bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase I study of cisplatin, vinorelbine, and concurrent thoracic radiotherapy for unresectable stage III non‐small cell lung cancer
Authors: Sekine Ikuo , Noda Kazumasa , Oshita Fumihiro , Yamada Kouzou , Tanaka Manabu , Yamashita Kosuke , Nokihara Hiroshi , Yamamoto Noboru , Kunitoh Hideo , Ohe Yuichiro , Tamura Tomohide , Kodama Tetsuro , Sumi Minako , Saijo Nagahiro
Published: August 2005

To determine the recommended phase II dose of vinorelbine in combination with cisplatin and thoracic radiotherapy (TRT) in patients with unresectable stage III non‐small cell lung cancer (NSCLC), 18 patients received cisplatin (80 μg/m2) on day 1 and vinorelbine (20 μg/m2 in level 1, and 25 μg/m2 in level 2) on days 1 and 8 every 4 weeks for 4 cycles. TRT consisted of a single dose of 2 Gy once daily for 3 weeks followed by a rest of 4 days, and then the same TRT for 3 weeks to a total dose of 60 Gy. Fifteen (83%) patients received 60 Gy of TRT and 14 (78%) patients received 4 cycles of chemotherapy. Ten (77%) of 13 patients at level 1 and all 5 patients at level 2 developed grade 3‐4 neutro‐penia. Four (31%) patients at level 1 and 3 (60%) patients at level 2 developed grade 3‐4 infection. None developed ≥grade 3 esophagitis or lung toxicity. Dose‐limiting toxicity was noted in 33% of the patients in level 1 and in 60% of the patients in level 2. The overall response rate (95% confidence interval) was 83% (59–96%) with 15 partial responses. The median survival time was 30.4 months, and the 1‐year, 2‐year, and 3‐year survival rates were 72%, 61%, and 50%, respectively. In conclusion, the recommended dose is the level 1 dose, and this regimen is feasible and promising in patients with stage III NSCLC.
A method for relating fault geometry, slip rate and uplift data above fault‐propagation folds
Authors: Hardy Stuart , Poblet Josep
Published: August 2005

Typically, the problem of constructing a balanced cross‐section across a fault‐propagation fold has been cast in terms of static entities such as fault dip, fold axial angles and limb dips. Increasingly, however, surficial data such as rates of uplift or erosion are becoming available above fault‐related folds. These data are often used to derive or constrain fault‐slip rates on deeper thrust faults and, ultimately, calculate horizontal shortening rates. However, where thrust faults are blind, there has been no simple method for relating fault geometry and slip to uplift data. This short contribution presents a series of new relationships (derived from velocity descriptions of deformation) that relate fault geometry and slip rate to measurements of uplift above flexural‐slip and trishear fault‐propagation folds. We examine the differences in uplift across such structures, their implications for the calculation of rates of fault slip and horizontal shortening and make comparisons with natural examples.
How does alluvial sedimentation at range fronts modify the erosional dynamics of mountain catchments?
Authors: Carretier S. , Lucazeau F.
Published: August 2005

At the geological time scale, the way in which the erosion of drainage catchments responds to tectonic uplift and climate changes depends on boundary conditions. In particular, sediment accumulation and erosion occurring at the edge of mountain ranges should influence the base level of mountain catchments, as well as sediment and water discharges. In this paper, we use a landform evolution model (LEM) to investigate how the presence of alluvial sedimentation at range fronts affects catchment responses to climatic or tectonic changes. This approach is applied to a 25 km × 50 km domain, in which the central part is uplifted progressively to simulate the growth of a small mountain range. The LEM includes different slope and river processes that can compete with each other. This competition leads to ‘transport‐limited’, ‘detachment‐limited’ or ‘mixed’ transport conditions in mountains at dynamic equilibrium. In addition, two end‐member algorithms (the channellized‐flow and the sheet‐flow regimes) have been included for the alluvial fan‐flow regime. The three transport conditions and the two flow algorithms represent six different models for which the responses to increase of rock uplift rate and/or cyclic variation of the precipitation rate are investigated.

Our results indicate that addition of an alluvial apron increases the long‐term mountain denudation. In response to uplift, mountain rivers adapt their profile in two successive stages; first by propagation of an erosion wave and then by slowly increasing their channel gradients. During the second stage, the erosion rate is almost uniform across the catchment area at any one time, which suggests that dynamic equilibrium has been reached, although the balance between erosion and rock uplift rates has not yet been achieved. This second stage is initiated by the uplift of the mountain river outlets because of sedimentation aggradation at the mountain front. The response time depends on the type of water flow imposed on the alluvial fans domains (× by 1.5 for channelized flow regime and by 10 for the sheet flow one).

