test, microscopy and immunofluorescent evaluation. Six gliomas are presented to demonstrate that these tissue fragments show good preservation of histological detail and tissue viability in culture. Utilization of this material may facilitate pathological interpretation by providing a more representative sample of tumor histology as well as an adequate and sterile biosource of material for tissue culture studies.

Differentiation of mycoplasmalike organisms (MLOs) in European fruit trees by PCR using specific primers derived from the sequence of a chromosomal fragment of the apple proliferation MLO.

PubMed Central

Jarausch, W; Saillard, C; Dosba, F; Bové, J M

1994-01-01

A 1.8-kb chromosomal DNA fragment of the mycoplasmalike organism (MLO) associated with apple proliferation was sequenced. Three putative open reading frames were observed on this fragment. The protein encoded by open reading frame 2 shows significant homologies with bacterial nitroreductases. From the nucleotide sequence four primer pairs for PCR were chosen to specifically amplify DNA from MLOs associated with European diseases of fruit trees. Primer pairs specific for (i) Malus-affecting MLOs, (ii) Malus- and Prunus-affecting MLOs, and (iii) Malus-, Prunus-, and Pyrus-affecting MLOs were obtained. Restriction enzyme analysis of the amplification products revealed restriction fragment length polymorphisms between Malus-, Prunus, and Pyrus-affecting MLOs as well as between different isolates of the apple proliferation MLO. No amplification with either primer pair could be obtained with DNA from 12 different MLOs experimentally maintained in periwinkle. Images PMID:7916180

The DFMS sensor of ROSINA onboard Rosetta: A computer-assisted approach to resolve mass calibration, flux calibration, and fragmentation issues

NASA Astrophysics Data System (ADS)

Dhooghe, Frederik; De Keyser, Johan; Altwegg, Kathrin; Calmonte, Ursina; Fuselier, Stephen; Hässig, Myrtha; Berthelier, Jean-Jacques; Mall, Urs; Gombosi, Tamas; Fiethe, Björn

2014-05-01

Rosetta will rendezvous with comet 67P/Churyumov-Gerasimenko in May 2014. The Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) instrument comprises three sensors: the pressure sensor (COPS) and two mass spectrometers (RTOF and DFMS). The double focusing mass spectrometer DFMS is optimized for mass resolution and consists of an ion source, a mass analyser and a detector package operated in analogue mode. The magnetic sector of the analyser provides the mass dispersion needed for use with the position-sensitive microchannel plate (MCP) detector. Ions that hit the MCP release electrons that are recorded digitally using a linear electron detector array with 512 pixels. Raw data for a given commanded mass are obtained as ADC counts as a function of pixel number. We have developed a computer-assisted approach to address the problem of calibrating such raw data. Mass calibration: Ion identification is based on their mass-over-charge (m/Z) ratio and requires an accurate correlation of pixel number and m/Z. The m/Z scale depends on the commanded mass and the magnetic field and can be described by an offset of the pixel associated with the commanded mass from the centre of the detector array and a scaling factor. Mass calibration is aided by the built-in gas calibration unit (GCU), which allows one to inject a known gas mixture into the instrument. In a first, fully automatic step of the mass calibration procedure, the calibration uses all GCU spectra and extracts information about the mass peak closest to the centre pixel, since those peaks can be identified unambiguously. This preliminary mass-calibration relation can then be applied to all spectra. Human-assisted identification of additional mass peaks further improves the mass calibration. Ion flux calibration: ADC counts per pixel are converted to ion counts per second using the overall gain, the individual pixel gain, and the total data accumulation time. DFMS can perform an internal scan to determine the pixel gain and related detector aging. The software automatically corrects for these effects to calibrate the fluxes. The COPS sensor can be used for an a posteriori calibration of the fluxes. Neutral gas number densities: Neutrals are ionized in the ion source before they are transferred to the mass analyser, but during this process fragmentation may occur. Our software allows one to identify which neutrals entered the instrument, given the ion fragments that are detected. First, multiple spectra with a limited mass range are combined to provide an overview of as many ion fragments as possible. We then exploit a fragmentation database to assist in figuring out the relation between entering species and recorded fragments. Finally, using experimentally determined sensitivities, gas number densities are obtained. The instrument characterisation (experimental determination of sensitivities, fragmentation patterns for the most common neutral species, etc.) has been conducted by the consortium using an instrument copy in the University of Bern test facilities during the cruise phase of the mission.

Measurements of the u valence quark distribution function in the proton and u quark fragmentation functions

NASA Astrophysics Data System (ADS)

Arneodo, M.; Arvidson, A.; Aubert, J. J.; Badelek, B.; Beaufays, J.; Bee, C. P.; Benchouk, C.; Berghoff, G.; Bird, I. G.; Blum, D.; Böhm, E.; De Bouard, X.; Brasse, F. W.; Braun, H.; Broll, C.; Brown, S. C.; Brück, H.; Calen, H.; Chima, J. S.; Ciborowski, J.; Clifft, R.; Coignet, G.; Combley, F.; Coughlan, J.; D'Agostini, G.; Dahlgren, S.; Dengler, F.; Derado, I.; Dreyer, T.; Drees, J.; Düren, M.; Eckardt, V.; Edwards, A.; Edwards, M.; Ernst, T.; Eszes, G.; Favier, J.; Ferrero, M. I.; Figiel, J.; Flauger, W.; Foster, J.; Gabathuler, E.; Gajewski, J.; Gamet, R.; Gayler, J.; Geddes, N.; Grafström, P.; Grard, F.; Haas, J.; Hagberg, E.; Hasert, F. J.; Hayman, P.; Heusse, P.; Jaffre, M.; Jacholkowska, A.; Janata, F.; Jancso, G.; Johnson, A. S.; Kabuss, E. M.; Kellner, G.; Korbel, V.; Krüger, A.; Krüger, J.; Kullander, S.; Landgraf, U.; Lanske, D.; Loken, J.; Long, K.; Maire, M.; Malecki, P.; Manz, A.; Maselli, S.; Mohr, W.; Montanet, F.; Montgomery, H. E.; Nagy, E.; Nassalski, J.; Norton, P. R.; Oakham, F. G.; Osborne, A. M.; Pascaud, C.; Pawlik, B.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pettingale, J.; Pietrzyk, B.; Poensgen, B.; Pötsch, M.; Renton, P.; Ribarics, P.; Rith, K.; Rondio, E.; Sandacz, A.; Scheer, M.; Schlagböhmer, A.; Schiemann, H.; Schmitz, N.; Schneegans, M.; Scholz, M.; Schouten, M.; Schröder, T.; Schultze, K.; Sloan, T.; Stier, H. E.; Studt, M.; Taylor, G. N.; Thenard, J. M.; Thompson, J. C.; De la Torre, A.; Toth, J.; Urban, L.; Urban, L.; Wallucks, W.; Whalley, M.; Wheeler, S.; Williams, W. S. C.; Wimpenny, S. J.; Windmolders, R.; Wolf, G.; European Muon Collaboration

1989-07-01

A new determination of the u valence quark distribution function in the proton is obtained from the analysis of identified charged pions, kaons, protons and antiprotons produced in muon-proton and muon-deuteron scattering. The comparison with results obtained in inclusive deep inelastic lepton-nucleon scattering provides a further test of the quark-parton model. The u quark fragmentation functions into positive and negative pions, kaons, protons and antiprotons are also measured.

[Anatomy of fractures of the inferior scapular angle].

PubMed

Bartoníček, J; Tuček, M; Malík, J

2018-01-01

The aim of this study is to describe the anatomy of fractures of the inferior angle and the adjacent part of the scapular body, based on 3D CT reconstructions. In a series of 375 scapular fractures, we identified a total of 20 fractures of the inferior angle of the scapular body (13 men, 7 women), with a mean patient age of 50 years (range 3373). In all fractures, 3D CT reconstructions were obtained, allowing an objective evaluation of the fracture pattern with a focus on the size and shape of the inferior angle fragment, propagation of the fracture line to the lateral and medial borders of the infraspinous part of the scapular body, fragment displacement and any additional fracture of the ipsilateral scapula and the shoulder girdle. We identified a total of 5 types of fracture involving the distal half of the infraspinous part of the scapular body. The first type, recorded in 5 cases, affected only the apex of the inferior angle, with a small part of the adjacent medial border. The second type, occurring in 4 cases, involved fractures separating the entire inferior angle. The third type, represented by 4 cases, was characterized by a fracture line starting medially close above the inferior angle and passing proximolaterally. The separated fragment had a shape of a big drop, carrying also the distal half of the lateral pillar in addition to the inferior angle. In the fourth type identified in 5 fractures, the separated fragment was formed both by the inferior angle and a variable part of the medial border. The fifth type, being by its nature a transition to the fracture of the infraspinous part of the body, was recorded in 2 cases, with the same V-shaped fragment. Fractures of the inferior angle and the adjacent part of the scapular body are groups of fractures differing from other infraspinous fractures of the scapular body. Although these fractures are highly variable in terms of shape, they have the same course of fracture line and the manner of displacement.Key words: scapula scapula fractures scapular body fractures inferior angle classification of scapular body fractures.

Negative electrospray ionization mass spectrometry: a method for sequencing and determining linkage position in oligosaccharides from branched hemicelluloses.

PubMed

Quéméner, Bernard; Vigouroux, Jacqueline; Rathahao, Estelle; Tabet, Jean Claude; Dimitrijevic, Aleksandra; Lahaye, Marc

2015-01-01

Xyloglucans of apple, tomato, bilberry and tamarind were hydrolyzed by commercial endo β-1-4-D-endoglucanase. The xylo-gluco-oligosaccharides (XylGos) released were separated on CarboPac PA 200 column in less than 15 min, and, after purification, they were structurally characterized by negative electrospray ionization mass spectrometry using a quadrupole time-of-flight (ESI-Q-TOF), a hybrid linear ion trap (LTQ)/Orbitrap and a hybrid quadrupole Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. In order to corroborate the fragmentation routes observed on XylGos, some commercial galacto-manno-oligosaccharides (GalMOs) and glucurono-xylo-oligosaccharides were also studied. The fragmentation pathways of the ionized GalMos were similar to those of XylGos ones. The product ion spectra were mainly characterized by prominent double cleavage (D) ions corresponding to the entire inner side chains. The directed fragmentation from the reducing end to the other end was observed for the main glycosylated backbone but also for the side-chains, allowing their complete sequencing. Relevant cross-ring cleavage ions from (0,2)X(j)-type revealed to be diagnostic of the 1-2-linked- glycosyl units from XylGos together with the 1-2-linked glucuronic acid unit from glucuronoxylans. Resonant activation in the LTQ Orbitrap allowed not only determining the type of all linkages but also the O-acetyl group location on fucosylated side-chains. Moreover, the fragmentation of the different side chains using the MS(n) capabilities of the LTQ/Orbitrap analyzer also allowed differentiating terminal arabinosyl and xylosyl substituents inside S and U side-chains of XylGos, respectively. The CID spectra obtained were very informative for distinction of isomeric structures differing only in their substitution pattern. These features together makes the fragmentation in negative ionization mode a relevant and powerful technique useful to highlight the subtle structural changes generally observed during the development of plant organs such as during fruit ripening and for the screening of cell wall mutants with altered hemicellulose structure. Copyright © 2015 John Wiley & Sons, Ltd.

