bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional characterization of both MAP kinases of the human malaria parasite Plasmodium falciparum by reverse genetics
Authors: Dorin‐Semblat Dominique , Quashie Neils , Halbert Jean , Sicard Audrey , Doerig Caroline , Peat Elizabeth , Ranford‐Cartwright Lisa , Doerig Christian 
Published: July 2007

SummaryThe kinome of the human malaria parasite Plasmodium falciparum includes two genes encoding mitogen‐activated protein kinase (MAPK) homologues, pfmap‐1 and pfmap‐2, but no clear orthologue of the MAPK kinase (MAPKK) family, raising the question of the mode of activation and function of the plasmodial MAPKs. Functional studies in the rodent malaria model Plasmodium berghei recently showed the map‐2 gene to be dispensable for asexual growth and gametocytogenesis, but essential for male gametogenesis in the mosquito vector. Here, we demonstrate by using a reverse genetics approach that the map‐2 gene is essential for completion of the asexual cycle of P. falciparum, an unexpected result in view of the non‐essentiality of the orthologous gene for P. berghei erythrocytic schizogony. This validates Pfmap‐2 as a potential target for chemotherapeutic intervention. In contrast, the other P. falciparum MAPK, Pfmap‐1, is required neither for in vitro schizogony and gametocytogenesis in erythrocytes, nor for gametogenesis and sporogony in the mosquito vector. However, Pfmap‐2 protein levels are elevated in pfmap‐1‐ parasites, suggesting that Pfmap‐1 fulfils an important function in asexual parasites that necessitates compensatory adaptation in parasites lacking this enzyme.
Type 3 peptide deformylases are required for oxidative phosphorylation in Trypanosoma brucei
Authors: Bouzaidi‐Tiali Nabile , Giglione Carmela , Bulliard Yannick , Pusnik Mascha , Meinnel Thierry , Schneider André 
Published: July 2007

SummaryPeptide deformylase (PDF) catalyses the removal of the formyl group from the first methionine of nascent proteins. Type 1 PDFs are found in bacteria and have orthologues in most eukaryotes. Type 2 PDFs are restricted to bacteria. Type 3 enzymes are found in Archaea and trypanosomatids and have not been studied experimentally yet. Thus, TbPDF1 and TbPDF2, the two PDF orthologues of the parasitic protozoa Trypanosoma brucei, are of type 3. An experimental analysis of these enzymes shows that both are mitochondrially localized, but that only TbPDF1 is essential for normal growth. Recombinant TbPDF1 exhibits PDF activity with a substrate specificity identical to that of bacterial enzymes. Consistent with these results, TbPDF1 is required for oxidative but not for mitochondrial substrate‐level phosphorylation. Ablation of TbPDF2, in contrast, does neither affect growth on standard medium nor oxidative phosphorylation. However, a reduced level of TbPDF2 slows down growth in a medium that selects for highly efficient oxidative phosphorylation. Furthermore, combined ablation of TbPDF1 and TbPDF2 results in an earlier growth arrest than is observed by downregulation of TbPDF1 alone. These results suggest that TbPDF2 is functionally linked to TbPDF1, and that it can influence the efficiency of oxidative phosphorylation.
A wide deep infrared look at the Pleiades with UKIDSS: new constraints on the substellar binary fraction and the low-mass initial mass function
Authors: Lodieu N. , Dobbie P. D. , Deacon N. R. , Hodgkin S. T. , Hambly N. C. , Jameson R. F. 
Published: July 2007