Cyclic variations of precipitation rate generate cyclic incisions in the alluvial apron. These incision pulses create knick‐points in the river profile in the case of ‘detachment‐limited’ and ‘mixed’ river conditions, which could be mistaken for tectonically induced knick‐points. ‘Transport‐limited’ conditions do not create such knick‐points, but nevertheless trigger erosion in catchments. The feedbacks linked to sedimentation and erosion at range front can therefore control catchment incision or aggradation. In addition, random river captures in the range front trigger auto‐cyclic erosion pulses in the catchment, capable of generating incision–aggradation cycles.
t(14;22)(q32;q11) in non‐Hodgkin lymphoma and myeloid leukaemia: molecular cytogenetic investigations
Authors: Aamot Hege Vangstein , Bjørnslett Merete , Delabie Jan , Heim Sverre
Published: August 2005

Two non‐Hodgkin lymphomas (NHL), one chronic lymphocytic leukaemia/small lymphocytic lymphoma and one diffuse large B‐cell lymphoma and three cases of myeloid leukaemia, two chronic (CML) and one acute (AML), showed, by G‐banding analysis, apparently identical chromosomal translocations t(14;22)(q32;q11), in three of the cases as the sole abnormality. Fluorescence in situ hybridisation (FISH) analysis with locus‐specific probes for ABL at 9q34 [bacterial artificial chromosomes (BACs) 835J22 and 1132H12], IGH at 14q32 [P1 artificial chromosome (PAC) 998D24] and IGL (PAC 1019H10) and BCR (BAC 74M14) at 22q11, as well as multicolour in situ hybridisation (M‐FISH) analyses were performed. A three‐way variant translocation of the classical t(9;22)(q34;q11), t(9;22;14)(q34;q11;q32), involving both BCR and ABL, was unravelled by the molecular cytogenetic investigations in the three myeloid leukaemia cases; a similar variant translocation has previously been reported in seven CML. The two cases of NHL (one NHL with a similar 14;22‐translocation has been reported previously) had no involvement of BCR or ABL, but instead the IGH and IGL genes were shown to be juxtaposed by the t(14;22)(q32;q11). How such a rearrangement with recombination of IGH and IGL might elicit a pathogenetic effect is completely unknown.
Combining prenylation inhibitors causes synergistic cytotoxicity, apoptosis and disruption of RAS‐to‐MAP kinase signalling in multiple myeloma cells
Authors: Morgan Michael A. , Sebil Tarkan , Aydilek Erdem , Peest Dietrich , Ganser Arnold , Reuter Christoph W. M.
Published: August 2005

The high incidence of activating RAS mutations, coupled with accumulating evidence linking RAS to multiple myeloma (MM) pathogenesis, indicate that novel therapies utilising inhibitors of RAS prenylation and signalling may be successful in the management of this disease. While preclinical studies investigating prenylation inhibitors, such as lovastatin, farnesyltransferase inhibitors (FTI) and geranylgeranyltransferase inhibitors (GGTI), have been promising, recent phase I/II clinical trials with FTI R115777 were disappointing, suggesting resistance to FTI monotherapy. To address this issue, the effects of FTI, GGTI and lovastatin alone and in combination were analysed in MM cell lines and primary cells. FTI treatment blocked H‐RAS processing, but was ineffective at inhibiting K‐ and N‐RAS prenylation because of alternative geranylgeranylation of these isoforms. However, combinations of FTI and GGTI or lovastatin were found to synergistically inhibit MM cell proliferation, migration, K‐ and N‐RAS processing, RAS‐to‐mitogen‐activated protein kinase signalling and to induce apoptosis. In contrast to FTI, lovastatin and some GGTI were found to cause intracellular accumulation of Rho proteins. Our results suggest that clinical efficacy of prenylation inhibitors in MM are limited by alternative prenylation of several small G‐proteins, such as RhoB, K‐ and N‐RAS. Furthermore, strategies combining FTI with GGTI or statins may provide greater efficacy in MM treatment.
Heterogeneous intracellular expression of B‐cell receptor components in B‐cell chronic lymphocytic leukaemia (B‐CLL) cells and effects of CD79b gene transfer on surface immunoglobulin levels in a B‐CLL‐derived cell line
Authors: Minuzzo Sonia , Indraccolo Stefano , Tosello Valeria , Piovan Erich , Cabrelle Anna , Trentin Livio , Semenzato Giampietro , Amadori Alberto
Published: August 2005

B‐cell chronic lymphocytic leukaemia (B‐CLL) cells display low amounts of surface immunoglobulins (sIg). To investigate the mechanisms underlying this phenomenon, we performed a thorough study of surface and intracellular expression of the B‐cell receptor (BCR) components in B‐CLL cells using flow cytometry. There was an heterogeneous pattern of expression. Overall, 20 of 22 samples showed reduced sIgM levels, compared with normal B cells. Among them, three (15%) had very low to undetectable intracellular IgM levels and variable amounts of CD79a and CD79b; nine (45%) had low intracellular CD79b levels but appreciable levels of IgM and CD79a; and eight (40%) had relatively normal intracellular levels of all BCR components. To investigate whether surface BCR levels could be controlled by the rate of CD79b synthesis, adenoviral vectors encoding CD79b were generated and used for gene transfer experiments. Delivery of CD79b to non‐B cells transfected with IgM and CD79a lead to high‐level expression of a functional BCR. Moreover, CD79b gene transfer in a B cell line derived from a B‐CLL patient and characterised by low intracellular levels of endogenous CD79b consistently increased sIgM levels. These findings indicate that the phenotype of B‐CLL cells in a subset of patients may depend primarily on poor CD79b expression, and suggest that upregulation of CD79b expression may correct the phenotype of these cells.
Chlorophenol binding to dissolved and particulate soil organic matter determined in controlled equilibrium systems
Authors: Frankki S. , Skyllberg U.
Published: August 2005