Spatial Pattern of Cell Damage in Tissue from Heavy Ions

NASA Technical Reports Server (NTRS)

Ponomarev, Artem L.; Huff, Janice L.; Cucinotta, Francis A.

2007-01-01

A new Monte Carlo algorithm was developed that can model passage of heavy ions in a tissue, and their action on the cellular matrix for 2- or 3-dimensional cases. The build-up of secondaries such as projectile fragments, target fragments, other light fragments, and delta-rays was simulated. Cells were modeled as a cell culture monolayer in one example, where the data were taken directly from microscopy (2-d cell matrix). A simple model of tissue was given as abstract spheres with close approximation to real cell geometries (3-d cell matrix), as well as a realistic model of tissue was proposed based on microscopy images. Image segmentation was used to identify cells in an irradiated cell culture monolayer, or slices of tissue. The cells were then inserted into the model box pixel by pixel. In the case of cell monolayers (2-d), the image size may exceed the modeled box size. Such image was is moved with respect to the box in order to sample as many cells as possible. In the case of the simple tissue (3-d), the tissue box is modeled with periodic boundary conditions, which extrapolate the technique to macroscopic volumes of tissue. For real tissue, specific spatial patterns for cell apoptosis and necrosis are expected. The cell patterns were modeled based on action cross sections for apoptosis and necrosis estimated based on BNL data, and other experimental data.

Patterns of [PSI+] aggregation allow insights into cellular organization of yeast prion aggregates

PubMed Central

Tyedmers, Jens

2012-01-01

The yeast prion phenomenon is very widespread and mounting evidence suggests that it has an impact on cellular regulatory mechanisms related to phenotypic responses to changing environments. Studying the aggregation patterns of prion amyloids during different stages of the prion life cycle is a first key step to understand major principles of how and where cells generate, organize and turn-over prion aggregates. The induction of the [PSI+] state involves the actin cytoskeleton and quality control compartments such as the Insoluble Protein Deposit (IPOD). An initially unstable transitional induction state can be visualized by overexpression of the prion determinant and displays characteristic large ring- and ribbon-shaped aggregates consisting of poorly fragmented bundles of very long prion fibrils. In the mature prion state, the aggregation pattern is characterized by highly fragmented, shorter prion fibrils that form aggregates, which can be visualized through tagging with fluorescent proteins. The number of aggregates formed varies, ranging from a single large aggregate at the IPOD to multiple smaller ones, depending on several parameters discussed. Aggregate units below the resolution of light microscopy that are detectable by fluorescence correlation spectroscopy are in equilibrium with larger aggregates in this stage and can mediate faithful inheritance of the prion state. Loss of the prion state is often characterized by reduced fragmentation of prion fibrils and fewer, larger aggregates. PMID:22449721

Vacuum ultraviolet photofragmentation of octadecane: photoionization mass spectrometric and theoretical investigation.

PubMed

Xu, Jing; Sang, Pengpeng; Zhao, Lianming; Guo, Wenyue; Qi, Fei; Xing, Wei; Yan, Zifeng

The photoionization and fragmentation of octadecane were investigated with infrared laser desorption/tunable synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry (IRLD/VUV PIMS) and theoretical calculations. Mass spectra of octadecane were measured at various photon energies. The fragment ions were gradually detected with the increase of photon energy. The main fragment ions were assigned to radical ions (C n H 2 n +1 + , n  = 4-11) and alkene ions (C n H 2 n + , n  = 5-10). The ionization energy of the precursor and appearance energy of ionic fragments were obtained by measuring the photoionization efficiency spectrum. Possible formation pathways of the fragment ions were discussed with the help of density functional theory calculations.

Genetic and Epigenetic Alterations of Brassica nigra Introgression Lines from Somatic Hybridization: A Resource for Cauliflower Improvement

PubMed Central

Wang, Gui-xiang; Lv, Jing; Zhang, Jie; Han, Shuo; Zong, Mei; Guo, Ning; Zeng, Xing-ying; Zhang, Yue-yun; Wang, You-ping; Liu, Fan

2016-01-01

Broad phenotypic variations were obtained previously in derivatives from the asymmetric somatic hybridization of cauliflower “Korso” (Brassica oleracea var. botrytis, 2n = 18, CC genome) and black mustard “G1/1” (Brassica nigra, 2n = 16, BB genome). However, the mechanisms underlying these variations were unknown. In this study, 28 putative introgression lines (ILs) were pre-selected according to a series of morphological (leaf shape and color, plant height and branching, curd features, and flower traits) and physiological (black rot/club root resistance) characters. Multi-color fluorescence in situ hybridization revealed that these plants contained 18 chromosomes derived from “Korso.” Molecular marker (65 simple sequence repeats and 77 amplified fragment length polymorphisms) analysis identified the presence of “G1/1” DNA segments (average 7.5%). Additionally, DNA profiling revealed many genetic and epigenetic differences among the ILs, including sequence alterations, deletions, and variation in patterns of cytosine methylation. The frequency of fragments lost (5.1%) was higher than presence of novel bands (1.4%), and the presence of fragments specific to Brassica carinata (BBCC 2n = 34) were common (average 15.5%). Methylation-sensitive amplified polymorphism analysis indicated that methylation changes were common and that hypermethylation (12.4%) was more frequent than hypomethylation (4.8%). Our results suggested that asymmetric somatic hybridization and alien DNA introgression induced genetic and epigenetic alterations. Thus, these ILs represent an important, novel germplasm resource for cauliflower improvement that can be mined for diverse traits of interest to breeders and researchers. PMID:27625659

Electron transfer driven decomposition of adenine and selected analogs as probed by experimental and theoretical methods

NASA Astrophysics Data System (ADS)

Cunha, T.; Mendes, M.; Ferreira da Silva, F.; Eden, S.; García, G.; Bacchus-Montabonel, M.-C.; Limão-Vieira, P.

2018-04-01

We report on a combined experimental and theoretical study of electron-transfer-induced decomposition of adenine (Ad) and a selection of analog molecules in collisions with potassium (K) atoms. Time-of-flight negative ion mass spectra have been obtained in a wide collision energy range (6-68 eV in the centre-of-mass frame), providing a comprehensive investigation of the fragmentation patterns of purine (Pu), adenine (Ad), 9-methyl adenine (9-mAd), 6-dimethyl adenine (6-dimAd), and 2-D adenine (2-DAd). Following our recent communication about selective hydrogen loss from the transient negative ions (TNIs) produced in these collisions [T. Cunha et al., J. Chem. Phys. 148, 021101 (2018)], this work focuses on the production of smaller fragment anions. In the low-energy part of the present range, several dissociation channels that are accessible in free electron attachment experiments are absent from the present mass spectra, notably NH2 loss from adenine and 9-methyl adenine. This can be understood in terms of a relatively long transit time of the K+ cation in the vicinity of the TNI tending to enhance the likelihood of intramolecular electron transfer. In this case, the excess energy can be redistributed through the available degrees of freedom inhibiting fragmentation pathways. Ab initio theoretical calculations were performed for 9-methyl adenine (9-mAd) and adenine (Ad) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.

Analysing Relationships Between Urban Land Use Fragmentation Metrics and Socio-Economic Variables

NASA Astrophysics Data System (ADS)

Sapena, M.; Ruiz, L. A.; Goerlich, F. J.

2016-06-01

Analysing urban regions is essential for their correct monitoring and planning. This is mainly accounted for the sharp increase of people living in urban areas, and consequently, the need to manage them. At the same time there has been a rise in the use of spatial and statistical datasets, such as the Urban Atlas, which offers high-resolution urban land use maps obtained from satellite imagery, and the Urban Audit, which provides statistics of European cities and their surroundings. In this study, we analyse the relations between urban fragmentation metrics derived from Land Use and Land Cover (LULC) data from the Urban Atlas dataset, and socio-economic data from the Urban Audit for the reference years 2006 and 2012. We conducted the analysis on a sample of sixty-eight Functional Urban Areas (FUAs). One-date and two-date based fragmentation indices were computed for each FUA, land use class and date. Correlation tests and principal component analysis were then applied to select the most representative indices. Finally, multiple regression models were tested to explore the prediction of socio-economic variables, using different combinations of land use metrics as explanatory variables, both at a given date and in a dynamic context. The outcomes show that demography, living conditions, labour, and transportation variables have a clear relation with the morphology of the FUAs. This methodology allows us to compare European FUAs in terms of the spatial distribution of the land use classes, their complexity, and their structural changes, as well as to preview and model different growth patterns and socio-economic indicators.

Habitat fragmentation effects depend on complex interactions between population size and dispersal ability: Modeling influences of roads, agriculture and residential development across a range of life-history characteristics [chapter 20

Treesearch

Samuel A. Cushman; Bradley W. Compton; Kevin McGarigal

2010-01-01

Habitat loss and fragmentation are widely believed to be the most important drivers of extinction (Leakey and Lewin 1995). The habitats in which organisms live are spatially structured at a number of scales, and these patterns interact with organism perception and behavior to drive population dynamics and community structure (Johnson et al. 1992). Anthropogenic habitat...

Analysis of Long Bone and Vertebral Failure Patterns.

DTIC Science & Technology

1983-03-01

apophyseal joints, lumbar spondylosis and low back pain in Jayson, M.I.V. (ed) The Lumbar Spine and Back Pain, Pitman Medical, pp. 83-114. PUBLICATIONS...NOTES Material in this report was presented at the International Society for the Study of the Lumbar Spine, Toronto, Canada, June 6-10, 1982. 19. KEY...intervertebral disc and end plate fragments were observed in the vertebral bodies (G84 L2 -3 ) of the upper lumbar levels. Also fragments of trabecular bone

Molecular Determination of Fasciola Spp. Isolates from Domestic Ruminants Fecal Samples in the Northwest of Iran

PubMed Central

IMANI BARAN, Abbas; CHERAGHI SARAY, Habib; KATIRAEE, Farzad

2017-01-01

Background: Fasciola species are the main causes for fascioliasis with great financial losses and are among the most important food/water-borne parasites worldwide. The basic proceedings such as epidemiology and effective control of fascioliasis rely mainly on precise identification of Fasciola species. The present study was conducted to determine the Fasciola species in ruminant fecal samples from East Azerbaijan Province in Iran. Methods: Overall, 2012 fecal samples were collected and processed initially for microscopic examination of Fasciola eggs in 2014–15. Then, recovered eggs were subjected to molecular identification. A fragment of 618 bp of the 28S rRNA gene pertaining to Fasciola genus was amplified under PCR. The amplified fragment was restricted by fast digest Ava II enzyme in order to a Restriction Fragment Length Polymorphism. Results: Based on microscopic examination, 72 samples were infected, from which, 10 and 62 cases pertained to cattle and sheep samples respectively. Based on RFLP, the PCR products restricted by the Ava II restriction enzyme produced 529 bp fragments only. According to the positive controls, all restriction patterns were related to Fasciola hepatica, while no restriction patterns were linked to F. gigantica. Conclusion: Based on PCR-RFLP, F. hepatica was dominant species in animals of the studied areas and no evidence of F. gigantica was observed. Therefore, further field studies to verify these results are suggested. PMID:28761485

The formation of new quasi-stationary vortex patterns from the interaction of two identical vortices in a rotating fluid

NASA Astrophysics Data System (ADS)

Sokolovskiy, Mikhail A.; Verron, Jacques; Carton, Xavier J.

