bluuebunny/crossref_metadata_2025_split huggingface dataset:
Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature‐sensitive
Authors: Hirata Akira , Kanai Tamotsu , Santangelo Thomas J. , Tajiri Momoko , Manabe Kenji , Reeve John N. , Imanaka Tadayuki , Murakami Katsuhiko S. 
Published: September 2008

SummaryAll archaeal genomes encode RNA polymerase (RNAP) subunits E and F that share a common ancestry with the eukaryotic RNAP subunits A43 and A14 (Pol I), Rpb7 and Rpb4 (Pol II), and C25 and C17 (Pol III). By gene replacement, we have isolated archaeal mutants of Thermococcus kodakarensis with the subunit F‐encoding gene (rpoF) deleted, but we were unable to isolate mutants lacking the subunit E‐encoding gene (rpoE). Wild‐type T. kodakarensis grows at temperatures ranging from 60°C to 100°C, optimally at 85°C, and the ΔrpoF cells grew at the same rate as wild type at 70°C, but much slower and to lower cell densities at 85°C. The abundance of a chaperonin subunit, CpkB, was much reduced in the ΔrpoF strain growing at 85°C and increased expression of cpkB, rpoF or rpoE integrated at a remote site in the genome, using a nutritionally regulated promoter, improved the growth of ΔrpoF cells. RNAP preparations purified from ΔrpoF cells lacked subunit F and also subunit E and a transcription factor TFE that co‐purifies with RNAP from wild‐type cells, but in vitro, this mutant RNAP exhibited no discernible differences from wild‐type RNAP in promoter‐dependent transcription, abortive transcript synthesis, transcript elongation or termination.
Localization of general and regulatory proteolysis in Bacillus subtilis cells
Authors: Kirstein Janine , Strahl Henrik , Molière Noël , Hamoen Leendert W. , Turgay Kürşad 
Published: September 2008

SummaryProtein degradation mediated by ATP‐dependent proteases, such as Hsp100/Clp and related AAA+ proteins, plays an important role in cellular protein homeostasis, protein quality control and the regulation of, e.g. heat shock adaptation and other cellular differentiation processes. ClpCP with its adaptor proteins and other related proteases, such as ClpXP or ClpEP of Bacillus subtilis, are involved in general and regulatory proteolysis. To determine if proteolysis occurs at specific locations in B. subtilis cells, we analysed the subcellular distribution of the Clp system together with adaptor and general and regulatory substrate proteins, under different environmental conditions. We can demonstrate that the ATPase and the proteolytic subunit of the Clp proteases, as well as the adaptor or substrate proteins, form visible foci, representing active protease clusters localized to the polar and to the mid‐cell region. These clusters could represent a compartmentalized place for protein degradation positioned at the pole close to where most of the cellular protein biosynthesis and also protein quality control are taking place, thereby spatially separating protein synthesis and degradation.
The RACK1 signal anchor protein from Trypanosoma brucei associates with eukaryotic elongation factor 1A: a role for translational control in cytokinesis
Authors: Regmi Sandesh , Rothberg Karen G. , Hubbard James G. , Ruben Larry 
Published: September 2008

SummaryRACK1 is a WD‐repeat protein that forms signal complexes at appropriate locations in the cell. RACK1 homologues are core components of ribosomes from yeast, plants and mammals. In contrast, a cryo‐EM analysis of trypanosome ribosomes failed to detect RACK1, thus eliminating an important translational regulatory mechanism. Here we report that TbRACK1 from Trypanosoma brucei associates with eukaryotic translation elongation factor‐1a (eEF1A) as determined by tandem MS of TAP‐TbRACK1 affinity eluates, co‐sedimentation in a sucrose gradient, and co‐precipitation assays. Consistent with these observations, sucrose gradient purified 80S monosomes and translating polysomes each contained TbRACK1. When RNAi was used to deplete cells of TbRACK1, a shift in the polysome profile was observed, while the phosphorylation of a ribosomal protein increased. Under these conditions, cell growth became hypersensitive to the translational inhibitor anisomycin. The kinetoplasts and nuclei were misaligned in the postmitotic cells, resulting in partial cleavage furrow ingression during cytokinesis. Overall, these findings identify eEF1A as a novel TbRACK1 binding partner and establish TbRACK1 as a component of the trypanosome translational apparatus. The synergy between anisomycin and TbRACK1 RNAi suggests that continued translation is required for complete ingression of the cleavage furrow.
Minitags for small molecules: detecting targets of reactive small molecules in living plant tissues using ‘click chemistry’
Authors: Kaschani Farnusch , Verhelst Steven H. L. , Van Swieten Paul F. , Verdoes Martijn , Wong Chung‐Sing , Wang Zheming , Kaiser Markus , Overkleeft Herman S. , Bogyo Matthew , Van Der Hoorn Renier A. L. 
Published: September 2008