We determined the sorption of 2,4‐dichlorophenol (DCP), 2,4,5‐trichlorophenol (TCP) and pentachlorophenol (PCP) to dissolved (DOM) and particulate soil organic matter (POM) from the same soil in controlled equilibrium systems, using14C‐labelled chlorophenols in combination with reversed‐phase high‐performance liquid chromatography (RP‐HPLC) and liquid scintillation. Associations of DCP, TCP and PCP to DOM and POM were satisfactorily described by linear adsorption isotherms. Together with the absence of substantial competition between DCP and TCP for binding sites, this indicates a hydrophobic partitioning mechanism. The organic carbon normalized partitioning coefficient (KOC) for the binding of DCP was similar in magnitude for POM (KPOC) and for DOM (KDOC), whereasKPOCfor the more hydrophobic compounds TCP and PCP were approximately one order of magnitude greater thanKDOC. On the basis of the relationships between log KOCand the organic carbon normalized partitioning coefficient (log KOW), the extent of association to POM increases more with the hydrophobicity of the chlorophenol than the extent of association to DOM. This holds for our data obtained for DOM and POM of similar origin, as well as for various sources of POM and DOM reported in the literature. Differences in the magnitude ofKPOCandKDOCin our study could not be accounted for by differences in gross carbon chemistry of POM and DOM, as determined by nuclear magnetic resonance (13C‐NMR) and X‐ray photoelectron spectroscopy (XPS). Thus, other factors such as the average size and capacity of hydrophobic moieties could explain differences in chlorophenol association between POM and DOM. We conclude thatKPOCandKDOCneed to be determined explicitly, when the transport and retention of chlorophenols is modelled, and not calculated from relationships between log KOCand log KOW.
NSF/SNAPs and p97/p47/VCIP135 are sequentially required for cell cycle‐dependent reformation of the ER network
Authors: Kano Fumi , Kondo Hisao , Yamamoto Akitsugu , Kaneko Yayoi , Uchiyama Keiji , Hosokawa Nobuko , Nagata Kazuhiro , Murata Masayuki
Published: August 2005

The endoplasmic reticulum (ER) has a characteristic polygonal structure with hallmark three‐way junctions. In a previous paper, we reconstituted the disruption of the pre‐existing ER network using mitotic cytosol from HeLa cells in streptolysin O (SLO)‐permeabilized CHO‐HSP cells (stably expressing GFP‐HSP47). In addition, we found that interphase cytosol induced reformation of the disrupted ER network into a continuous network structure. Here, we show that the reformation of the ER network is accomplished through two sequential fusion reactions. The first process is mediated by NSF/α and γ‐SNAPs, and involves the generation of typical membranous intermediate structures that connect the disrupted ER tubules. A subsequent fusion is mediated by p97/p47/VCIP135, which has been shown to be required for homotypic fusion events in Golgi cisternae regrowth after mitosis. In addition, we also found that both fusion processes involve the t‐SNARE, syntaxin 18.
Unfolding of higher DNA structures formed by the d(CGG) triplet repeat by UP1 protein
Authors: Fukuda Hirokazu , Katahira Masato , Tanaka Etsuko , Enokizono Yoshiaki , Tsuchiya Naoto , Higuchi Kumiko , Nagao Minako , Nakagama Hitoshi
Published: August 2005

Fragile X syndrome is caused by expansion of a d(CGG) triplet repeat in the 5′‐untranslated region of the first exon of the FMR1 gene resulting in silencing of the gene. The d(CGG) repeat has been reported to form hairpin and quadruplex structures in vitro, and formation of these higher structures could be responsible for its unstable expansion in the syndrome, although molecular mechanisms underlying the repeat expansion still remain elusive. We have previously proved that UP1, a proteolytic product of hnRNP A1, unfolds the intramolecular quadruplex structures of d(GGCAG)5 and d(TTAGGG)4 and abrogates the arrest of DNA synthesis at d(GGG)n sites. Here, we demonstrate that the d(CGG) repeat forms a peculiar DNA structure, which deviates from the canonical B‐form structure. In addition, UP1 was demonstrated by CD spectrum analysis to unfold this characteristic higher structure of the d(CGG) repeat and to abrogate the arrest of DNA synthesis at the site. This ability of UP1 suggests that unfolding of unusual DNA structures of a triplet repeat is required for DNA synthesis processes.
Comparison of some properties on the different types of pestil: a traditional product in Turkey
Authors: Cagindi Ozlem , Otles Semih
Published: August 2005

Pestil is a traditional dried fruit snack, which is consumed in Turkey. Wheat starch is mixed with different clarified fruit juices such as grape, mulberry, apricot or plum and cooked using traditional techniques. In this work the proximate chemical composition (moisture, ash, fat, crude protein and total carbohydrate), energy value and thickness of grape, apricot and mulberry pestils were investigated. The colour properties (Hunter L, a and b) were determined by a Minolta Chroma‐Meter and the mineral content (Ca, Fe, K, Mg, Na, Cu, Zn, Mn) of each product was determined by inductively coupled plasma atomic emission spectrometry (ICP‐AES). The carbohydrate value of pestil samples ranged between 73.7 and 82.4% and energy value was between 321.5 and 356.4 kcal 100 g−1. Mulberry pestil was a better source of energy than grape and apricot pestils. Apricot pestils were rich in calcium, sodium and zinc, and mulberry pestil samples were rich in magnesium.
The effect of coagulants on the texture of chhana (an acid and heat coagulated product made from milk)
Authors: Bandyopadhyay Mahuya , Chakraborty Runu , Raychaudhuri Utpal
Published: August 2005