2018-06-01

Within the framework of the quasi-geostrophic approximation, the interactions of two identical initially circular vortex patches are studied using the contour dynamics/surgery method. The cases of barotropic vortices and of vortices in the upper layer of a two-layer fluid are considered. Diagrams showing the end states of vortex interactions and, in particular, the new regime of vortex triplet formation are constructed for a wide range of external parameters. This paper shows that, in the nonlinear evolution of two such (like-signed) vortices, the filaments and vorticity fragments surrounding the merged vortex often collapse into satellite vortices. Therefore, the conditions for the formation and the quasi-steady motions of a new type of triplet-shaped vortex structure are obtained.

Melodic cues for metre.

PubMed

Vos, P G; van Dijk, A; Schomaker, L

1994-01-01

A method of time-series analysis and a time-beating experiment were used to test the structural and perceptual validity of notated metre. Autocorrelation applied to the flow of melodic intervals between notes from thirty fragments of compositions for solo instruments by J S Bach strongly supported the validity of bar length specifications. Time-beating data, obtained with four stimuli from the same set, played in an expressionless mode, and presented under categorically distinct tempos to different subgroups of musically trained subjects, were rather inconsistent with respect to tapped bar lengths. However, taps were most frequently given to the events in the stimuli that corresponded with the first beats according to the score notations. No significant effects of tempo on tapping patterns were observed. The findings are discussed in comparison with other examinations of metre inference from musical compositions.

Primary structure of the hemoglobin alpha-chain of rose-ringed parakeet (Psittacula krameri).

PubMed

Islam, A; Beg, O U; Persson, B; Zaidi, Z H; Jörnvall, H

1988-10-01

The structure of the hemoglobin alpha-chain of Rose-ringed Parakeet was determined by sequence degradations of the intact subunit, the CNBr fragments, and peptides obtained by digestion with staphylococcal Glu-specific protease and trypsin. Using this analysis, the complete alpha-chain structure of 21 avian species is known, permitting comparisons of the protein structure and of avian relationships. The structure exhibits differences from previously established avian alpha-chains at a total of 61 positions, five of which have residues unique to those of the parakeet (Ser-12, Gly-65, Ser-67, Ala-121, and Leu-134). The analysis defines hemoglobin variation within an additional avian order (Psittaciformes), demonstrates distant patterns for evaluation of relationships within other avian orders, and lends support to taxonomic conclusions from molecular data.

Optical model analyses of galactic cosmic ray fragmentation in hydrogen targets

NASA Technical Reports Server (NTRS)

Townsend, Lawrence W.

1993-01-01

Quantum-mechanical optical model methods for calculating cross sections for the fragmentation of galactic cosmic ray nuclei by hydrogen targets are presented. The fragmentation cross sections are calculated with an abrasion-ablation collision formalism. Elemental and isotopic cross sections are estimated and compared with measured values for neon, sulfur, and calcium ions at incident energies between 400A MeV and 910A MeV. Good agreement between theory and experiment is obtained.

Dynamics and pattern of a managed coniferous forest landscape in Oregon.

Treesearch

T.A. Spies; W.J. Ripple; G.A. Bradshaw

1994-01-01

We examined the process of fragmentation in a managed forest landscape by comparing rates and patterns of disturbance (primarily clear-cutting) and regrowth between 1972 and 1988 using Landsat imagery. A 2589-km2 managed forest landscape in western Oregon was classified into two forest types, closed-canopy conifer forest (CF) (typically, > 60% conifer cover) and...

The landscape context of forest and grassland in the United States

Treesearch

Kurt H. Riitters

2011-01-01

As development introduces competing land uses into forest and grassland landscapes, the public expresses concern for landscape patterns through headline issues such as urban sprawl and fragmentation. Resource managers need a deeper understanding of the causes and consequences of landscape patterns to know if, where, and how to take any needed actions. The spatial...

Landscape pattern and context of forest and grassland in Alaska, Hawaii, and Puerto Rico

Treesearch

Kurt H. Riitters

2012-01-01

As development introduces competing land uses into forest and grassland landscapes, the public concerns for landscape patterns are expressed through headline issues such as urban sprawl and forest fragmentation. The task for resource managers is to maintain an appropriate balance of biodiversity, water quality, recreation experience, and other amenities in forest and...

Shifts in reproductive assurance strategies and inbreeding costs associated with habitat fragmentation in Central American mahogany

PubMed Central

Breed, Martin F; Gardner, Michael G; Ottewell, Kym M; Navarro, Carlos M; Lowe, Andrew J

2012-01-01

The influence of habitat fragmentation on mating patterns and progeny fitness in trees is critical for understanding the long-term impact of contemporary landscape change on the sustainability of biodiversity. We examined the relationship between mating patterns, using microsatellites, and fitness of progeny, in a common garden trial, for the insect-pollinated big-leaf mahogany, Swietenia macrophylla King, sourced from forests and isolated trees in 16 populations across Central America. As expected, isolated trees had disrupted mating patterns and reduced fitness. However, for dry provenances, fitness was negatively related to correlated paternity, while for mesic provenances, fitness was correlated positively with outcrossing rate and negatively with correlated paternity. Poorer performance of mesic provenances is likely because of reduced effective pollen donor density due to poorer environmental suitability and greater disturbance history. Our results demonstrate a differential shift in reproductive assurance and inbreeding costs in mahogany, driven by exploitation history and contemporary landscape context. PMID:22381041

Clinical proteomics: Applications for prostate cancer biomarker discovery and detection.

PubMed

Petricoin, Emanuel F; Ornstein, David K; Liotta, Lance A

2004-01-01

The science of proteomics comprises much more than simply generating lists of proteins that change in expression as a cause of or consequence of pathophysiology. The goal of proteomics should be to characterize the information flow through the intercellular protein circuitry that communicates with the extracellular microenvironment and then ultimately to the serum/plasma macroenvironment. Serum proteomic pattern diagnostics is a new type of proteomic concept in which patterns of ion signatures generated from high dimensional mass spectrometry data are used as diagnostic classifiers. This recent approach has exciting potential for clinical utility of diagnostic patterns because low molecular weight metabolites, peptides, and protein fragments may have higher accuracy than traditional biomarkers of cancer detection. Intriguingly, we now have discovered that this diagnostic information exists in a bound state, complexed with circulating highly abundant carrier proteins. These diagnostic fragments may one day be harvested by circulating nanoparticles, designed to absorb, enrich, and amplify the repertoire of diagnostic biomarkers generated-even at the critical, initial stages of carcinogenesis. Copyright 2004 Elsevier Inc.

Salt Weathering on Mars

NASA Astrophysics Data System (ADS)

Jagoutz, E.

2006-12-01

Large well rounded boulders and angular rock fragments characterizes the Martian landscape as seen on the recent excellent quality photos. Analyzing the different rock-shapes indicates a time sequence of emplacement, fragmentation and transport of different rocks on Mars, which might give interesting insight into transport and weathering processes. Larger commonly well rounded boulders were emplaced onto gravel plains. After emplacement, these rocks were fragmented and disassembled. Nests of angular rock fragments are marking the locations of preexisting larger rocks. Frequently it is possible to reconstruct larger rounded rocks from smaller angular fragments. In other cases transport after fragmentation obscured the relationship of the fragments. However, a strewn field of fragments is still reminiscent of the preexisting rock. Mechanical salt weathering could be a plausible explanation for the insitu fragmentation of larger rounded blocks into angular fragments. Impact or secondary air fall induced fragmentation produces very different patterns, as observed around impact crates on Earth. Salt weathering of rocks is a common process in terrestrial environments. Salt crystallization in capillaries causes fragmentation of rocks, irrespective of the process of salt transportation and concentration. On Earth significant salt weathering can be observed in different climatic environments: in the transition zone of alluvial aprons and salt playas in desserts and in dry valleys of Antarctica. In terrestrial semi-arid areas the salt is transported by salt solution, which is progressively concentrated by evaporation. In Antarctic dry valleys freeze-thaw cycles causes salt transportation and crystallization resulting in rock fragmentation. This salt induced process can lead to complete destruction of rocks and converts rocks to fine sand. The efficient breakdown of rocks is dominating the landscape in some dry valleys of the Earth but possibly also on Mars. (Malin, 1974). However, irrespectively of the climatic environment a liquid brine is a necessity for salt induced fragmentation of rocks.M. C. Malin (1974) JGR Vol 79,26 p 3888-3894

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

PubMed Central

Diaz, Naryttza N; Krause, Lutz; Goesmann, Alexander; Niehaus, Karsten; Nattkemper, Tim W

2009-01-01

Background Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning. Results Our novel strategy was extensively evaluated using the leave-one-out cross validation strategy on fragments of variable length (800 bp – 50 Kbp) from 373 completely sequenced genomes. TACOA is able to classify genomic fragments of length 800 bp and 1 Kbp with high accuracy until rank class. For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus). Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown". We compared the classification accuracy of TACOA with the latest intrinsic classifier PhyloPythia using 63 recently published complete genomes. For fragments of length 800 bp and 1 Kbp the overall accuracy of TACOA is higher than that obtained by PhyloPythia at all taxonomic ranks. For all fragment lengths, both methods achieved comparable high specificity results up to rank class and low false negative rates are also obtained. Conclusion An accurate multi-class taxonomic classifier was developed for environmental genomic fragments. TACOA can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp. The proposed method is transparent, fast, accurate and the reference set can be easily updated as newly sequenced genomes become available. Moreover, the method demonstrated to be competitive when compared to the most current classifier PhyloPythia and has the advantage that it can be locally installed and the reference set can be kept up-to-date. PMID:19210774

Peptide Fragmentation by Corona Discharge Induced Electrochemical Ionization

PubMed Central

Lloyd, John R.; Hess, Sonja

2010-01-01

Fundamental studies have greatly improved our understanding of electrospray, including the underlying electrochemical reactions. Generally regarded as disadvantageous, we have recently shown that corona discharge (CD) can be used as an effective method to create a radical cation species [M]+•, thus optimizing the electrochemical reactions that occur on the surface of the stainless steel (SS) electrospray capillary tip. This technique is known as CD initiated electrochemical ionization (CD-ECI). Here, we report on the fundamental studies using CD-ECI to induce analytically useful in-source fragmentation of a range of molecules that complex transition metals. Compounds that have been selectively fragmented using CD-ECI include enolate forming phenylglycine containing peptides, glycopeptides, nucleosides and phosphopeptides. Collision induced dissociation (CID) or other activation techniques were not necessary for CD-ECI fragmentation. A four step mechanism was proposed: 1. Complexation using either Fe in the SS capillary tip material or Cu(II) as an offline complexation reagent; 2. Electrochemical oxidation of the complexed metal and thus formation of a radical cation (e.g.; Fe - e− → Fe +•); 3. Radical fragmentation of the complexed compound. 4. Electrospray ionization of the fragmented neutrals. Fragmentation patterns resembling b- and y-type ions were observed and allowed the localization of the phosphorylation sites. PMID:20869880

Nucleon localization and fragment formation in nuclear fission

DOE PAGES

Zhang, C. L.; Schuetrumpf, B.; Nazarewicz, W.