SummarySmall molecules offer unprecedented opportunities for plant research since plants respond to, metabolize, and react with a diverse range of endogenous and exogenous small molecules. Many of these small molecules become covalently attached to proteins. To display these small molecule targets in plants, we introduce a two‐step labelling method for minitagged small molecules. Minitags are small chemical moieties (azide or alkyne) that are inert under biological conditions and have little influence on the membrane permeability and specificity of the small molecule. After labelling, proteomes are extracted under denaturing conditions and minitagged proteins are coupled to reporter tags through a ‘click chemistry’ reaction. We introduce this two‐step labelling procedure in plants by studying the well‐characterized targets of E‐64, a small molecule cysteine protease inhibitor. In contrast to biotinylated E‐64, minitagged E‐64 efficiently labels vacuolar proteases in vivo. We displayed, purified and identified targets of a minitagged inhibitor that targets the proteasome and cysteine proteases in living plant cells. Chemical interference assays with inhibitors showed that MG132, a frequently used proteasome inhibitor, preferentially inhibits cysteine proteases in vivo. The two‐step labelling procedure can be applied on detached leaves, cell cultures, seedlings and other living plant tissues and, when combined with photoreactive groups, can be used to identify targets of herbicides, phytohormones and reactive small molecules selected from chemical genetic screens.
Methyl jasmonate differentially affects tocopherol content and tyrosine amino transferase activity in cultured cells of Amaranthus caudatus and Chenopodium quinoa
Authors: Antognoni F. , Faudale M. , Poli F. , Biondi S. 
Published: September 2008

AbstractTocopherols are lipid‐soluble compounds synthesised exclusively by photosynthetic organisms. In this study, in vitro callus cultures were established from two plants that are naturally rich in tocopherols, Amaranthus caudatus and Chenopodium quinoa, in order to examine whether callus cultures were able to produce these compounds at levels comparable to those observed in planta. In both species, cotyledon explants produced the best callus induction and, once established, callus cultures were grown under two different hormonal treatments to check for effects of growth and to induce chloroplast differentiation in the cells. A rapid differentiation of chloroplasts occurred only in C. quinoa cell aggregates grown in the presence of benzyladenine, leading to the production of a homogeneous green callus. In both species, only α‐tocopherol was produced by callus cultures, although levels were much lower than in planta, and the production was not influenced by the hormonal conditions. Interestingly, cell cultures of the two species responded in different ways to methyl jasmonate (MJ). In A. caudatus cultures, treatment with 100 μm MJ increased the production of α‐tocopherol up to fivefold, and the inductive effect was influenced by the hormonal composition of the medium. This increase in α‐tocopherol was associated with a proportional increase in tyrosine aminotransferase (TAT) activity, one of the key enzymes involved in tocopherol biosynthesis. By contrast, in C. quinoa cultures, elicitation with MJ did not have any effect, neither on tocopherol production, nor on TAT activity. These results are discussed in relation to chloroplast differentiation and the interplay between jasmonates and phytohormones.
High chloroplast haplotype diversity in Greek populations of beech (Fagus sylvatica L.)
Authors: Hatziskakis S. , Papageorgiou A. C. , Gailing O. , Finkeldey R. 
Published: September 2008

