bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstruction of a human mitochondrial complex I mutation in the unicellular green alga Chlamydomonas
Authors: Larosa Véronique , Coosemans Nadine , Motte Patrick , Bonnefoy Nathalie , Remacle Claire 
Published: January 2012

SummaryDefects in complex I (NADH:ubiquinone oxidoreductase (EC 1.6.5.3)) are the most frequent cause of human respiratory disorders. The pathogenicity of a given human mitochondrial mutation can be difficult to demonstrate because the mitochondrial genome harbors large numbers of polymorphic base changes that have no pathogenic significance. In addition, mitochondrial mutations are usually found in the heteroplasmic state, which may hide the biochemical effect of the mutation. We propose that the unicellular green alga Chlamydomonas could be used to study such mutations because (i) respiratory complex‐deficient mutants are viable and mitochondrial mutations are found in the homoplasmic state, (ii) transformation of the mitochondrial genome is feasible, and (iii) Chlamydomonas complex I is similar to that of humans. To illustrate this proposal, we introduced a Leu157Pro substitution into the Chlamydomonas ND4 subunit of complex I in two recipient strains by biolistic transformation, demonstrating that site‐directed mutagenesis of the Chlamydomonas mitochondrial genome is possible. This substitution did not lead to any respiratory enzyme defects when present in the heteroplasmic state in a patient with chronic progressive external ophthalmoplegia. When present in the homoplasmic state in the alga, the mutation does not prevent assembly of whole complex I (950 kDa) and the NADH dehydrogenase activity of the peripheral arm of the complex is mildly affected. However, the NADH:duroquinone oxidoreductase activity is strongly reduced, suggesting that the substitution could affect binding of ubiquinone to the membrane domain. The in vitro defects correlate with a decrease in dark respiration and growth rate in vivo.
Non‐random distribution of extensive chromosome rearrangements in Brassica napus depends on genome organization
Authors: Nicolas Stéphane D. , Monod Hervé , Eber Frédérique , Chèvre Anne‐Marie , Jenczewski Eric 
Published: January 2012

SummaryChromosome rearrangements are common, but their dynamics over time, mechanisms of occurrence and the genomic features that shape their distribution and rate are still poorly understood. We used allohaploid Brassica napus (AC, n = 19) as a model to analyze the effect of genomic features on the formation and diversity of meiotically driven chromosome rearrangements. We showed that allohaploid B. napus meiosis leads to extensive new structural diversity. Almost every allohaploid offspring carried a unique combination of multiple rearrangements throughout the genome, and was thus structurally differentiated from both its haploid parent and its sister plants. This large amount of genome reshuffling was remarkably well‐tolerated in the heterozygous state, as neither male nor female fertility were strongly reduced, and meiosis behavior was normal in most cases. We also used a quantitative statistical model, which accounted for 75% of the observed variation in rearrangement rates, to show that the distribution of meiotically driven chromosome rearrangements was not random but was shaped by three principal genomic features. In descending order of importance, the rate of marker loss increased strongly with genetic distance from the centromere, the degree of collinearity between chromosomes, and the genome of origin (A < C). Overall, our results demonstrate that B. napus accumulates a large number of genetic changes, but these rearrangements are not randomly distributed in the genome. The structural genetic diversity produced by the allohaploid pathway and its role in the evolution of polyploid species compared to diploid meiosis are discussed.
Visual marker and Agrobacterium‐delivered recombinase enable the manipulation of the plastid genome in greenhouse‐grown tobacco plants
Authors: Tungsuchat‐Huang Tarinee , Maliga Pal 
Published: January 2012