2016-12-27

An electron localization measure was originally introduced to characterize chemical bond structures in molecules. Recently, a nucleon localization based on Hartree-Fock densities has been introduced to investigate α-cluster structures in light nuclei. Compared to the local nucleonic densities, the nucleon localization function has been shown to be an excellent indicator of shell effects and cluster correlations. In this work, using the spatial nucleon localization measure, we investigated the emergence of fragments in fissioning heavy nuclei using the self-consistent energy density functional method with a quantified energy density functional optimized for fission studies. We studied the particle densities and spatial nucleonmore » localization distributions along the fission pathways of 264Fm, 232Th, and 240Pu. We demonstrated that the fission fragments were formed fairly early in the evolution, well before scission. To illustrate the usefulness of the localization measure, we showed how the hyperdeformed state of 232Th could be understood in terms of a quasimolecular state made of 132Sn and 100Zr fragments. Compared to nucleonic distributions, the nucleon localization function more effectively quantifies nucleonic clustering: its characteristic oscillating pattern, traced back to shell effects, is a clear fingerprint of cluster/fragment configurations. This is of particular interest for studies of fragment formation and fragment identification in fissioning nuclei.« less

Amplified Fragment Length Polymorphism Fingerprinting of Pseudomonas Strains from a Poultry Processing Plant

PubMed Central

Geornaras, Ifigenia; Kunene, Nokuthula F.; von Holy, Alexander; Hastings, John W.

1999-01-01

Molecular typing has been used previously to identify and trace dissemination of pathogenic and spoilage bacteria associated with food processing. Amplified fragment length polymorphism (AFLP) is a novel DNA fingerprinting technique which is considered highly reproducible and has high discriminatory power. This technique was used to fingerprint 88 Pseudomonas fluorescens and Pseudomonas putida strains that were previously isolated from plate counts of carcasses at six processing stages and various equipment surfaces and environmental sources of a poultry abattoir. Clustering of the AFLP patterns revealed a high level of diversity among the strains. Six clusters (clusters I through VI) were delineated at an arbitrary Dice coefficient level of 0.65; clusters III (31 strains) and IV (28 strains) were the largest clusters. More than one-half (52.3%) of the strains obtained from carcass samples, which may have represented the resident carcass population, grouped together in cluster III. By contrast, 43.2% of the strains from most of the equipment surfaces and environmental sources grouped together in cluster IV. In most cases, the clusters in which carcass strains from processing stages grouped corresponded to the clusters in which strains from the associated equipment surfaces and/or environmental sources were found. This provided evidence that there was cross-contamination between carcasses and the abattoir environment at the DNA level. The AFLP data also showed that strains were being disseminated from the beginning to the end of the poultry processing operation, since many strains associated with carcasses at the packaging stage were members of the same clusters as strains obtained from carcasses after the defeathering stage. PMID:10473382

Identification and quantification of VOCs by proton transfer reaction time of flight mass spectrometry: An experimental workflow for the optimization of specificity, sensitivity, and accuracy

PubMed Central

Hanna, George B.

2018-01-01

Abstract Proton transfer reaction time of flight mass spectrometry (PTR‐ToF‐MS) is a direct injection MS technique, allowing for the sensitive and real‐time detection, identification, and quantification of volatile organic compounds. When aiming to employ PTR‐ToF‐MS for targeted volatile organic compound analysis, some methodological questions must be addressed, such as the need to correctly identify product ions, or evaluating the quantitation accuracy. This work proposes a workflow for PTR‐ToF‐MS method development, addressing the main issues affecting the reliable identification and quantification of target compounds. We determined the fragmentation patterns of 13 selected compounds (aldehydes, fatty acids, phenols). Experiments were conducted under breath‐relevant conditions (100% humid air), and within an extended range of reduced electric field values (E/N = 48–144 Td), obtained by changing drift tube voltage. Reactivity was inspected using H3O+, NO+, and O2 + as primary ions. The results show that a relatively low (<90 Td) E/N often permits to reduce fragmentation enhancing sensitivity and identification capabilities, particularly in the case of aldehydes using NO+, where a 4‐fold increase in sensitivity is obtained by means of drift voltage reduction. We developed a novel calibration methodology, relying on diffusion tubes used as gravimetric standards. For each of the tested compounds, it was possible to define suitable conditions whereby experimental error, defined as difference between gravimetric measurements and calculated concentrations, was 8% or lower. PMID:29336521

Amplified fragment length polymorphism fingerprinting of Pseudomonas strains from a poultry processing plant.

PubMed

Geornaras, I; Kunene, N F; von Holy, A; Hastings, J W

1999-09-01

Molecular typing has been used previously to identify and trace dissemination of pathogenic and spoilage bacteria associated with food processing. Amplified fragment length polymorphism (AFLP) is a novel DNA fingerprinting technique which is considered highly reproducible and has high discriminatory power. This technique was used to fingerprint 88 Pseudomonas fluorescens and Pseudomonas putida strains that were previously isolated from plate counts of carcasses at six processing stages and various equipment surfaces and environmental sources of a poultry abattoir. Clustering of the AFLP patterns revealed a high level of diversity among the strains. Six clusters (clusters I through VI) were delineated at an arbitrary Dice coefficient level of 0.65; clusters III (31 strains) and IV (28 strains) were the largest clusters. More than one-half (52.3%) of the strains obtained from carcass samples, which may have represented the resident carcass population, grouped together in cluster III. By contrast, 43.2% of the strains from most of the equipment surfaces and environmental sources grouped together in cluster IV. In most cases, the clusters in which carcass strains from processing stages grouped corresponded to the clusters in which strains from the associated equipment surfaces and/or environmental sources were found. This provided evidence that there was cross-contamination between carcasses and the abattoir environment at the DNA level. The AFLP data also showed that strains were being disseminated from the beginning to the end of the poultry processing operation, since many strains associated with carcasses at the packaging stage were members of the same clusters as strains obtained from carcasses after the defeathering stage.

[Cone-beam computed tomography in paleoanthropology].

PubMed

Vasil'ev, A Iu; Buzhilova, A P; Egorova, E A; Makarova, D V; Berezina, N Ia; Zorina, I S; Khartanovich, V I

2014-01-01

To study the capabilities of cone-bean computed tomography (CBCT) in estimating the bone structure when analyzing anthropological findings. Twenty-four bone fragments (remains) of Napoléon Bonaparte Imperial Army soldiers who had died at a Königsberg military hospital during their retreat from Russia in the War of 1812 were examined by CBCT. A total of 28 tubular bones with different injury healing signs and a skull with maxillofacial trauma marks were investigated. Furthermore, an object from D.G. Rokhlin's paleopathological collection was used to analyze a complicated humeral infectious process. CBCT was performed by individually selecting the scanning foldings, physicotechnical conditions and regimens in relation to the anatomic location and size of fragments. Processing of the obtained images reveled fractures of different bones in 19 (65.5%) cases. The signs of ununited fractures were visualized in 20.7% of the samples. Image post-processing showed intraarticular consolidated fractures in 13.8% of the anthropological findings. The CBCT examination of bone fragments exhibited the signs of their fusion. A wound pattern was established in 31% of the samples. The specific features of a bone amputation stump could be characterized in detail in 17.2% of the anthropological findings. 51.7% of the cases were found to have signs of sustained bone inflammatory diseases of various genesis, which in 41.4% of them were presented by linear, bulbar, and assimilated periostal reactions and significantly detectable on CBCT scans. Sequestral cavities were imaged in 31% of the fragments. The CBCT images are characterized by high informative value (from 7.5 to 10.6 pixels/mm), optimal spatial resolution, definition, and hardness. The software of CBCT involves the parameters and possible postprocessing of images (building of panoramic and mulplanar reconstructions, assessment of the density characteristics of tissues), which allow an analysis of anthropological material, by needlessly destroying them.

Proteolytic processing of endogenous and recombinant beta 4 integrin subunit

PubMed Central

1992-01-01

The alpha 6 beta 4 integrin is a receptor involved in the interaction of epithelial cells with basement membranes. This integrin is unique among the known integrins in that its beta 4 subunit has a large cytoplasmic domain. The function of this cytoplasmic domain is not known. In this paper we show that the beta 4 subunit undergoes proteolytic processing in cultured cells and provide evidence that this also happens in tissues. Immunoprecipitation experiments indicated that the cytoplasmic domain of beta 4 is susceptible to a calcium-dependent protease present in cellular extracts. In vitro assays with purified calpain showed that this enzyme can cleave beta 4 at two distinct sites in the cytoplasmic domain, generating truncated molecules of 165 and 130 kD. Immunoblotting experiments performed on cultured epithelial cells using an antibody to a peptide modeled after the COOH-terminus of the beta 4 subunit showed 70-kD fragments and several fragments of molecular masses between 185 and 115 kD. Similar fragments were detected in CHO cells transfected with the full-length beta 4 cDNA, but not in control transfected cells or in cells transfected with a mutant cDNA lacking the epitope of the cytoplasmic peptide antibody. The sizes of the fragments indicated that both the intracellular and extracellular domains of beta 4 are proteolytically processed. To examine the processing of the beta 4 subunit in epithelial tissues in vivo, human skin frozen sections were stained with antibodies to the ectodomain or the cytoplasmic domain of beta 4. The distinct staining patterns obtained with the two types of antibodies provided evidence that beta 4 is proteolytically processed in vivo in skin. Analogous experiments performed on sections of the cornea suggested that beta 4 is not proteolytically processed at a detectable level in this tissue. Thus, cleavage of the beta 4 subunit occurs in a tissue-specific fashion. These results suggest a potential mechanism of modulating the activities of the alpha 6 beta 4 integrin. PMID:1500432

Towards optimized methods to study viral impacts on soil microbial carbon cycling

NASA Astrophysics Data System (ADS)

Trubl, G. G.; Roux, S.; Jang, H. B.; Solonenko, N.; Sullivan, M. B.; Rich, V. I.