Chhana (a heat and acid coagulated milk protein mass and an Indian equivalent to cottage cheese) can be used as a raw material for the manufacture of various types of sweets popular all over India. Texture Profile Analysis (TPA), using an Instron Universal Testing Machine, was used to determine the effect of different coagulants on the textural characteristics of chhana. Chhana was made using three different coagulants: citric acid, lactic acid and calcium lactate, at five different concentrations, 0.5, 1, 2, 4 and 8%. Two types of dilution media, distilled water and acid whey, were used. The textural characteristics obtained when aqueous 0.5% citric acid, aqueous 0.5% lactic acid and 4–8% calcium lactate solutions, using acid whey as the solvent, gave similar TPA readings to normal chhana.
The performance of a methyl cellulose‐treated coating during the frying of a poultry product
Authors: Maskat Mohamad Y. , Yip Ho H. , Mahali Haryani M.
Published: August 2005

The performance of coatings treated with a range of methyl cellulose (MC) concentrations during the frying of coated chicken breasts was investigated. Chicken breasts were immersed in 0, 1 and 2.5% MC solution and then coated with a commercial coating mix. The coated chicken breasts were then fried at an initial temperature of 190 °C. Parameters measured included coating pickup, coating loss, cooked yield and frying loss. Results showed a significant increase in coating pickup with the use of 1 and 2.5% MC, which may have been due to the higher viscosity and binding ability of the MC layer. The use of 2.5% MC produced lower coating loss and frying loss and also a higher cooked yield.
A comparison between olive oil and extra‐virgin olive oil used as covering liquids in canned dried tomatoes: hydrolytic and oxidative degradation during storage
Authors: Baiano Antonietta , Gomes Tommaso , Caponio Francesco
Published: August 2005

The hydrolytic and oxidative degradation of olive oil and extra‐virgin olive oil, used as covering liquids in canned dried tomatoes, was studied during storage by means of conventional (acidity, peroxide value, p‐anisidine value) and non conventional (polar compounds) analyses. The effects of the addition of spices were also considered. The hydrolysis and oxidation of olive oil increased faster and was higher than that of extra‐virgin olive oil in terms of absolute values but some other indices, such as percentage of oligopolymers and percentage of oxidized triglycerides, increased faster in extra‐virgin olive oil than in olive oil. The antioxidant effect given by a higher concentration of polyphenols in the extra‐virgin olive oil was shown by a reduced amount of secondary oxidation. However, olive oil and extra‐virgin olive oils showed similar behaviour in terms of peroxide formation.
Purification of yeast proteinase A from fresh beer and its specificity on foam proteins
Authors: Wang Zhao‐Yue , He Guo‐Qing , Liu Zhong‐Shan , Ruan Hui , Chen Qi‐He , Xiong Hao‐Ping
Published: August 2005

Yeast proteinase A from fresh beer was first purified with Sephadex G‐100 column chromatography and the active fractions reached to 5.3‐fold purification with 7% of yield. After purification with DEAE Sephadex A50, proteinase A activity increased to be 10.1 times of the initial with 1% of yield. When identifying the sample from chromatography by sodium dodecyl sulphate‐polyacrylamide gel electrophoresis (SDS‐PAGE), only one protein band with 42 kDa was observed, this indicated that the enzyme was purified. The pattern of electrophoresis of hydrolysed beer by crude proteinase A did not show lipid transfer protein (LTP) on the gel. The result of SDS‐PAGE of interaction mixture of purified proteinase A and beer also indicated that LTP was decomposed.
Influence of different treatments on dehydrated cauliflower quality
Authors: Kadam Dattatreya Mahadev , Lata  , Samuel David Vijay Kumar , Pandey Alok Kumar
Published: August 2005

Fresh cauliflower was cut into florets, blanched, treated and spread in trays to dry by means of a solar drying process. The influences of packaging materials, blanching time, and potassium metabisulphite (KMS) concentration levels on the quality of solar dehydrated cauliflower up to 6 months of storage were studied. Ascorbic acid (vitamin C) present in fresh cauliflower was 74.61 mg (100 g)−1. Results revealed that ascorbic acid concentration decreased with an increase in blanching time but its retention was high in cauliflower dehydrated by solar drying. Dehydrated cauliflower had 581.37 mg (100 g)−1 of ascorbic acid in samples treated with 0.5, 1.0 and 1.5% of KMS with 3 min blanching at day zero. Washing cauliflower florets in tap water reduced the microbial load as compared with the unwashed sample. Processed and dehydrated cauliflower, packed in three types of packaging materials did not show presence of fungi even after storage for 6 months. In almost all samples, permissible levels of bacterial counts were observed after 6 months of storage. All the samples were also found to be free from Escherichia coli. It was found that blanched samples (blanching done for 7 min) treated with 0.5% KMS, dehydrated and then packed in laminated aluminium foil (LF) were the best in regard with nutritional and microbiological quality of dehydrated cauliflower.
Consumer acceptance of high‐fibre muffins and rusks baked with red palm olein
Authors: Scholtz Susanna C. , Bosman Magdalena J. C.
Published: August 2005