Abstract
We present the results of a deep wide-field near-infrared survey of 12 deg2 of the Pleiades conducted as part of the United Kingdom Infrared Telescope (UKIRT) Infrared Deep Sky Survey (UKIDSS) Galactic Cluster Survey (GCS). We have extracted over 340 high-probability proper motion (PM) members down to 0.03 M⊙ using a combination of UKIDSS photometry and PM measurements obtained by cross-correlating the GCS with data from the Two Micron All Sky Survey, the Isaac Newton Telescope and the Canada–France–Hawaii Telescope. Additionally, we have unearthed 73 new candidate brown dwarf (BD) members on the basis of five-band UKIDSS photometry alone. We have identified 23 substellar multiple system candidates out of 63 candidate BDs from the (Y−K, Y) and (J−K, J) colour–magnitude diagrams, yielding a binary frequency of 28–44 per cent in the 0.075−0.030 M⊙ mass range. Our estimate is three times larger than the binary fractions reported from high-resolution imaging surveys of field ultracool dwarfs and Pleiades BDs. However, it is marginally consistent with our earlier ‘peculiar’ photometric binary fraction of 50 ± 10 per cent presented by Pinfield et al., in good agreement with the 32–45 per cent binary fraction derived from the recent Monte Carlo simulations of Maxted & Jeffries and compatible with the 26 ± 10 per cent frequency recently estimated by Basri & Reiners. A tentative estimate of the mass ratios from photometry alone seems to support the hypothesis that binary BDs tend to reside in near equal-mass ratio systems. In addition, the recovery of four Pleiades members targeted by high-resolution imaging surveys for multiplicity studies suggests that half of the binary candidates may have separations below the resolution limit of the Hubble Space Telescope or current adaptive optics facilities at the distance of the Pleiades (a ∼7 au). Finally, we have derived luminosity and mass functions from the sample of photometric candidates with membership probabilities. The mass function is well modelled by a lognormal peaking at 0.24 M⊙ and is in agreement with previous studies in the Pleiades.
Elevated CO2 and temperature alter net ecosystem C exchange in a young Douglas fir mesocosm experiment
Authors: TINGEY DAVID T. , LEE E. HENRY , PHILLIPS DONALD L. , RYGIEWICZ PAUL T. , WASCHMANN RONALD S. , JOHNSON MARK G. , OLSZYK DAVID M. 
Published: July 2007

ABSTRACTWe investigated the effects of elevated CO2 (EC) [ambient CO2 (AC) + 190 ppm] and elevated temperature (ET) [ambient temperature (AT) + 3.6 °C] on net ecosystem exchange (NEE) of seedling Douglas fir (Pseudotsuga menziesii) mesocosms. As the study utilized seedlings in reconstructed soil–litter–plant systems, we anticipated greater C losses through ecosystem respiration (Re) than gains through gross photosynthesis (GPP), i.e. negative NEE. We hypothesized that: (1) EC would increase GPP more than Re, resulting in NEE being less negative; and (2) ET would increase Re more than GPP, resulting in NEE being more negative. We also evaluated effects of CO2 and temperature on light inhibition of dark respiration. Consistent with our hypothesis, NEE was a smaller C source in EC, not because EC increased photosynthesis but rather because of decreased respiration resulting in less C loss. Consistent with our hypothesis, NEE was more negative in ET because Re increased more than GPP. The light level that inhibited respiration varied seasonally with little difference among CO2 and temperature treatments. In contrast, the degree of light inhibition of respiration was greater in AC than EC. In our system, respiration was the primary control on NEE, as EC and ET caused greater changes in respiration than photosynthesis.
Evidence for sporangial dispersal leading to a single infection event and a sudden high incidence of grapevine downy mildew
Authors: Gobbin D. , Bleyer G. , Keil S. , Kassemeyer H. H. , Gessler C. 
Published: July 2007

In a German vineyard (PRO) between 10 and 13 June 2004, the incidence of grapevine downy mildew (Plasmopara viticola) increased abruptly from 0 to 99%. Infected vines bore on average between 45 and 60 lesions each, corresponding to about 220 000 lesions ha−1 in a non‐aggregated distribution. A second vineyard (FUT), approximately 50 m distant from PRO, had been inoculated 3 weeks before the abrupt increase in incidence of disease in PRO. Using microsatellites to ascertain the sources of inoculum and likelihood and extent of interplot spread from FUT to PRO, 555 samples were collected and 20 unique genotypes were identified, of which one caused 80% of the sampled lesions in both vineyards. Three genotypes responsible for 95% of the lesions in FUT and PRO were identified as the genotypes originally established through earlier inoculations in FUT. This is the first report of definitive and quantitative evidence of sporangial migration up to 130 m in a single infection event. The utility of molecular tools to address practical epidemiological issues in this pathosystem is illustrated. The results of this study provide an example of how P. viticola was able to rapidly colonize European vineyards after the pathogen was introduced from North America in 1878.
DWARF10, an RMS1/MAX4/DAD1 ortholog, controls lateral bud outgrowth in rice
Authors: Arite Tomotsugu , Iwata Hirotaka , Ohshima Kenji , Maekawa Masahiko , Nakajima Masatoshi , Kojima Mikiko , Sakakibara Hitoshi , Kyozuka Junko 
Published: July 2007