2016-12-01

Permafrost contains 50% of global soil carbon and is rapidly thawing. While the fate of this carbon is currently unknown, it will undoubtedly be shaped by microbes and their associated viruses, which modulate host activities via mortality and metabolic control. However, little is known about soil viruses generally and their impact on terrestrial biogeochemistry; this is partially due to the presence of inhibitory substances (e.g. humic acids) in soils that interfere with sample processing and sequence-based metagenomics surveys. To address this problem, we examined viral populations in three different peat soils along a permafrost thaw gradient. These samples yielded low viral DNA recoveries, and shallow metagenomic sequencing, but still resulted in the recovery of 40 viral genome fragments. Genome- and network-based classification suggested that these new references represented 11 viral clusters, and ecological patterns (based upon non-redundant fragment recruitment) showed that viral populations were distinct in each habitat. Although only 31% of the genes could be functionally classified, pairwise genome comparisons classified 63% of the viruses taxonomically. Additionally, comparison of the 40 viral genome fragments to 53 previously recovered fragments from the same site showed no overlap, suggesting only a small portion of the resident viral community has been sampled. A follow-up experiment was performed to remove more humics during extraction and thereby obtain better viral metagenomes. Three DNA extraction protocols were tested (CTAB, PowerSoil, and Wizard columns) and the DNA was further purified with an AMPure clean-up. The PowerSoil kit maximized DNA yield (3x CTAB and 6x Wizard), and yielded the purest DNA (based on NanoDrop 260:230 ratio). Given the important roles of viruses in biogeochemical cycles in better-studied systems, further research and humic-removal optimization on these thawing permafrost-associated viral communities is needed to clarify their involvement in carbon cycle feedbacks.

Monitoring and Predicting Land-use Changes and the Hydrology of the Urbanized Paochiao Watershed in Taiwan Using Remote Sensing Data, Urban Growth Models and a Hydrological Model.

PubMed

Lin, Yu-Pin; Lin, Yun-Bin; Wang, Yen-Tan; Hong, Nien-Ming

2008-02-04

Monitoring and simulating urban sprawl and its effects on land-use patterns andhydrological processes in urbanized watersheds are essential in land-use and waterresourceplanning and management. This study applies a novel framework to the urbangrowth model Slope, Land use, Excluded land, Urban extent, Transportation, andHillshading (SLEUTH) and land-use change with the Conversion of Land use and itsEffects (CLUE-s) model using historical SPOT images to predict urban sprawl in thePaochiao watershed in Taipei County, Taiwan. The historical and predicted land-use datawas input into Patch Analyst to obtain landscape metrics. This data was also input to theGeneralized Watershed Loading Function (GWLF) model to analyze the effects of futureurban sprawl on the land-use patterns and watershed hydrology. The landscape metrics ofthe historical SPOT images show that land-use patterns changed between 1990-2000. TheSLEUTH model accurately simulated historical land-use patterns and urban sprawl in thePaochiao watershed, and simulated future clustered land-use patterns (2001-2025). TheCLUE-s model also simulated land-use patterns for the same period and yielded historical trends in the metrics of land-use patterns. The land-use patterns predicted by the SLEUTHand CLUE-s models show the significant impact urban sprawl will have on land-usepatterns in the Paochiao watershed. The historical and predicted land-use patterns in thewatershed tended to fragment, had regular shapes and interspersion patterns, but wererelatively less isolated in 2001-2025 and less interspersed from 2005-2025 compared withland-use pattern in 1990. During the study, the variability and magnitude of hydrologicalcomponents based on the historical and predicted land-use patterns were cumulativelyaffected by urban sprawl in the watershed; specifically, surface runoff increasedsignificantly by 22.0% and baseflow decreased by 18.0% during 1990-2025. The proposedapproach is an effective means of enhancing land-use monitoring and management ofurbanized watersheds.

Gas-phase study on uridine: Conformation and X-ray photofragmentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Itälä, Eero, E-mail: ersita@utu.fi; Kooser, Kuno; Levola, Helena

2015-05-21

Fragmentation of RNA nucleoside uridine, induced by carbon 1s core ionization, has been studied. The measurements by combined electron and ion spectroscopy have been performed in gas phase utilizing synchrotron radiation. As uridine is a combination of d-ribose and uracil, which have been studied earlier with the same method, this study also considers the effect of chemical environment and the relevant functional groups. Furthermore, since in core ionization the initial core hole is always highly localized, charge migration prior to fragmentation has been studied here. This study also demonstrates the destructive nature of core ionization as in most cases themore » C 1s ionization of uridine leads to concerted explosions producing only small fragments with masses ≤43 amu. In addition to fragmentation patterns, we found out that upon evaporation the sugar part of the uridine molecule attains hexagonal form.« less

Indirect double photoionization of water

NASA Astrophysics Data System (ADS)

Resccigno, T. N.; Sann, H.; Orel, A. E.; Dörner, R.

2011-05-01

The vertical double ionization thresholds of small molecules generally lie above the dissociation limits corresponding to formation of two singly charged fragments. This gives the possibility of populating singly charged molecular ions by photoionization in the Franck-Condon region at energies below the lowest dication state, but above the dissociation limit into two singly charged fragment ions. This process can produce a superexcited neutral fragment that autoionizes at large internuclear separation. We study this process in water, where absorption of a photon produces an inner-shell excited state of H2O+ that fragments to H++OH*. The angular distribution of secondary electrons produced by OH* when it autoionizes produces a characteristic asymmetric pattern that reveals the distance, and therefore the time, at which the decay takes place. LBNL, Berkeley, CA, J. W. Goethe Universität, Frankfurt, Germany. Work performed under auspices of US DOE and supported by OBES, Div. of Chemical Sciences.

Avian persistence in fragmented rainforest.

PubMed

Lens, Luc; Van Dongen, Stefan; Norris, Ken; Githiru, Mwangi; Matthysen, Erik

2002-11-08

What factors determine the persistence of species in fragmented habitats? To address this question, we studied the relative impacts of forest deterioration and fragmentation on bird species in 12 rainforest fragments in Kenya, combining 6 years of individual capture-recapture data with measurements of current captures and museum specimens. Species mobility, as estimated from species-specific dispersal rates, and tolerance to habitat deterioration, as estimated from change in fluctuating asymmetry with increasing habitat disturbance, explained 88% of the variation in patch occupancy among eight forest bird species. Occupancy increased with mobility and with tolerance to deterioration, where both variables contributed equally to this relationship. We conclude that individual-level study, such as of dispersal behavior and phenotypic development, can predict patterns of persistence at the species level. More generally, for conservation tactics to stand a high chance of success, they should include action both within sites, to minimize habitat deterioration, and across landscapes, to maximize dispersal.

Clinicopathologic Association and Prognostic Value of Microcystic, Elongated, and Fragmented (MELF) Pattern in Endometrial Endometrioid Carcinoma.

PubMed

Kihara, Atsushi; Yoshida, Hiroshi; Watanabe, Reiko; Takahashi, Kenta; Kato, Tomoyasu; Ino, Yoshinori; Kitagawa, Masanobu; Hiraoka, Nobuyoshi

2017-07-01

Microcystic, elongated, and fragmented (MELF) pattern is seen in the invasive front of some endometrial endometrioid carcinomas. Although MELF pattern can be expected as an indicator of patient outcomes, its prognostic significance remains unclear. This study was conducted to elucidate clinicopathologic features and the prognostic impact of MELF pattern in patients with endometrial endometrioid carcinoma. We retrospectively analyzed data of 479 consecutive patients with endometrial endometrioid carcinoma that had been surgically resected. In 45 of 427 patients (11%) with low-grade endometrioid carcinoma, MELF pattern was found, but it was found in none of the 52 patients with high-grade endometrioid carcinoma. Among the patients with low-grade endometrioid carcinoma, MELF pattern was associated significantly with larger tumor size, myometrial invasion of more than 50%, advanced International Federation of Gynecology and Obstetrics stages, lymphovascular space invasion, lymph node metastasis, papillary architecture, and mucinous differentiation. However, survival analysis revealed that the patients with MELF pattern showed no significantly worse prognosis than those without MELF pattern either in disease-specific survival or in recurrence-free survival. MELF was not a significant prognosticator after adjustment for International Federation of Gynecology and Obstetrics stage (disease-specific survival [hazard ratio, 1.47; 95% confidence interval, 0.28-7.67; P=0.64], recurrence-free survival [hazard ratio, 0.98, 95% confidence interval, 0.32-2.99, P=0.98]). Immunohistochemical analysis revealed that MELF pattern was positive for p16 and p21 and almost negative for Ki-67 labeling, which suggested that tumor cells in MELF pattern were involved in growth arrest or cellular senescence. We conclude that MELF pattern could have little impact on outcomes of patients with low-grade endometrial endometrioid carcinoma.

Rock fragment movement in shallow rill flow - A laboratory study

NASA Astrophysics Data System (ADS)

Becker, Kerstin; Wirtz, Stefan; Seeger, Manuel; Gronz, Oliver; Remke, Alexander; Iserloh, Thomas; Brings, Christine; Casper, Markus; Ries, Johannes B.

2014-05-01

Studies concerning rill erosion mainly deal with the erosion and transport of fine material. The transport of rock fragments is examined mostly for mountain rivers. But there are important differences between the conditions and processes in rivers and in rills: (1) In most cases, the river cuts into a coarse substrate, where fine material is sparse, whereas rill erosion occurs on arable land. So the main part of the substrate is fine material and only single rock fragments influence the processes. (2) In rivers, the water depth is relatively high. There are a lot of studies about hydraulic parameters in such flows, but there is almost nothing known about hydraulic conditions in surface runoff events of a few centimeters. Additionally, little information exists about the rock fragment movement as a part of rill erosion processes on arable land. This knowledge should be increased because rock fragments cause non-stationary water turbulences in rills, which enhance the erosive force of flowing water. Field experiments can only show the fact that a certain rock fragment has moved: The starting point and the final position can be estimated. But the moving path and especially the initiation of the movement is not detectable under field conditions. Hence, we developed a laboratory setup to analyze the movement of rock fragments depending on rock fragment properties (size, form), slope gradient, flow velocity and surface roughness. By observing the rock fragments with cameras from two different angles we are able (1) to measure the rotation angles of a rock fragment during the experiment and (2) to deduce different rock fragment movement patterns. On this poster we want to present the experimental setup, developed within the scope of a master thesis, and the results of these experiments.

Long-term demographic consequences of habitat fragmentation to a tropical understory bird community

USGS Publications Warehouse

Korfanta, N.M.; Newmark, W.D.; Kauffman, M.J.