SummarySuccessful manipulation of the plastid genome (ptDNA) has been carried out so far only in tissue‐culture cells, a limitation that prevents plastid transformation being applied in major agronomic crops. Our objective is to develop a tissue‐culture independent protocol that enables manipulation of plastid genomes directly in plants to yield genetically stable seed progeny. We report that in planta excision of a plastid aurea bar gene (bar au) is detectable in greenhouse‐grown plants by restoration of the green pigmentation in tobacco leaves. The P1 phage Cre or PhiC31 phage Int site‐specific recombinase was delivered on the Agrobacterium T‐DNA injected at the axillary bud site, resulting in the excision of the target‐site flanked marker gene. Differentiation of new apical meristems was forced by decapitating the plants above the injection site. The new shoot apex that differentiated at the injection site contained bar au‐free plastids in 30–40% of the injected plants, of which 7% transmitted the bar au‐free plastids to the seed progeny. The success of obtaining seed with bar au‐free plastids depended on repeatedly forcing shoot development from axillary buds, a process that was guided by the size and position of green sectors in the leaves. The success of in planta plastid marker excision proved that manipulation of the plastid genomes is feasible within an intact plant. Extension of the protocol to in planta plastid transformation depends on the development of new protocols for the delivery of transforming DNA encoding visual markers.
Inducible NAD overproduction in Arabidopsis alters metabolic pools and gene expression correlated with increased salicylate content and resistance to Pst‐AvrRpm1
Authors: Pétriacq Pierre , de Bont Linda , Hager Jutta , Didierlaurent Laure , Mauve Caroline , Guérard Florence , Noctor Graham , Pelletier Sandra , Renou Jean‐Pierre , Tcherkez Guillaume , Gakière Bertrand 
Published: January 2012

SummaryPlant development and function are underpinned by redox reactions that depend on co‐factors such as nicotinamide adenine dinucleotide (NAD). NAD has recently been shown to be involved in several signalling pathways that are associated with stress tolerance or defence responses. However, the mechanisms by which NAD influences plant gene regulation, metabolism and physiology still remain unclear. Here, we took advantage of Arabidopsis thaliana lines that overexpressed the nadC gene from E. coli, which encodes the NAD biosynthesis enzyme quinolinate phosphoribosyltransferase (QPT). Upon incubation with quinolinate, these lines accumulated NAD and were thus used as inducible systems to determine the consequences of an increased NAD content in leaves. Metabolic profiling showed clear changes in several metabolites such as aspartate‐derived amino acids and NAD‐derived nicotinic acid. Large‐scale transcriptomic analyses indicated that NAD promoted the induction of various pathogen‐related genes such as the salicylic acid (SA)‐responsive defence marker PR1. Extensive comparison with transcriptomic databases further showed that gene expression under high NAD content was similar to that obtained under biotic stress, eliciting conditions or SA treatment. Upon inoculation with the avirulent strain of Pseudomonas syringae pv. tomato Pst‐AvrRpm1, the nadC lines showed enhanced resistance to bacteria infection and exhibited an ICS1‐dependent build‐up of both conjugated and free SA pools. We therefore concluded that higher NAD contents are beneficial for plant immunity by stimulating SA‐dependent signalling and pathogen resistance.
In vivo visualization of RNA in plants cells using the λN22 system and a GATEWAY‐compatible vector series for candidate RNAs
Authors: Schönberger Johannes , Hammes Ulrich Z. , Dresselhaus Thomas 
Published: January 2012

SummaryThe past decade has seen a tremendous increase in RNA research, which has demonstrated that RNAs are involved in many more processes than were previously thought. The dynamics of RNA synthesis towards their regulated activity requires the interplay of RNAs with numerous RNA binding proteins (RBPs). The localization of RNA, a mechanism for controlling translation in a spatial and temporal fashion, requires processing and assembly of RNA into transport granules in the nucleus, transport towards cytoplasmic destinations and regulation of its activity. Compared with animal model systems little is known about RNA dynamics and motility in plants. Commonly used methods to study RNA transport and localization are time‐consuming, and require expensive equipment and a high level of experimental skill. Here, we introduce the λN22 RNA stem‐loop binding system for the in vivo visualization of RNA in plant cells. The λN22 system consists of two components: the λN22 RNA binding peptide and the corresponding box‐B stem loops. We generated fusions of λN22 to different fluorophores and a GATEWAY vector series for the simple fusion of any target RNA 5′ or 3′ to box‐B stem loops. We show that the λN22 system can be used to detect RNAs in transient expression assays, and that it offers advantages compared with the previously described MS2 system. Furthermore, the λN22 system can be used in combination with the MS2 system to visualize different RNAs simultaneously in the same cell. The toolbox of vectors generated for both systems is easy to use and promises significant progress in our understanding of RNA transport and localization in plant cells.
Host conservatism, host shifts and diversification across three trophic levels in two Neotropical forests
Authors: WILSON J. S. , FORISTER M. L. , DYER L. A. , O’CONNOR J. M. , BURLS K. , FELDMAN C. R. , JARAMILLO M. A. , MILLER J. S. , RODRÍGUEZ‐CASTAÑEDA G. , TEPE E. J. , WHITFIELD J. B. , YOUNG B. 
Published: January 2012