AbstractThe distribution of chloroplast DNA (cpDNA) variations in Greek beech (Fagus sylvatica L.) populations was studied using chloroplast microsatellite markers. Thirteen haplotypes were identified from 40 populations by combining three different primers. Most of the cpDNA variation was distributed among populations, but a considerable variation was also observed within populations. The total diversity was very high for all regions. The Nst/Gst comparison was significant, indicating phylogenetic subdivision, but no strong spatial structure was detected, suggesting complex post‐glacial migration patterns. Possible scenarios explaining this diversity pattern include the existence of several separated refugia in the region, the recolonisation of mountains by different beech lineages and the formation of an introgression zone between two different beech subspecies in the eastern part of the country.
Ice encapsulation protects rather than disturbs the freezing lichen
Authors: Bjerke J. W. 
Published: September 2008

AbstractArctic and alpine terricolous lichens are adapted to harsh environments and are tolerant to extremely low temperatures when metabolically inactive. However, there are reports indicating that freezing can be lethal to metabolically active lichens. With a projected warmer and more unstable climate, winter precipitation at high latitudes will fall more frequently as rain, causing snowmelt and encapsulating terricolous lichens in ice or exposing them to large temperature fluctuations. Lichens are a major winter food source for reindeer in most parts of the circumpolar region. A laboratory experiment tested how three hydrated reindeer forage lichen species covered by snow, encapsulated in ice, or uncovered responded to storage at freezing temperatures and subsequent warming. Photosynthetic performance (maximal fluorescence of dark‐adapted samples and net photosynthetic rates) was significantly lower in lichens not insulated by snow or ice, whereas there were few differences between the snow and ice treatments. It is suggested that snow and ice provide sufficiently moist environments to improve extracellular and reduce intracellular ice nucleation activity. Ice encapsulation, which is often lethal to vascular plants, did not have any negative effects on the studied lichens. The results indicate that complete snow and ice melt followed by refreezing can be detrimental to terricolous lichen ecosystems. Reduced lichen biomass will have a negative effect both on reindeer winter survival and the indigenous peoples who herd reindeer.
Pollination by deceit in Paphiopedilum barbigerum (Orchidaceae): a staminode exploits the innate colour preferences of hoverflies (Syrphidae)
Authors: Shi J. , Luo Y.‐B. , Bernhardt P. , Ran J.‐C. , Liu Z.‐J. , Zhou Q. 
Published: September 2008

Abstract Paphiopedilum barbigerum T. Tang et F. T. Wang, a slipper orchid native to southwest China and northern Vietnam, produces deceptive flowers that are self‐compatible but incapable of mechanical self‐pollination (autogamy). The flowers are visited by females of Allograpta javana and Episyrphus balteatus (Syrphidae) that disperse the orchid’s massulate pollen onto the receptive stigmas. Measurements of insect bodies and floral architecture show that the physical dimensions of these two fly species correlate with the relative positions of the receptive stigma and dehiscent anthers of P. barbigerum. These hoverflies land on the slippery centralised wart located on the shiny yellow staminode and then fall backwards through the labellum entrance. They are temporarily trapped in the inflated chamber composed of the interconnected labellum and column. The attractive staminode of P. barbigerum strongly reflects the colour yellow (500–560 nm), a colour preferred innately by most pollen‐eating members of the Syrphidae. No scent molecules were detected using GC mass spectrometry analysis, showing that the primary attractant in this system is visual, not olfactory. Pollination‐by‐deceit in P. barbigerum is contrasted with its congener, P. dianthum, a brood site mimic that is pollinated by ovipositing females of E. balteatus. As the natural rate of fruit set in P. barbigerum (mean 26.3% pooled over three seasons) is lower than that of P. dianthum (mean 58.5% over two seasons), the evolution of false brood sites in some Paphiopedilum spp. should be selectively advantageous as they may provide an increase in the attention and return rates of dependable pollinators to flowers that always lack a reward.
Population genetic structure inMyrtus communisL. in a chronically fragmented landscape in the Mediterranean: can gene flow counteract habitat perturbation?
Authors: Albaladejo R. G. , Carrillo L. F. , Aparicio A. , Fernández‐Manjarrés J. F. , González‐Varo J. P. 
Published: September 2008