2012-01-01

Tropical deforestation continues to cause population declines and local extinctions in centers of avian diversity and endemism. Although local species extinctions stem from reductions in demographic rates, little is known about how habitat fragmentation influences survival of tropical bird populations or the relative importance of survival and fecundity in ultimately shaping communities. We analyzed 22 years of mark-recapture data to assess how fragmentation influenced apparent survival, recruitment, and realized population growth rate within 22 forest understory bird species in the Usambara Mountains, Tanzania. This represents the first such effort, in either tropical or temperate systems, to characterize the effect of deforestation on avian survival across such a broad suite of species. Long-term demographic analysis of this suite of species experiencing the same fragmented environment revealed considerable variability in species' responses to fragmentation, in addition to general patterns that emerged from comparison among species. Across the understory bird community as a whole, we found significantly lower apparent survival and realized population growth rate in small fragments relative to large, demonstrating fragmentation effects to demographic rates long after habitat loss. Demographic rates were depressed across five feeding guilds, suggesting that fragmentation sensitivity was not limited to insectivores. Seniority analyses, together with a positive effect of fragmentation on recruitment, indicated that depressed apparent survival was the primary driver of population declines and observed extinctions. We also found a landscape effect, with lower vital rates in one mountain range relative to another, suggesting that fragmentation effects may add to other large-scale drivers of population decline. Overall, realized population growth rate (λ) estimates were < 1 for most species, suggesting that future population persistence even within large forest fragments is uncertain in this biodiversity hotspot.

Renormalization of the fragmentation equation: exact self-similar solutions and turbulent cascades.

PubMed

Saveliev, V L; Gorokhovski, M A

2012-12-01

Using an approach developed earlier for renormalization of the Boltzmann collision integral [Saveliev and Nanbu, Phys. Rev. E 65, 051205 (2002)], we derive an exact divergence form for the fragmentation operator. Then we reduce the fragmentation equation to the continuity equation in size space, with the flux given explicitly. This allows us to obtain self-similar solutions and to find the integral of motion for these solutions (we call it the bare flux). We show how these solutions can be applied as a description of cascade processes in three- and two-dimensional turbulence. We also suggested an empirical cascade model of impact fragmentation of brittle materials.

Cloning, bacterial expression and crystallization of Fv antibody fragments

NASA Astrophysics Data System (ADS)

E´, Jean-Luc; Boulot, Ginette; Chitarra, V´ronique; Riottot, Marie-Madeleine; Souchon, H´le`ne; Houdusse, Anne; Bentley, Graham A.; Narayana Bhat, T.; Spinelli, Silvia; Poljak, Roberto J.

1992-08-01

The variable Fv fragments of antibodies, cloned in recombinant plasmids, can be expressed in bacteria as functional proteins having immunochemical properties which are very similar or identical with those of the corresponding parts of the parent eukaryotic antibodies. They offer new possibilities for the study of antibody-antigen interactions since the crystals of Fv fragments and of their complexes with antigen reported here diffract X-rays to a higher resolution that those obtained with the cognate Fab fragments. The Fv approach should facilitate the structural study of the combining site of antibodies and the further characterization of antigen-antibody interactions by site-directed mutagenesis experiments.

Bone fragments a body can make

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stout, S.D.; Ross, L.M. Jr.

Data obtained from various analytical techniques applied to a number of small bone fragments recovered from a crime scene were used to provide evidence for the occurrence of a fatality. Microscopic and histomorphometric analyses confirmed that the fragments were from a human skull. X-ray microanalysis of darkened areas on the bone fragments revealed a chemical signature that matched the chemical signature of a shotgun pellet recovered at the scene of the crime. The above findings supported the deoxyribonucleic acid (DNA) fingerprint evidence which, along with other evidence, was used to convict a man for the murder of his wife, evenmore » though her body was never recovered.« less

Relativistic corrections to heavy quark fragmentation to S-wave heavy mesons

NASA Astrophysics Data System (ADS)

Sang, Wen-Long; Yang, Lan-Fei; Chen, Yu-Qi

2009-07-01

The relativistic corrections of order v2 to the fragmentation functions for the heavy quark to S-wave heavy quarkonia are calculated in the framework of the nonrelativistic quantum chromodynamics factorization formula. We derive the fragmentation functions by using the Collins-Soper definition in both the Feynman gauge and the axial gauge. We also extract them through the process Z0→Hq qmacr in the limit MZ/m→∞. We find that all results obtained by these two different methods and in different gauges are the same. We estimate the relative size of the relativistic corrections to the fragmentation functions.

Relativistic corrections to heavy quark fragmentation to S-wave heavy mesons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sang Wenlong; Yang Lanfei; Chen Yuqi

The relativistic corrections of order v{sup 2} to the fragmentation functions for the heavy quark to S-wave heavy quarkonia are calculated in the framework of the nonrelativistic quantum chromodynamics factorization formula. We derive the fragmentation functions by using the Collins-Soper definition in both the Feynman gauge and the axial gauge. We also extract them through the process Z{sup 0}{yields}Hqq in the limit M{sub Z}/m{yields}{infinity}. We find that all results obtained by these two different methods and in different gauges are the same. We estimate the relative size of the relativistic corrections to the fragmentation functions.

Generalized Boltzmann-Type Equations for Aggregation in Gases

NASA Astrophysics Data System (ADS)

Adzhiev, S. Z.; Vedenyapin, V. V.; Volkov, Yu. A.; Melikhov, I. V.

2017-12-01

The coalescence and fragmentation of particles in a dispersion system are investigated by applying kinetic theory methods, namely, by generalizing the Boltzmann kinetic equation to coalescence and fragmentation processes. Dynamic equations for the particle concentrations in the system are derived using the kinetic equations of motion. For particle coalescence and fragmentation, equations for the particle momentum, coordinate, and mass distribution functions are obtained and the coalescence and fragmentation coefficients are calculated. The equilibrium mass and velocity distribution functions of the particles in the dispersion system are found in the approximation of an active terminal group (Becker-Döring-type equation). The transition to a continuum description is performed.

Using hadron-in-jet data in a global analysis of D* fragmentation functions

NASA Astrophysics Data System (ADS)

Anderle, Daniele P.; Kaufmann, Tom; Stratmann, Marco; Ringer, Felix; Vitev, Ivan

2017-08-01

We present a novel global QCD analysis of charged D*-meson fragmentation functions at next-to-leading order accuracy. This is achieved by making use of the available data for single-inclusive D*-meson production in electron-positron annihilation, hadron-hadron collisions, and, for the first time, in-jet fragmentation in proton-proton scattering. It is shown how to include all relevant processes efficiently and without approximations within the Mellin moment technique, specifically for the in-jet fragmentation cross section. The presented technical framework is generic and can be straightforwardly applied to future analyses of fragmentation functions for other hadron species, as soon as more in-jet fragmentation data become available. We choose to work within the zero mass variable flavor number scheme which is applicable for sufficiently high energies and transverse momenta. The obtained optimum set of parton-to-D* fragmentation functions is accompanied by Hessian uncertainty sets which allow one to propagate hadronization uncertainties to other processes of interest.

Searching for substructures in fragment spaces.

PubMed

Ehrlich, Hans-Christian; Volkamer, Andrea; Rarey, Matthias

2012-12-21

A common task in drug development is the selection of compounds fulfilling specific structural features from a large data pool. While several methods that iteratively search through such data sets exist, their application is limited compared to the infinite character of molecular space. The introduction of the concept of fragment spaces (FSs), which are composed of molecular fragments and their connection rules, made the representation of large combinatorial data sets feasible. At the same time, search algorithms face the problem of structural features spanning over multiple fragments. Due to the combinatorial nature of FSs, an enumeration of all products is impossible. In order to overcome these time and storage issues, we present a method that is able to find substructures in FSs without explicit product enumeration. This is accomplished by splitting substructures into subsubstructures and mapping them onto fragments with respect to fragment connectivity rules. The method has been evaluated on three different drug discovery scenarios considering the exploration of a molecule class, the elaboration of decoration patterns for a molecular core, and the exhaustive query for peptides in FSs. FSs can be searched in seconds, and found products contain novel compounds not present in the PubChem database which may serve as hints for new lead structures.

Geostatistics and Geographic Information System to Analyze the Spatial Distribution of the Diversity of Anastrepha Species (Diptera: Tephritidae): the Effect of Forest Fragments in an Urban Area.

PubMed

Garcia, A G; Araujo, M R; Uramoto, K; Walder, J M M; Zucchi, R A

2017-12-08

Fruit flies are among the most damaging insect pests of commercial fruit in Brazil. It is important to understand the landscape elements that may favor these flies. In the present study, spatial data from surveys of species of Anastrepha Schiner (Diptera: Tephritidae) in an urban area with forest fragments were analyzed, using geostatistics and Geographic Information System (GIS) to map the diversity of insects and evaluate how the forest fragments drive the spatial patterns. The results indicated a high diversity of species associated with large fragments, and a trend toward lower diversity in the more urbanized area, as the fragment sizes decreased. We concluded that the diversity of Anastrepha species is directly and positively related to large and continuous forest fragments in urbanized areas, and that combining geostatistics and GIS is a promising method for use in insect-pest management and sampling involving fruit flies. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Analysis and performance assessment of a fragment retransmission scheme for energy efficient IEEE 802.11 WLANs.

PubMed

Mafole, Prosper; Aritsugi, Masayoshi

2016-01-01

Backoff-free fragment retransmission (BFFR) scheme enhances the performance of legacy MAC layer fragmentation by eliminating contention overhead. The eliminated overhead is the result of backoff executed before a retransmission attempt is made when fragment transmission failure occurs within a fragment burst. This paper provides a mathematical analysis of BFFR energy efficiency and further assesses, by means of simulations, the energy efficiency, throughput and delay obtained when BFFR is used. The validity of the new scheme is evaluated in different scenarios namely, constant bit rate traffic, realistic bursty internet traffic, node mobility, rigid and elastic flows and their combinations at different traffic loads. We also evaluate and discuss the impact of BFFR on MAC fairness when the number of nodes is varied from 4 to 10. It is shown that BFFR has advantages over legacy MAC fragmentation scheme in all the scenarios.

Organization of nif gene cluster in Frankia sp. EuIK1 strain, a symbiont of Elaeagnus umbellata.

PubMed

Oh, Chang Jae; Kim, Ho Bang; Kim, Jitae; Kim, Won Jin; Lee, Hyoungseok; An, Chung Sun

2012-01-01

The nucleotide sequence of a 20.5-kb genomic region harboring nif genes was determined and analyzed. The fragment was obtained from Frankia sp. EuIK1 strain, an indigenous symbiont of Elaeagnus umbellata. A total of 20 ORFs including 12 nif genes were identified and subjected to comparative analysis with the genome sequences of 3 Frankia strains representing diverse host plant specificities. The nucleotide and deduced amino acid sequences showed highest levels of identity with orthologous genes from an Elaeagnus-infecting strain. The gene organization patterns around the nif gene clusters were well conserved among all 4 Frankia strains. However, characteristic features appeared in the location of the nifV gene for each Frankia strain, depending on the type of host plant. Sequence analysis was performed to determine the transcription units and suggested that there could be an independent operon starting from the nifW gene in the EuIK strain. Considering the organization patterns and their total extensions on the genome, we propose that the nif gene clusters remained stable despite genetic variations occurring in the Frankia genomes.