AbstractHost–parasite systems have been models for understanding the connection between shifts in resource use and diversification. Despite theoretical expectations, ambiguity remains regarding the frequency and importance of host switches as drivers of speciation in herbivorous insects and their parasitoids. We examine phylogenetic patterns with multiple genetic markers across three trophic levels using a diverse lineage of geometrid moths (Eois), specialist braconid parasitoids (Parapanteles) and plants in the genusPiper. Host–parasite associations are mapped onto phylogenies, and levels of cospeciation are assessed. We find nonrandom patterns of host use within both the moth and wasp phylogenies. The moth–plant associations in particular are characterized by small radiations of moths associated with unique host plants in the same geographic area (i.e. closely related moths using the same host plant species). We suggest a model of diversification that emphasizes an interplay of factors including host shifts, vicariance and adaptation to intraspecific variation within hosts.
Divergence of ovipositor length and egg shape in a brood parasitic bitterling fish through the use of different mussel hosts
Authors: KITAMURA J. , NAGATA N. , NAKAJIMA J. , SOTA T. 
Published: January 2012

AbstractBitterling fishes deposit their eggs on the gills of living mussels using a long ovipositor. We examined whether ovipositor length (OL) and egg shape correlated with differences in host mussel species in the family Unionidae among populations of the tabira bitterling (Acheilognathus tabira) in Japan. Bitterling populations that use mussels in the sub‐family Anodontinae possessed longer ovipositors and more elongated eggs than those using mussels of Unioninae, as expected from the difference in host size between the sub‐families (anodontine mussels are larger than unionine mussels). Based on a robust phylogeny of A. tabira populations, we demonstrated that the evolution of both OL and egg shape were correlated with host differences, but not with each other, suggesting that these traits have been selected for independently. Our study demonstrates how adaptive traits for brood parasitism may diverge with host shift due to different host availability and/or interspecific competition for hosts.
Changes in reciprocal herkogamy during the tristyly–distyly transition inOxalis alpinaincrease efficiency in pollen transfer
Authors: BAENA‐DíAZ F. , FORNONI J. , SOSENSKI P. , MOLINA‐FREANER F. E. , WELLER S. G. , PÉREZ‐ISHIWARA R. , DOMÍNGUEZ C. A. 
Published: January 2012

AbstractAlthough the spatial separation of sexual organs within a flower (herkogamy) has been interpreted as a mechanism that promotes efficient pollen transfer, there have been few attempts to relate variation in herkogamy to probabilities of pollen flow. Here, we used a heterostylous species with variation in reciprocal herkogamy to test this hypothesis. We measured legitimate and illegitimate pollen flow with fluorescent dyes in four selected populations ofOxalis alpinacorresponding to the extremes of a previously reported evolutionary gradient from tristyly to distyly. After the breakdown of tristyly, the observed increment in reciprocal herkogamy between the long and short morphs was associated with a 30% increase in the proportion of dye received from compatible illegitimate pollinations. In all populations, the most likely effective pollen vectors were twoHeterosarusbee species. Our results support the adaptive value of reciprocal herkogamy in promoting efficient pollen transfer in heterostylous species.
The adaptive significance of mandibular symphyseal fusion in mammals
Authors: SCOTT J. E. , HOGUE A. S. , RAVOSA M. J. 
Published: January 2012