AbstractAncient managed landscapes provide ideal opportunities to assess the consequences of habitat fragmentation on the patterns of genetic diversity and gene flow in long‐lived plant species. Using amplified fragment length polymorphism (AFLP) and allozyme markers, we quantified seed‐mediated gene flow and population genetic diversity and structure in 14 populations ofMyrtus communis(myrtle), a common endozoochorous shrub species of forest patches in lowland agricultural Mediterranean areas. Overall, allozyme diversity for myrtle was low (P95 = 25%; A = 1.411; He = 0.085) compared to other known populations, and a significant portion of populations (57%) had lower levels of allelic diversity and/or heterozygosity than expected at random, as shown by simulated resampling of the whole diversity of the landscape. We found significant correlations between allozyme variability and population size and patch isolation, but no significant inbreeding in any population. Genetic differentiation among populations for both allozyme and AFLP markers was significant (ΦST = 0.144 and ΦST = 0.142, respectively) but an isolation‐by‐distance pattern was not detected. Assignment tests on AFLP data indicated a high immigration rate in the populations (ca.20–22%), likely through effective seed dispersal across the landscape by birds and mammals. Our results suggest that genetic isolation is not the automatic outcome of habitat destruction since substantial levels of seed‐mediated gene flow are currently detectable. However, even moderate rates of gene flow seem insufficient in this long‐lived species to counteract the genetic erosion and differentiation imposed by chronic habitat destruction.
Systematization, Distribution and Territory of the Middle Cerebral Artery on the Brain Surface in Chinchilla (Chinchilla lanigera)
Authors: De Araujo A. C. P. , Campos R. 
Published: September 2008

SummaryThe aim of the present study was to analyse thirty chinchilla (Chinchilla lanigera) brains, injected with latex, and to systematize and describe the distribution and the vascularization territories of the middle cerebral artery. This long vessel, after it has originated from the terminal branch of the basilar artery, formed the following collateral branches: rostral, caudal and striated (perforating) central branches. After crossing the lateral rhinal sulcus, the middle cerebral artery emitted a sequence of rostral and caudal convex hemispheric cortical collateral branches on the convex surface of the cerebral hemisphere to the frontal, parietal, temporal and occipital lobes. Among the rostral convex hemispheric branches, a trunk was observed, which reached the frontal and parietal lobes and, in a few cases, the occipital lobe. The vascular territory of the chinchilla’s middle cerebral artery included, in the cerebral hemisphere basis, the lateral cerebral fossa, the caudal third of the olfactory trigone, the rostral two‐thirds of the piriform lobe, the lateral olfactory tract, and most of the convex surface of the cerebral hemisphere, except for a strip between the cerebral longitudinal fissure and the vallecula, which extended from the rostral to the caudal poles bordering the cerebral transverse fissure.
Myelinated, synapsing cultures of murine spinal cord – validation as an in vitro model of the central nervous system
Authors: Thomson C. E. , McCulloch M. , Sorenson A. , Barnett S. C. , Seed B. V. , Griffiths I. R. , McLaughlin M. 
Published: September 2008

AbstractResearch in central nervous system (CNS) biology and pathology requires in vitro models, which, to recapitulate the CNS in vivo, must have extensive myelin and synapse formation under serum‐free (defined) conditions. However, finding such a model has proven difficult. The technique described here produces dense cultures of myelinated axons, with abundant synapses and nodes of Ranvier, that are suitable for both morphological and biochemical analysis. Cellular and molecular events were easily visualised using conventional microscopy. Ultrastructurally, myelin sheaths were of the appropriate thickness relative to axonal diameter (G‐ratio). Production of myelinated axons in these cultures was consistent and repeatable, as shown by statistical analysis of multiple experimental repeats. Myelinated axons were so abundant that from one litter of embryonic mice, myelin was produced in amounts sufficient for bulk biochemical analysis. This culture method was assessed for its ability to generate an in vitro model of the CNS that could be used for both neurobiological and neuropathological research. Myelin protein kinetics were investigated using a myelin fraction isolated from the cultures. This fraction was found to be superior, quantitatively and qualitatively, to the fraction recovered from standard cultures of dissociated oligodendrocytes, or from brain slices. The model was also used to investigate the roles of specific molecules in the pathogenesis of inflammatory CNS diseases. Using the defined conditions offered by this culture system, dose‐specific, inhibitory effects of inflammatory cytokines on myelin formation were demonstrated, unequivocally. The method is technically quick, easy and reliable, and should have wide application to CNS research.
Embryonic motor activity and implications for regulating motoneuron axonal pathfinding in zebrafish
Authors: Menelaou Evdokia , Husbands Erin E. , Pollet Robin G. , Coutts Christopher A. , Ali Declan W. , Svoboda Kurt R. 
Published: September 2008