Dual Fragment Impact of PBX Charges

NASA Astrophysics Data System (ADS)

Haskins, Peter; Briggs, Richard; Leeming, David; White, Nathan; Cheese, Philip; DE&S MoD UK Team; Ordnance Test Solutions Ltd Team

2017-06-01

Fragment impact can pose a significant hazard to many systems containing explosives or propellants. Testing for this threat is most commonly carried out using a single fragment. However, it can be argued that an initial fragment strike (or strikes) could sensitise the energetic material to subsequent impacts, which may then lead to a more violent reaction than would have been predicted based upon single fragment studies. To explore this potential hazard we have developed the capability to launch 2 fragments from the same gun at a range of velocities, and achieve impacts on an acceptor charge with good control over the spatial and temporal separation of the strikes. In this paper we will describe in detail the experimental techniques we have used, both to achieve the dual fragment launch and observe the acceptor charge response. In addition, we will describe the results obtained against PBX filled explosive targets; discuss the mechanisms controlling the target response and their significance for vulnerability assessment. Results of these tests have clearly indicated the potential for detonation upon the second strike, at velocities well below those needed for shock initiation by a single fragment.

Home Range and Ranging Behaviour of Bornean Elephant (Elephas maximus borneensis) Females

PubMed Central

Alfred, Raymond; Ahmad, Abd Hamid; Payne, Junaidi; Williams, Christy; Ambu, Laurentius Nayan; How, Phua Mui; Goossens, Benoit

2012-01-01

Background Home range is defined as the extent and location of the area covered annually by a wild animal in its natural habitat. Studies of African and Indian elephants in landscapes of largely open habitats have indicated that the sizes of the home range are determined not only by the food supplies and seasonal changes, but also by numerous other factors including availability of water sources, habitat loss and the existence of man-made barriers. The home range size for the Bornean elephant had never been investigated before. Methodology/Principal Findings The first satellite tracking program to investigate the movement of wild Bornean elephants in Sabah was initiated in 2005. Five adult female elephants were immobilized and neck collars were fitted with tracking devices. The sizes of their home range and movement patterns were determined using location data gathered from a satellite tracking system and analyzed by using the Minimum Convex Polygon and Harmonic Mean methods. Home range size was estimated to be 250 to 400 km2 in a non-fragmented forest and 600 km2 in a fragmented forest. The ranging behavior was influenced by the size of the natural forest habitat and the availability of permanent water sources. The movement pattern was influenced by human disturbance and the need to move from one feeding site to another. Conclusions/Significance Home range and movement rate were influenced by the degree of habitat fragmentation. Once habitat was cleared or converted, the availability of food plants and water sources were reduced, forcing the elephants to travel to adjacent forest areas. Therefore movement rate in fragmented forest was higher than in the non-fragmented forest. Finally, in fragmented habitat human and elephant conflict occurrences were likely to be higher, due to increased movement bringing elephants into contact more often with humans. PMID:22347469

Experimental Investigation of the Influence of Confining Stress on Hard Rock Fragmentation Using a Conical Pick

NASA Astrophysics Data System (ADS)

Li, Xibing; Wang, Shaofeng; Wang, Shanyong

2018-01-01

High geostress is a prominent condition in deep excavations and affects the cuttability of deep hard rock. This study aims to determine the influence of confining stress on hard rock fragmentation as applied by a conical pick. Using a true triaxial test apparatus, static and coupled static and dynamic loadings from pick forces were applied to end faces of cubic rock specimens to break them under biaxial, uniaxial and stress-free confining stress conditions. The cuttability indices (peak pick force, insertion depth and disturbance duration), failure patterns and fragment sizes were measured and compared to estimate the effects of confining stress. The results show that the rock cuttabilities decreased in order from rock breakages under stress-free conditions to uniaxial confining stress and then to biaxial confining stress. Under biaxial confining stress, only flake-shaped fragments were stripped from the rock surfaces under the requirements of large pick forces or disturbance durations. As the level of uniaxial confining stress increased, the peak pick force and the insertion depth initially increased and then decreased, and the failure patterns varied from splitting to partial splitting and then to rock bursts with decreasing average fragment sizes. Rock bursts will occur under elastic compression via ultra-high uniaxial confining stresses. There are two critical uniaxial confining stress levels, namely stress values at which peak pick forces begin to decrease and improve rock cuttability, and those at which rock bursts initially occur and cutting safety decreases. In particular, hard rock is easiest to split safely and efficiently under stress-free conditions. Moreover, coupled static preloading and dynamic disturbance can increase the efficiency of rock fragmentation with increasing preloading levels and disturbance amplitudes. The concluding remarks confirm hard rock cuttability using conical pick, which can improve the applicability of mechanical excavation in deep hard rock masses.

Optical model calculations of 14.6A GeV silicon fragmentation cross sections

NASA Technical Reports Server (NTRS)

Townsend, Lawrence W.; Khan, Ferdous; Tripathi, Ram K.

1993-01-01

An optical potential abrasion-ablation collision model is used to calculate hadronic dissociation cross sections for a 14.6 A GeV(exp 28) Si beam fragmenting in aluminum, tin, and lead targets. The frictional-spectator-interaction (FSI) contributions are computed with two different formalisms for the energy-dependent mean free path. These estimates are compared with experimental data and with estimates obtained from semi-empirical fragmentation models commonly used in galactic cosmic ray transport studies.

Conversion of fullerenes to diamond

DOEpatents

Gruen, Dieter M.

1994-01-01

A method of forming synthetic hydrogen defect free diamond or diamond like films on a substrate. The method involves providing vapor containing fullerene molecules with or without an inert gas, providing a device to impart energy to the fullerene molecules, fragmenting at least in part some of the fullerene molecules in the vapor or energizing the molecules to incipient fragmentation, ionizing the fullerene molecules, impinging ionized fullerene molecules on the substrate to assist in causing fullerene fragmentation to obtain a thickness of diamond on the substrate.

Arthroscopically assisted knee contracture release secondary to melorheostosis: a case report.

PubMed

Claramunt, Raúl Torres; López, Xavier Pelfort; Palou, Enric Cáceres; García, Joan C Monllau; Verdie, Lluís Puig

2011-02-01

Melorheostosis is a rare non-hereditary bone disease characterized by a radiographic pattern of flowing hyperostosis along the cortex with sclerotomal distribution. We report a case of a patient with severe knee contracture and a restricted range of motion caused by intraarticular bone fragment and hyperostotic bone lesions secondary to melorheostosis. An arthroscopically assisted approach was used successfully in order to remove free bone fragments and to release the hyperostotic lesions in the bone cortex of the distal femur.

Genomic and transcriptomic alterations following intergeneric hybridization and polyploidization in the Chrysanthemum nankingense×Tanacetum vulgare hybrid and allopolyploid (Asteraceae).

PubMed

Qi, Xiangyu; Wang, Haibin; Song, Aiping; Jiang, Jiafu; Chen, Sumei; Chen, Fadi

2018-01-01

Allopolyploid formation involves two major events: interspecific hybridization and polyploidization. A number of species in the Asteraceae family are polyploids because of frequent hybridization. The effects of hybridization on genomics and transcriptomics in Chrysanthemum nankingense×Tanacetum vulgare hybrids have been reported. In this study, we obtained allopolyploids by applying a colchicine treatment to a synthesized C. nankingense × T. vulgare hybrid. Sequence-related amplified polymorphism (SRAP), methylation-sensitive amplification polymorphism (MSAP), and high-throughput RNA sequencing (RNA-Seq) technologies were used to investigate the genomic, epigenetic, and transcriptomic alterations in both the hybrid and allopolyploids. The genomic alterations in the hybrid and allopolyploids mainly involved the loss of parental fragments and the gain of novel fragments. The DNA methylation level of the hybrid was reduced by hybridization but was restored somewhat after polyploidization. There were more significant differences in gene expression between the hybrid/allopolyploid and the paternal parent than between the hybrid/allopolyploid and the maternal parent. Most differentially expressed genes (DEGs) showed down-regulation in the hybrid/allopolyploid relative to the parents. Among the non-additive genes, transgressive patterns appeared to be dominant, especially repression patterns. Maternal expression dominance was observed specifically for down-regulated genes. Many methylase and methyltransferase genes showed differential expression between the hybrid and parents and between the allopolyploid and parents. Our data indicate that hybridization may be a major factor affecting genomic and transcriptomic changes in newly formed allopolyploids. The formation of allopolyploids may not simply be the sum of hybridization and polyploidization changes but also may be influenced by the interaction between these processes.

Molecular characterization of human and animal Echinococcus granulosus isolates in Isfahan, Iran.

PubMed

Shahnazi, Mojtaba; Hejazi, Hosein; Salehi, Mansour; Andalib, Ali Reza

2011-01-01

Cystic hydatid disease (CHD) is one of the most important zoonotic diseases in different parts of Iran. While it causes major health problem, there is limited information about its transmission cycles and reservoirs of human infection. Therefore we aimed to characterize the existence Echinococcus granulosus cysts in humans and animals in the province of Isfahan, central region of Iran. We collected hydatid cysts from the liver and lungs of patients who underwent surgery procedure and also cysts were obtained from domestic animals at slaughterhouses. DNA was extracted from the protoscoleces and examined by polymerase chain reaction (PCR) of rDNA internal transcribed spacer1 (ITS1-PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP). In addition, fragments of the genes coding for mitochondrial cytochrome c oxidase subunit 1 (CO1) and NADH dehydrogenase 1 (ND1) were sequenced. Among the two different identified strains/genotypes (sheep and camel), the sheep strain was shown to be the most common genotype of E. granulosus affecting humans, sheep, cattle, goats and occasionally camels. Nine out of 26 camel samples were infected with sheep strain. However the camel genotype was observed in humans, camels and cattle. Seventeen out of 26 camel isolates, 6 out of 31 human and 5 out of 14 cattle samples were infected with the camel genotype. The camel genotypes had PCR and RFLP patterns which were different from the PCR and RFLP patterns of the rest of isolates (sheep strain). The results of this study showed that the 'camel' strain was actual source of infection to humans which circulates between intermediate hosts including camels and cattle, and it confirms the camel-dog transmission cycle in Isfahan. Copyright © 2010 Elsevier B.V. All rights reserved.