AbstractThe mandibular symphyseal joint is remarkably variable across major mammalian clades, ranging in adults from unfused (amphiarthrosis) to partially fused (synarthrosis) to completely ossified (synostosis). Experimental work conducted on primates suggests that greater ossification of the symphysis is a response to increased recruitment of the balancing‐side (i.e. nonchewing side) jaw‐adductor muscles during forceful unilateral biting and chewing, with increased fusion strengthening the symphysis against correspondingly elevated joint stresses. It is thus expected that species with diets composed primarily of foods that require high‐magnitude bite forces and/or repetitive loading to process will be characterized by greater degrees of symphyseal ossification than species with relatively easy‐to‐process diets (i.e. food items typified by low toughness and/or low stiffness). However, comparative support for this idea is limited. We tested this hypothesis in four dietarily diverse mammalian clades characterized by variation in symphyseal fusion – the Strepsirrhini, Marsupialia, Feliformia, and Caniformia. We scored fusion in adult specimens of 292 species, assigned each to a dietary category based on literature accounts, and tested for an association between these two variables using Pagel’s test for the correlated evolution of binary characters. Results indicate that greater fusion is associated with diets composed of resistant items in strepsirrhines, marsupials, and feliforms, providing some support for the hypothesis. However, no such relationship was detected in caniforms, suggesting that factors other than dietary mechanical properties influence symphyseal ossification. Future work should focus on such factors, as well as those that favour an unfused mandibular symphysis.
LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces
Authors: Ytournel F. , Teyssèdre S. , Roldan D. , Erbe M. , Simianer H. , Boichard D. , Gilbert H. , Druet T. , Legarra A. 
Published: January 2012

SummarySimulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re‐create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long‐range LD, allowing optimization of fine‐mapping strategies.
Calla lily chlorotic spot virus from Spider Lily (Hymenocallis litteralis) and Tobacco (Nicotiana tabacum) in the South‐west of China
Authors: Liu Yating , Lu Xiuping , Zhi Long , Zheng Yuanxian , Chen Xuejiao , Xu Yue , Wu Fajing , Li Yongzhong 
Published: January 2012

AbstractLeaf samples were collected from four spider lily and tobacco plants with tospovirus‐like symptoms in Yunnan province. The nucleocapsid ORFs of the four isolates were obtained by RT‐PCR, cloning and sequencing of the amplified products. Nucleotide sequences of the obtained amplicons were more than 90% identical to that of Calla lily chlorotic spot virus (CCSV) isolates deposited in the GenBank database. The virus induced systematic leaf necrosis, chlorotic lesions, rugosity and deformation on mechanically inoculated experimental hosts. This is the first report of CCSV in mainland China, and also on spider lily and tobacco.
Parrotfish mediation in coral mortality and bioerosion by the encrusting, excavating sponge Cliona tenuis
Authors: Márquez Juan Carlos , Zea Sven 
Published: January 2012

AbstractThe parrotfish Sparisoma viride often grazes live coral from edges undermined by the Caribbean encrusting and excavating sponge Cliona tenuis. To test whether parrotfish biting action has an effect on the dynamics of the sponge–coral interaction, we manipulated access of parrotfishes to the sponge–coral border in two species of massive corals. When parrotfish had access to the border, C. tenuis advanced significantly more slowly into the coral Siderastrea siderea than into the coral Diploria strigosa. When fish bites were prevented, sponge spread into S. siderea was further slowed down but remained the same for D. strigosa. Additionally, a thinner layer of the outer coral skeleton was removed by bioerosion when fish were excluded, a condition more pronounced in D. strigosa than in S. siderea. Thus, the speed of sponge‐spread and the extent of bioerosion by parrotfish was coral species‐dependent. It is hypothesized that coral skeleton architecture is the main variable associated with such dependency. Cliona tenuis spread is slow when undermining live S. siderea owing to the coral’s compact skeleton. The coral’s smooth and hard surface promotes a wide and shallow parrotfish bite morphology, which allows the sponge to overgrow the denuded area and thus advance slightly faster. On the less compact skeleton of the brain coral, D. strigosa, sponge spread is more rapid. This coral’s rather uneven surface sustains narrower and deeper parrotfish bites which do not facilitate the already fast sponge progress. Parrotfish corallivory thus acts synergistically with C. tenuis to further harm corals whose skeletal architecture slows sponge lateral spread. In addition, C. tenuis also appears to mediate the predator–prey fish–coral interaction by attracting parrotfish biting.
Combining echo sounding, sediment and biological data to map benthic habitats in a coastal area of the Persian Gulf
Authors: Haghi Mahsa , Savari Ahmad , Kochanian Preeta , Nabavi Mohammad Bagher , Nami Mohammad Hasan , Zakeri Mohammad , Bodaghi Mohammad 
Published: January 2012