AbstractZebrafish embryos exhibit spontaneous contractions of the musculature as early as 18–19 h post fertilization (hpf) when removed from their protective chorion. These movements are likely initiated by early embryonic central nervous system activity. We have made the observation that narrowminded mutant embryos (hereafter, nrd −/−) lack normal embryonic motor output upon dechorionation. However, these mutants can swim and respond to tactile stimulation by larval stages of development. nrd −/− embryos exhibit defects in neural crest development, slow muscle development and also lack spinal mechanosensory neurons known as Rohon–Beard (RB) neurons. At early developmental stages (i.e. 21–22 hpf) and while still in their chorions, nrd siblings (nrd +/?) exhibited contractions of the musculature at a rate similar to wild‐type embryos. Anatomical analysis indicated that RB neurons were present in the motile embryos, but absent in the non‐motile embryos, indicating that the non‐motile embryos were nrd −/− embryos. Further anatomical analysis of nrd −/− embryos revealed errors in motoneuron axonal pathfinding that persisted into the larval stage of development. These errors were reversed when nrd −/− embryos were raised in high [K+] beginning at 21 hpf, indicating that the abnormal axonal phenotypes may be related to a lack of depolarizing activity early in development. When activity was blocked with tricaine in wild‐type embryos, motoneuron phenotypes were similar to the motoneuron phenotypes in nrd −/− embryos. These results implicate early embryonic activity in conjunction with other factors as necessary for normal motoneuron development.
UK Multinationals' Effective Use of Financial Currency‐Hedge Techniques: Estimating and Explaining Foreign Exchange Exposure Using Bilateral Exchange Rates
Authors: Makar Stephen D. , Huffman Stephen P. 
Published: September 2008

AbstractUsing a unique dataset of recently available accounting disclosures, this study examines the relationship between UK multinationals' stock returns and changes in the principal exchange rate to which each firm is most exposed. We find more firms with significant foreign exchange exposure estimates using this firm‐specific principal currency data, compared with those exposure estimates using the broad exchange rate index data prevalent in prior studies. The cross‐sectional variations in such principal‐currency exposure estimates are explained in relation to the financial currency‐hedge techniques that each firm specifically identifies as being used to manage its currency risk. In particular, we provide evidence that firms effectively use foreign currency derivatives and foreign‐denominated debt to reduce the currency risk associated with the bilateral exchange rate to which they are most exposed. This study is important to both the academic and the practitioner communities because it represents the first use of publicly available UK disclosures to improve the estimation and explanation of foreign exchange exposure.
International Variation in Bank Accounting Information Content
Authors: Zhao Ronald , He Yihong 
Published: September 2008

AbstractThis study explores the cross‐country impact of financial system and banking regulations on the information content of bank earnings and book value. Test results provide empirical evidence that financial system and banking regulations have a joint effect on the association of equity price with earnings and book value components in Germany, France, the United Kingdom and United States. This effect is explainable by the objective bank function, which shows that earnings of the period determine the terminal book value, thus consistent with the clean surplus accounting approach. Cross‐country variation in bank accounting information content calls for caution in interpreting international bank financial and operating ratios.
Analyst Following, Institutional Investors and Pricing of Future Earnings: Evidence from Korea
Authors: Choi Bobae , Jung Kooyul 
Published: September 2008

AbstractThis paper examines the role of sophisticated investors in pricing future earnings in Korea. Using the future earnings response coefficient (FERC) model, we test the effect of analyst following and institutional ownership on the informativeness of stock returns for future earnings. We find that the informativeness of stock returns for future earnings, measured as the FERC, increases with the analyst following and institutional ownership. We also investigate how the recently introduced Regulation Fair Disclosure in Korea affects the informativeness of stock returns for future earnings and its relation with analyst following and institutional ownership. The results show that the regulation decreases the FERC in general and its relation with analyst following, suggesting that analysts' superior ability is impaired after the regulation.