Study the fragment size distribution in dynamic fragmentation of laser shock loding tin

NASA Astrophysics Data System (ADS)

He, Weihua; Xin, Jianting; Chu, Genbai; Shui, Min; Xi, Tao; Zhao, Yongqiang; Gu, Yuqiu

2017-06-01

Characterizing the distribution of fragment size produced from dynamic fragmentation process is very important for fundamental science like predicting material dymanic response performance and for a variety of engineering applications. However, only a few data about fragment mass or size have been obtained due to its great challenge in its dynamic measurement. This paper would focus on investigating the fragment size distribution from the dynamic fragmentation of laser shock-loaded metal. Material ejection of tin sample with wedge shape groove in the free surface is collected with soft recovery technique. Via fine post-shot analysis techniques including X-ray micro-tomography and the improved watershed method, it is found that fragments can be well detected. To characterize their size distributions, a random geometric statistics method based on Poisson mixtures was derived for dynamic heterogeneous fragmentation problem, which leads to a linear combinational exponential distribution. Finally we examined the size distribution of laser shock-loaded tin with the derived model, and provided comparisons with other state-of-art models. The resulting comparisons prove that our proposed model can provide more reasonable fitting result for laser shock-loaded metal.

Temporal Changes in Forest Contexts at Multiple Extents: Three Decades of Fragmentation in the Gran Chaco (1979-2010), Central Argentina.

PubMed

Frate, Ludovico; Acosta, Alicia T R; Cabido, Marcelo; Hoyos, Laura; Carranza, Maria Laura

2015-01-01

The context in which a forest exists strongly influences its function and sustainability. Unveiling the multi-scale nature of forest fragmentation context is crucial to understand how human activities affect the spatial patterns of forests across a range of scales. However, this issue remains almost unexplored in subtropical ecosystems. In this study, we analyzed temporal changes (1979-2010) in forest contexts in the Argentinean dry Chaco at multiple extents. We classified forests over the last three decades based on forest context amount (Pf) and structural connectivity (Pff), which were measured using a moving window approach fixed at eight different extents (from local, ~ 6 ha, to regional, ~ 8300 ha). Specific multi-scale forest context profiles (for the years 1979 and 2010) were defined by projecting Pf vs. Pff mean values and were compared across spatial extents. The distributions of Pf across scales were described by scalograms and their shapes over time were compared. The amount of agricultural land and rangelands across the scales were also analyzed. The dry Chaco has undergone an intensive process of fragmentation, resulting in a shift from landscapes dominated by forests with gaps of rangelands to landscapes where small forest patches are embedded in agricultural lands. Multi-scale fragmentation analysis depicted landscapes in which local exploitation, which perforates forest cover, occurs alongside extensive forest clearings, reducing forests to small and isolated patches surrounded by agricultural lands. In addition, the temporal diminution of Pf's variability along with the increment of the mean slope of the Pf 's scalograms, indicate a simplification of the spatial pattern of forest over time. The observed changes have most likely been the result of the interplay between human activities and environmental constraints, which have shaped the spatial patterns of forests across scales. Based on our results, strategies for the conservation and sustainable management of the dry Chaco should take into account both the context of each habitat location and the scales over which a forest pattern might be preserved, altered or restored.

Temporal Changes in Forest Contexts at Multiple Extents: Three Decades of Fragmentation in the Gran Chaco (1979-2010), Central Argentina

PubMed Central

Frate, Ludovico; Acosta, Alicia T. R.; Cabido, Marcelo; Hoyos, Laura; Carranza, Maria Laura

2015-01-01

The context in which a forest exists strongly influences its function and sustainability. Unveiling the multi-scale nature of forest fragmentation context is crucial to understand how human activities affect the spatial patterns of forests across a range of scales. However, this issue remains almost unexplored in subtropical ecosystems. In this study, we analyzed temporal changes (1979–2010) in forest contexts in the Argentinean dry Chaco at multiple extents. We classified forests over the last three decades based on forest context amount (P f) and structural connectivity (P ff), which were measured using a moving window approach fixed at eight different extents (from local, ~ 6 ha, to regional, ~ 8300 ha). Specific multi-scale forest context profiles (for the years 1979 and 2010) were defined by projecting P f vs. P ff mean values and were compared across spatial extents. The distributions of P f across scales were described by scalograms and their shapes over time were compared. The amount of agricultural land and rangelands across the scales were also analyzed. The dry Chaco has undergone an intensive process of fragmentation, resulting in a shift from landscapes dominated by forests with gaps of rangelands to landscapes where small forest patches are embedded in agricultural lands. Multi-scale fragmentation analysis depicted landscapes in which local exploitation, which perforates forest cover, occurs alongside extensive forest clearings, reducing forests to small and isolated patches surrounded by agricultural lands. In addition, the temporal diminution of P f’s variability along with the increment of the mean slope of the P f ‘s scalograms, indicate a simplification of the spatial pattern of forest over time. The observed changes have most likely been the result of the interplay between human activities and environmental constraints, which have shaped the spatial patterns of forests across scales. Based on our results, strategies for the conservation and sustainable management of the dry Chaco should take into account both the context of each habitat location and the scales over which a forest pattern might be preserved, altered or restored. PMID:26630387

Environmental Occurrence of Madurella mycetomatis, the Major Agent of Human Eumycetoma in Sudan

PubMed Central

Ahmed, Abdalla; Adelmann, Daniel; Fahal, Ahmed; Verbrugh, Henri; Belkum, Alex van; Hoog, Sybren de

2002-01-01

Madurella mycetomatis is the main causative agent of human eumycetoma, a severe debilitating disease endemic in Sudan. It has been suggested that eumycetoma has a soil-borne or thorn prick-mediated origin. For this reason, efforts were undertaken to culture M. mycetomatis from soil samples (n = 43) and thorn collections (n = 35) derived from areas in which it is endemic. However, ribosomal sequencing data revealed that the black fungi obtained all belonged to other fungal species. In addition, we performed PCR-mediated detection followed by restriction fragment length polymorphism (RFLP) analysis for the identification of M. mycetomatis DNA from the environmental samples as well as biopsies from patients with mycetoma. In the case of the Sudanese soil samples, 17 out of 74 (23%) samples were positive for M. mycetomatis DNA. Among the thorn collections, 1 out of 22 (5%) was positive in the PCR. All PCR RFLP patterns clearly indicated the presence of M. mycetomatis. In contrast, 15 Dutch and English control soil samples were all negative. Clinically and environmentally obtained fungal PCR products share the same PCR RFLP patterns, suggesting identity, at least at the species level. These observations support the hypothesis that eumycetoma is primarily environmentally acquired and suggest that M. mycetomatis needs special conditions for growth, as direct isolation from the environment seems to be impossible. PMID:11880433

Season-modulated responses of Neotropical bats to forest fragmentation.

PubMed

Ferreira, Diogo F; Rocha, Ricardo; López-Baucells, Adrià; Farneda, Fábio Z; Carreiras, João M B; Palmeirim, Jorge M; Meyer, Christoph F J

2017-06-01

Seasonality causes fluctuations in resource availability, affecting the presence and abundance of animal species. The impacts of these oscillations on wildlife populations can be exacerbated by habitat fragmentation. We assessed differences in bat species abundance between the wet and dry season in a fragmented landscape in the Central Amazon characterized by primary forest fragments embedded in a secondary forest matrix. We also evaluated whether the relative importance of local vegetation structure versus landscape characteristics (composition and configuration) in shaping bat abundance patterns varied between seasons. Our working hypotheses were that abundance responses are species as well as season specific, and that in the wet season, local vegetation structure is a stronger determinant of bat abundance than landscape-scale attributes. Generalized linear mixed-effects models in combination with hierarchical partitioning revealed that relationships between species abundances and local vegetation structure and landscape characteristics were both season specific and scale dependent. Overall, landscape characteristics were more important than local vegetation characteristics, suggesting that landscape structure is likely to play an even more important role in landscapes with higher fragment-matrix contrast. Responses varied between frugivores and animalivores. In the dry season, frugivores responded more to compositional metrics, whereas during the wet season, local and configurational metrics were more important. Animalivores showed similar patterns in both seasons, responding to the same group of metrics in both seasons. Differences in responses likely reflect seasonal differences in the phenology of flowering and fruiting between primary and secondary forests, which affected the foraging behavior and habitat use of bats. Management actions should encompass multiscale approaches to account for the idiosyncratic responses of species to seasonal variation in resource abundance and consequently to local and landscape scale attributes.

Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs

PubMed Central

2011-01-01

Background Various solutions have been introduced for the identification of post-translational modification (PTM) from tandem mass spectrometry (MS/MS) in proteomics field but the identification of peptide modifiers, such as Ubiquitin (Ub) and ubiquitin-like proteins (Ubls), is still a challenge. The fragmentation of peptide modifier produce complex shifted ion mass patterns in combination with other PTMs, which makes it difficult to identify and locate the PTMs on a protein sequence. Currently, most PTM identification methods do not consider the complex fragmentation of peptide modifier or deals it separately from the other PTMs. Results We developed an advanced PTM identification method that inspects possible ion patterns of the most known peptide modifiers as well as other known biological and chemical PTMs to make more comprehensive and accurate conclusion. The proposed method searches all detectable mass differences of measured peaks from their theoretical values and the mass differences within mass tolerance range are grouped as mass shift classes. The most possible locations of multiple PTMs including peptide modifiers can be determined by evaluating all possible scenarios generated by the combination of the qualified mass shift classes.The proposed method showed excellent performance in the test with simulated spectra having various PTMs including peptide modifiers and in the comparison with recently developed methods such as QuickMod and SUMmOn. In the analysis of HUPO Brain Proteome Project (BPP) datasets, the proposed method could find the ubiquitin modification sites that were not identified by other conventional methods. Conclusions This work presents a novel method for identifying bothpeptide modifiers that generate complex fragmentation patternsand PTMs that are not fragmented during fragmentation processfrom tandem mass spectra. PMID:22373085

An optimized OPC and MDP flow for reducing mask write time and mask cost

NASA Astrophysics Data System (ADS)

Yang, Ellyn; Li, Cheng He; Park, Se Jin; Zhu, Yu; Guo, Eric

2010-09-01

In the process of optical proximity correction, layout edge or fragment is migrating to proper position in order to minimize edge placement error (EPE). During this fragment migration, several factors other than EPE can be also taken into account as a part of cost function for optimal fragment displacement. Several factors are devised in favor of OPC stability, which can accommodate room for high mask error enhancement factor (MEEF), lack of process window, catastrophic pattern failure such as pinch/bridge and improper fragmentation. As technology node becomes finer, there happens conflict between OPC accuracy and stability. Especially for metal layers, OPC has focused on the stability by loss of accurate OPC results. On this purpose, several techniques have been introduced, which are target smoothing, process window aware OPC, model-based retargeting and adaptive OPC. By utilizing those techniques, OPC enables more stabilized patterning, instead of realizing design target exactly on wafer. Inevitably, post-OPC layouts become more complicated because those techniques invoke additional edge, or fragments prior to correction or during OPC iteration. As a result, jogs of post OPC layer can be dramatically increased, which results in huge number of shot count after data fracturing. In other words, there is trade-off relationship between data complexity and various methods for OPC stability. In this paper, those relationships have been investigated with respect to several technology nodes. The mask shot count reduction is achieved by reducing the number of jogs with which EPE difference are within pre-specified value. The effect of jog smoothing on OPC output - in view of OPC performance and mask data preparation - was studied quantitatively for respective technology nodes.