The acceptance of, preference for and consumption intent for high‐fibre muffins and/or rusks baked with either red palm olein (RPO) or sunflower oil (SFO, as control) were evaluated by two consumer groups of 144 and 67 consumers, respectively, in order to determine the possibility of their successful inclusion as carriers for oils in a subsequent nutrition intervention trial. A five‐point hedonic and food action rating scale was used for sensory evaluation. SFO muffins and rusks scored significantly higher than RPO products on a number of hedonic dimensions and were thus more acceptable to the average consumer. Sensory attributes of SFO and RPO products received high scores by consumers from both groups (≥4.0 on five‐point scale), and consumers intended to eat them often (at least one per day). The RPO products were satisfactory in terms of acceptance and complied with requirements for use in the subsequent nutrition intervention trial.
Improving colour extraction and stability in red wines: the use of maceration enzymes and enological tannins
Authors: Bautista‐Ortín A. B. , Martínez‐Cutillas A. , Ros‐García J. M. , López‐Roca J. M. , Gómez‐Plaza E.
Published: August 2005

Two commercially available maceration enzymes and two enological tannins were tested in Monastrell wines to determine their suitability for improving the chromatic characteristics, colour stability and sensory properties of the resulting wines. The greatest differences for all the wines, when comparing with the control wine, were observed at the beginning of the winemaking process, any differences diminishing in the finished wines. One of the enzyme‐treated wines was used showed hardly any difference from the control wine, whereas the other enzyme‐treated wine showed an improvement in their chromatic and sensory characteristics. The use of two different enological tannins did not provide any improvement in the chromatic and sensory characteristics of the wines, imparting a higher yellow colour and resulting in lower scores in the colour and aroma sensory characteristics, accompanied by a higher astringency, dryness and bitter sensory sensations.
Individual wrapping of radishes with food packaging film
Authors: Chu Chun‐Lung George , Liu Wei Tang , Ma Jianhua
Published: August 2005

When ‘Taibai’ radishes were individually wrapped with food packaging film, they had a reduced weight and firmness loss and a decreased formation of internal sponginess. When stored at 1 °C, wrapped radishes lost 0.01% of their fresh weight per day when compared with the 0.28% weight loss per day for unwrapped radishes. When stored at 5 °C, wrapped radishes lost 0.02–0.03% of their fresh weight per day when compared with the 0.78% weight loss per day of unwrapped radishes. Wrapped radishes stored for 88 days at 5 °C or 165 days at 1 °C maintained their firmness better than unwrapped radishes. Wrapped radishes had significantly less internal sponginess than unwrapped radishes.
Reduced reproductive success and offspring survival in fragmented populations of the forest herbPhyteuma spicatum
Authors: KOLB ANNETTE
Published: August 2005

Habitat fragmentation, which reduces the size and increases the isolation of populations, is a major threat to biodiversity. ForPhyteuma spicatum, a self‐incompatible, rare understorey herb in deciduous forests of north‐western Germany, I tested the hypotheses that: (i) fitness (in terms of reproductive success) is reduced in small or isolated populations, (ii) reproduction in small populations is reduced by pollen limitation and (iii) genetic effects cause fitness reductions in small populations.

I compared the reproductive success of plants ofPhyteumain 14 populations of different size and degree of isolation. Seed production was, as predicted, positively related to population size but was also influenced by plant size, although not by population isolation, density or habitat quality.

I performed supplemental hand‐pollinations in 10 of the 14 populations using pollen from the same population (test for pollen quantity) or from another large population (pollen quality). The proportional difference in seed production between hand‐pollinated plants and open‐pollinated controls increased with decreasing population size, indicating pollinator limitation of reproduction in small populations. There was no difference between the two hand‐pollination treatments, suggesting that a sufficient number of cross‐compatible mates was available even in the smallest populations.

Progeny from the 14 populations were grown for 32 weeks in a common environment. There was no effect of population size on germination, but final seedling survival was positively related to population size, and this relationship was more pronounced in the glasshouse than under more favourable growing conditions in a common garden. Genetic effects may thus reduce fitness (here measured in terms of survival) in plants from small populations, making them more susceptible to environmental stress.

The results suggest that both reproduction and offspring performance may be reduced in small populations even of long‐lived species such asPhyteuma spicatum. Different processes, such as pollen limitation and genetic deterioration, may interact and affect local population dynamics and the persistence of species in fragmented landscapes.
Successional dynamics of woody seedling communities in wet tropical secondary forests
Authors: CAPERS ROBERT S. , CHAZDON ROBIN L. , BRENES ALVARO REDONDO , ALVARADO BRAULIO VILCHEZ
Published: August 2005

Chronosequence studies have found that shrubs and lianas are generally more abundant in early stages of tropical forest succession, whereas canopy trees and palms become more abundant and species‐rich in older stages and mature forests.

We analysed changes in woody seedling communities over 5 years in four second‐growth forests (initially 13–26 years after pasture abandonment) in Costa Rica. We recorded community‐level changes in woody seedling density, species density, species richness and composition in six woody life‐forms: canopy trees, subcanopy trees, canopy palms, understorey palms, shrubs and lianas. We evaluated these changes in relation to annualized recruitment and mortality rates for each life‐form.

Seedling density declined in all four sites over the 5 years, whereas Shannon diversity and the proportion of rare species increased. Species richness and evenness increased in all but the oldest site.

Canopy palm, understorey palm and canopy tree seedlings increased in species richness and relative abundance, whereas shrub and liana relative abundance declined. Canopy trees accounted for 34–42% of all new recruits. Detrended correspondence analysis showed that species composition was initially highly distinct within each forest site and remained distinct over the 5‐year period.