AbstractMapping surveys of coastal benthic habitat in Qeshm Island Geopark, Persian Gulf, were conducted using a combination of biological, sedimentological and echo‐sounding data. The survey area covered approximately 233 km2 in a depth range of 5–25 m, and the data were acquired from a single beam echo sounder, grab, video and still photography. Sediment and macrofauna samples were collected by grab at 76 stations and subjected to classification and ordination analyses. Two acoustic classes were identified differentiating along the near/offshore axis. Sediment texture was dominated by fine grain sizes, with five distinct sub‐sediment types. In total, 214 macrobenthic taxa were identified, of which polychaetes accounted for 60%. Other dominant groups included young sponges, nematodes, malacostracan crustacean, bivalves, ostracods and ophiuroids. Underwater videos and still photos integrated the macrofaunal and sedimentary data and revealed a range of biogenic sedimentary features such as burrows and tubes. The biological data identified six main biological assemblages showing an inshore/offshore pattern. The macrobenthic abundance did not demonstrate a significant difference with depth, although polychaetes were positively correlated with depth. The highest abundance and species richness were observed at median depths. Species distribution and diversity did not show any correlation with sediment type. A preliminary habitat mapping of the south coast of the Qeshm Island Geopark has been carried out, integrating acoustic, sediment and biological data.
Candida‐Agglutinationstiter bei ausgewählten Krankheitsgrappen:* Candida Agglutination Titres in Selected Groups of Diseases
Authors: Hübner Ursula , Heidenbluth Ingeburg , Heerdegen Edith 
Published: January 2012

Zusammenfassung: Die Candida‐Agglutinationstiter von 431 Patienten, davon 378 mit Dermatosen, 40 mit Tumoren und ITS‐Patienten und 13 Leukosekranken, wurden unter Berücksichtigung der Sproßpilzbesiedlung der Haut, des Magen‐Darm‐Kanales oder mehrerer Organe ausgewertet. Die Häufigkeitsverteilungen der Titer der Patienten mit und ohne Pilznachweis ließen zwei deutlich unterscheidbare Kollektive erkennen. Hohe Werte wuden vorwiegend bei Besiedlung mehrerer Organsysteme gefunden. Diese traten bevozugt in den Gruppen der Kranken mit Tumoren, unter Intensivpflege, mit immunsuppressiver Dauertherapie und mit Diabetes mellitus auf. Eine absolute Trennung zwischen pathologiscben und Normal‐Titern ist nicht möglich. Der Wert 1:256 wird als kritischer Punkt angesehen.Summary: Candida agglutination titres of 431 patients‐378 with skin diseases, 40 with neoplasms or under intensive therapeutical care and 13 with leukemia‐were analysed with regard to yeast colonization of the skin, the gastro‐intestinal tract or several other organs. Distribution of antibody titres in the two groups of patients with and without demonstration of fungi showed two distinct collectives. High levels were found predominantly in connection with colonization of several organs. This was mainly the case in patients with neoplasms, those under intensive care or long‐term immunosuppressive therapy or in patients with diabetes mellitus. An unequivocal distinction between pathological and normal titres is impossible. A titer of 1:256, however, seems to mark the critical point.