Shifts in life‐form were correlated with declining light availability during succession. Across sites, median light availability at the end of the study period in 2003 was positively correlated with recruitment rates of understorey palms, shrubs and lianas, and was negatively correlated with mortality rates of canopy trees and palms.

Observed changes among seedling communities mirrored those described in chronosequence studies on plants in larger size classes, lending support to the assumptions of chronosequence studies in Neotropical forests.

The results demonstrate the importance of seedling recruitment and mortality in determining the course of succession. Convergence occurs in some community properties, such as relative abundance within life‐forms, but not in others, such as species composition. Finally, the results illustrate the value of studying plant community dynamics at the level of woody life‐forms, especially in hyperdiverse systems such as tropical forests.
Experimental invasion by legumes reveals non‐random assembly rules in grassland communities
Authors: TURNBULL LINDSAY A. , RAHM SABINE , BAUDOIS OKSANA , EICHENBERGER‐GLINZ SUSANN , WACKER LUCA , SCHMID BERNHARD
Published: August 2005

Although experimental studies usually reveal that resistance to invasion increases with species diversity, observational studies sometimes show the opposite trend. The higher resistance of diverse plots to invasion may be partly due to the increased probability of a plot containing a species with similar resource requirements to the invader.

We conducted a study of the invasibility of monocultures belonging to three different functional groups by seven sown species of legume. By only using experimentally established monocultures, rather than manipulating the abundance of particular functional groups, we removed both species diversity and differences in underlying abiotic conditions as potentially confounding variables.

We found that legume monocultures were more resistant than monocultures of grasses or non‐leguminous forbs to invasion by sown legumes but not to invasion by other unsown species. The functional group effect remained after controlling for differences in total biomass and the average height of the above‐ground biomass.

The relative success of legume species and types also varied with monoculture characteristics. The proportional biomass of climbing legumes increased strongly with biomass height in non‐leguminous forb monocultures, while it declined with biomass height in grass monocultures. Trifolium pratense was the most successful invader in grass monocultures, while Vicia cracca was the most successful in non‐leguminous forb monocultures.

Our results suggest that non‐random assembly rules operate in grassland communities both between and within functional groups. Legume invaders found it much more difficult to invade legume plots, while grass and non‐leguminous forb plots favoured non‐climbing and climbing legumes, respectively. If plots mimic monospecific patches, the effect of these assembly rules in diverse communities might depend upon the patch structure of diverse communities. This dependency on patch structure may contribute to differences in results of research from experimental vs. natural communities.
Lipopolysaccharide Increases γ‐Aminobutyric Acid Synthesis in Medial Preoptic Neurones in Association with Inhibition of Steroid‐Induced Luteinising Hormone Surge in Female Rats
Authors: Akema T. , He D. , Sugiyama H.
Published: September 2005

Lipopolysaccharide (LPS), an endotoxin produced by Gram‐negative bacteria, inhibits gonadotrophin secretion and ovulation in female mammals. The present study was undertaken to examine whether γ‐aminobutyric acid (GABA)‐synthesising neurones in the medial preoptic area (mPOA) may be involved in the inhibition by LPS of progesterone‐induced luteinising hormone (LH) surge in ovariectomised oestrogen‐primed rats. An intravenous injection of LPS (10 µg) at noon significantly increased the content of glutamic acid decarboxylase 67 (GAD67), a GABA‐synthesising enzyme, in brain tissues including the mPOA. LPS treatment also significantly increased the number of detectable GAD67‐immunoreactive (ir) as well as GABA‐ir cells in the mPOA, compared to control rats. The same LPS challenge completely eliminated the steroid‐induced LH surge, which was normally induced in control rats in the afternoon. A local injection of muscimol (100 ng), a GABAA receptor agonist, into the mPOA also significantly attenuated the LH surge, mimicking the effect of LPS. These results suggest that LPS stimulates GABA synthesis in preoptic neurones, which in turn inhibit the LH surge in female rats. The results also support the hypothesis that diminution of the GABAergic suppressive activity in the mPOA permits the LH surge to be induced.
Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation
Authors: KNOWLES L. LACEY , RICHARDS CORINNE L.
Published: September 2005

Determining what factors affect the structuring of genetic variation is key to deciphering the relative roles of different evolutionary processes in species differentiation. Such information is especially critical to understanding how the frequent shifts and fragmentation of species distributions during the Pleistocene translates into species differences, and why the effect of such rapid climate change on patterns of species diversity varies among taxa. Studies of mitochondrial DNA (mtDNA) have detected significant population structure in many species, including those directly impacted by the glacial cycles. Yet, understanding the ultimate consequence of such structure, as it relates to how species divergence occurs, requires demonstration that such patterns are also shared with genomic patterns of differentiation. Here we present analyses of amplified fragment length polymorphisms (AFLPs) in the montane grasshopper Melanoplus oregonensis to assess the evolutionary significance of past demographic events and associated drift‐induced divergence as inferred from mtDNA. As an inhabitant of the sky islands of the northern Rocky Mountains, this species was subject to repeated and frequent shifts in species distribution in response to the many glacial cycles. Nevertheless, significant genetic structuring of M. oregonensis is evident at two different geographic and temporal scales: recent divergence associated with the recolonization of the montane meadows in individual sky islands, as well as older divergence associated with displacements into regional glacial refugia. The genomic analyses indicate that drift‐induced divergence, despite the lack of long‐standing geographic barriers, has significantly contributed to species divergence during the Pleistocene. Moreover, the finding that divergence associated with past demographic events involves the repartitioning of ancestral variation without significant reductions of genomic diversity has intriguing implications — namely, the further amplification of drift‐induced divergence by selection.
Introgression in natural populations of bioindicators: a case study of Carabus splendens and Carabus punctatoauratus
Authors: STREIFF R. , VEYRIER R. , AUDIOT P. , MEUSNIER S. , BROUAT C.
Published: September 2005

The evolutionary importance of hybridization in wild plants and animals has become increasingly widely recognized in the last decade. In practical terms, hybridization provides an exceptionally tough set of problems for conservation biologists. We illustrate this in a case study of two Carabidae species widely used to evaluate the impact of human activities on biodiversity. These two species live in a complex mosaic of sympatry/allopatry and are known to hybridize in controlled conditions. Hybridization has not been quantified in natural populations to date due to the lack of a simple set of phenotypic traits for identifying hybrids. We thus screened for hybrids in natural populations, by multilocus genotyping at nine microsatellite loci. A high level of genetic differentiation between these two taxa was observed, as shown by allelic frequency distributions. Two Bayesian assignment procedures without obligatory pure taxon references were used to infer different classes of hybrids (F1, F2 and backcrosses) and mixture proportions between the two species. A low level of hybridization (F1 genotypes) was observed in natural populations, contrasting with results obtained in controlled conditions. A high level of introgression was, however, detected at three of 12 sites, as revealed by the detection of backcrossed genotypes. This interspecific gene flow was detected in a limited zone of the common geographical range of the two species and was not related to the pattern of sympatry/allopatry. We then considered the origin and repercussions of this introgression, based on intraspecific genetic diversity and geographical structure.
A fork‐clearing role for UvrD
Authors: Florés Maria‐José , Sanchez Nicolas , Michel Bénédicte
Published: August 2005

The inactivation of a replication protein causes the disassembly of the replication machinery and creates a need for replication reactivation. In several replication mutants, restart occurs after the fork has been isomerized into a four‐armed junction, a reaction called replication fork reversal. The repair helicase UvrD is essential for replication fork reversal upon inactivation of the polymerase (DnaE) or the β‐clamp (DnaN) subunits of the Escherichia coli polymerase III, and for the viability of dnaEts and dnaNts mutants at semi‐permissive temperature. We show here that the inactivation of recA, recFOR, recJ or recQ recombination genes suppresses the requirement for UvrD for replication fork reversal and suppresses the lethality conferred by uvrD inactivation to Pol IIIts mutants at semi‐permissive temperature. We propose that RecA binds inappropriately to blocked replication forks in the dnaEts and dnaNts mutants in a RecQ‐ RecJ‐ RecFOR‐dependent way and that UvrD acts by removing RecA or a RecA‐made structure, allowing replication fork reversal. This work thus reveals the existence of a futile reaction of RecA binding to blocked replication forks, that requires the action of UvrD for fork‐clearing and proper replication restart.
Inferring the genetic network of m‐xylene metabolism through expression profiling of the xyl genes of Pseudomonas putida mt‐2
Authors: Velázquez Francisco , Parro Víctor , de Lorenzo Víctor
Published: August 2005

A subgenomic array of structural and regulatory genes of the TOL plasmid pWW0 of Pseudomonas putida mt‐2 has been constructed to sort out the interplay between m‐xylene catabolism and the environmental stress brought about by this aromatic chemical. To this end, xyl sequences were spotted along with groups of selected P. putida genes, the transcription of which become descriptors of distinct physiological conditions. The expression of the TOL pathway in response to pathway substrates was thus profiled, uncovering a regulatory network that overcomes and expands the predictions made by projecting known data from individual promoters. First, post‐transcriptional checks appear to mitigate the burden caused by non‐productive induction of the TOL operons. Second, the fate of different segments of the polycistronic mRNAs from the upper and lower TOL operons varies depending on the metabolism of their inducers. Finally, m‐xylene triggers a noticeable heat shock, the onset of which does interfere with optimal expression of catabolic genes. These results reveal a degree of regulatory partnership between TOL plasmid‐encoded functions and host physiology that go beyond transcription initiation control.
Antibiotic‐induced expression of a cryptic cpb2 gene in equine β2‐toxigenic Clostridium perfringens
Authors: Vilei Edy M. , Schlatter Yvonne , Perreten Vincent , Straub Reto , Popoff Michel R. , Gibert Maryse , Gröne Andrea , Frey Joachim
Published: August 2005

The cpb2 gene of β2‐toxigenic Clostridium perfringens isolated from horses, cattle, sheep, human and pigs was sequenced. The cpb2 gene of equine and other non‐porcine isolates differed from porcine isolates by the absence of an adenine in a poly A tract immediately downstream of the start codon in all non‐porcine C. perfringens strains. This deletion involved formation of a cryptic gene harbouring a premature stop codon after only nine amino acid codons, while the full β2‐toxin protein consists of 265 amino acids. Immunoblots carried out with antibodies directed against a recombinant β2‐toxin showed the absence of expression of the β2‐toxin in equine and the other non‐porcine strains under standard culture conditions. However, treatment of C. perfringens with the aminoglycosides gentamicin or streptomycin was able to induce expression of the cpb2 gene in a representative equine strain of this group, presumably by frameshifting. The presence of the β2‐toxin was revealed by immunohistology in tissue samples of small and large intestine from horses with severe typhlocolitis that had been treated before with gentamicin. This result may explain the finding that antibiotic treatment of horses affected by β2‐toxigenic C. perfringens leads to a more accentuated and fatal progression of equine typhlocolitis. Clinical observations show a reduced appearance of strong typhlocolitis in horses with intestinal complications admitted to hospital care since the standard use of gentamicin has been abandoned. This is the first report on expression of a bacterial toxin gene by antibiotic‐induced ribosomal frameshifting.
The Yersinia pestis type III secretion needle plays a role in the regulation of Yop secretion
Authors: Torruellas Julie , Jackson Michael W. , Pennock Jeffry W. , Plano Gregory V.
Published: August 2005

Activation of bacterial virulence‐associated type III secretion systems (T3SSs) requires direct contact between a bacterium and a eukaryotic cell. In Yersinia pestis, the cytosolic LcrG protein and a cytosolic YopN‐TyeA complex function to block T3S in the presence of extracellular calcium and prior to contact with a eukaryotic cell. The mechanism by which the bacterium senses extracellular calcium and/or cell contact and transmits these signals to the cytosolic compartment is unknown. We report here that YscF, a small protein that polymerizes to form the external needle of the T3SS, is essential for the calcium‐dependent regulation of T3S. Alanine‐scanning mutagenesis was used to identify YscF mutants that secrete virulence proteins in the presence and absence of calcium and prior to contact with a eukaryotic cell. Interestingly, one of the YscF mutants that exhibited constitutive T3S was unable to translocate secreted proteins across the eukaryotic plasma membrane. These data indicate that the YscF needle is a multifunctional structure that participates in virulence protein secretion, in translocation of virulence proteins across eukaryotic membranes and in the cell contact‐ and calcium‐dependent regulation of T3S.
ABC‐type neutral amino acid permease N‐I is required for optimal diazotrophic growth and is repressed in the heterocysts of Anabaena sp. strain PCC 7120
Authors: Picossi Silvia , Montesinos María Luz , Pernil Rafael , Lichtlé Christiane , Herrero Antonia , Flores Enrique
Published: August 2005

Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that can fix N2 in differentiated cells called heterocysts. The products of Anabaena open reading frames (ORFs) all1046, all1047, all1284, alr1834 and all2912 were identified as putative elements of a neutral amino acid permease. Anabaena mutants of these ORFs were strongly affected (1–12% of the wild‐type activity) in the transport of Pro, Phe, Leu and Gly and also impaired (17–30% of the wild‐type activity) in the transport of Ala and Ser. These results identified those ORFs as the nat genes encoding the N‐I neutral amino acid permease. According to amino acid sequence homologies, natA (all1046) and natE (all2912) encode ATPases, natC (all1047) and natD (all1284) encode transmembrane proteins, and natB (alr1834) encodes a periplasmic substrate‐binding protein of an ABC‐type uptake transporter. The natA, natC, natD and natE mutants showed defects in Gln and His uptake that were not observed in the natB mutant suggesting that NatB is not a binding protein for Gln or His. The nat mutants released hydrophobic amino acids to the medium, and amino acid release took place at higher levels in cultures incubated in the absence of combined N than in the presence of nitrate. Alanine was the amino acid released at highest levels, and its release was impaired in a mutant unable to develop heterocysts. The nat mutants were also impaired in diazotrophic growth, with natA, natC, natD and natE mutants showing more severe defects than the natB mutant. Expression of natA and natC, which constitute an operon, natCA, as well as of natB was studied and found to take place in vegetative cells but not in the heterocysts. These results indicate that the N‐I permease is necessary for normal growth of Anabaena sp. strain PCC 7120 on N2, and that this permease has a role in the diazotrophic filament specifically in the vegetative cells.
Cytoplasmic degradation of ssrA‐tagged proteins
Authors: Farrell Christopher M. , Grossman Alan D. , Sauer Robert T.
Published: August 2005

Degradation of ssrA‐tagged proteins is a central feature of protein‐quality control in all bacteria. In Escherichia coli, the ATP‐dependent ClpXP and ClpAP proteases are thought to participate in this process, but their relative contributions to degradation of ssrA‐tagged proteins in vivo have been uncertain because two adaptor proteins, ClpS and SspB, can modulate proteolysis of these substrates. Here, intracellular levels of these protease components and adaptors were determined during exponential growth and  as  cells  entered  early  stationary  phase.  Levels  of ClpA and ClpP increased about threefold during this transition, whereas ClpX, ClpS and SspB levels remained nearly constant. Using GFP‐ssrA expressed from the chromosome as a degradation reporter, the effects of altered concentrations of different protease components or adaptor proteins were explored. Both ClpXP and ClpAP degraded GFP‐ssrA in the cell, demonstrating that wild‐type levels of SspB and ClpS do not inhibit ClpAP completely. Upon entry into stationary phase, increased levels of ClpAP resulted in increased degradation of ssrA‐tagged substrates. As measured by maximum turnover rates, ClpXP degradation of GFP‐ssrA in vivo was significantly more efficient than in vitro. Surprisingly, ClpX‐dependent ClpP‐independent degradation of GFP‐ssrA was also observed. Thus, unfolding of this substrate by ClpX appears to enhance intracellular degradation by other proteases.