SummaryPlant architecture is mostly determined by shoot branching patterns. Apical dominance is a well‐known control mechanism in the development of branching patterns, but little is known regarding its role in monocots such as rice. Here, we show that the concept of apical dominance can be applied to tiller bud outgrowth of rice. In dwarf10 (d10), an enhanced branching mutant of rice, apical dominance can be observed, but the inhibitory effects of the apical meristem was reduced. D10 is a rice ortholog of MAX4/RMS1/DAD1 that encodes a carotenoid cleavage dioxygenase 8 and is supposed to be involved in the synthesis of an unidentified inhibitor of shoot branching. D10 expression predominantly occurs in vascular cells in most organs. Real‐time polymerase chain reaction analysis revealed that accumulation of D10 mRNA is induced by exogenous auxin. Moreover, D10 expression is upregulated in six branching mutants, d3, d10, d14, d17, d27 and high tillering dwarf (htd1). No such effects were found for D3 or HTD1, the MAX2 and MAX3 orthologs, respectively, of rice. These findings imply that D10 transcription might be a critical step in the regulation of the branching inhibitor pathway. In addition, we present observations that suggest that FINE CULM1 (FC1), a rice ortholog of teosinte branched 1 (tb1), possibly works independently of the branching inhibitor pathway.
Microbial uranium immobilization independent of nitrate reduction
Authors: Madden Andrew S. , Smith April C. , Balkwill David L. , Fagan Lisa A. , Phelps Tommy J. 
Published: July 2007

SummaryAt many uranium processing and handling facilities, including sites in the US Department of Energy (DOE) complex, high levels of nitrate are present as co‐contamination with uranium in groundwater. The daunting prospect of complete nitrate removal prior to the reduction of uranium provides a strong incentive to explore bioremediation strategies that allow for uranium bioreduction and stabilization in the presence of nitrate. Typical in situ strategies involving the stimulation of metal‐reducing bacteria are hindered by low‐pH environments and require that the persistent nitrate must first and continuously be removed or transformed prior to uranium being a preferred electron acceptor. This work investigated the possibility of stimulating nitrate‐indifferent, pH‐tolerant microorganisms to achieve bioreduction of U(VI) despite nitrate persistence. Enrichments from U‐contaminated sediments demonstrated nearly complete reduction of uranium with very little loss of nitrate from pH 5.7–6.2 using methanol or glycerol as a carbon source. Bacterial 16S rRNA genes were amplified from uranium‐reducing enrichments (pH 5.7–6.2) and sequenced. Phylogenetic analyses classified the clone sequences into four distinct clusters. Data from sequencing and terminal‐restriction fragment length polymorphism (T‐RFLP) profiles indicated that the majority of the microorganisms stimulated by these enrichment conditions consisted of low G+C Gram‐positive bacteria most closely related to Clostridium and Clostridium‐like organisms. This research demonstrates that the stimulation of a natural microbial community to immobilize U through bioreduction is possible without the removal of nitrate.
Diversity and abundance of aerobic and anaerobic ammonium‐oxidizing bacteria in freshwater sediments of the Xinyi River (China)
Authors: Zhang Ying , Ruan Xiao‐Hong , Op den Camp Huub J. M. , Smits Toine J. M. , Jetten Mike S. M. , Schmid Markus C. 
Published: July 2007

SummaryHere we report on the biodiversity and abundance of aerobic and anaerobic ammonium‐oxidizing bacteria in sediment samples from the Xinyi River, Jinagsu Province (China). The biodiversity of aerobic ammonium‐oxidizing bacteria in the sediment was assessed using the amoA gene as functional marker. The retrieved amoA clones were affiliated to environmental sequences from freshwater habitats. The closest cultivated relative was Nitrosomonas urea. Anaerobic ammonium‐oxidizing (anammox) bacteria were studied using anammox and planctomycete‐specific 16S rRNA gene primers. The sediments contained 16S rRNA genes and bacterial cells closely related to the known anammox bacterium Candidatus‘Brocadia anammoxidans’. Anaerobic continuous flow reactors were set up to enrich anammox organisms from the sediments. After an adaptation period of about 25 days the reactors started to consume ammonium and nitrite, indicating that the anammox reaction was occurring with a rate of 41–58 nmol cm−3 h−1. Community analysis of the enrichments by quantitative fluorescence in situ hybridization showed an increase in the abundance of anammox bacteria from < 1% to 6 ± 2% of the total population. Analysis of the 16S rRNA genes showed that the enriched anammox organisms were related to the Candidatus‘Scalindua’ genus.
Quantitative analyses of the abundance and composition of ammonia‐oxidizing bacteria and ammonia‐oxidizing archaea of a Chinese upland red soil under long‐term fertilization practices
Authors: He Ji‐zheng , Shen Ju‐pei , Zhang Li‐mei , Zhu Yong‐guan , Zheng Yuan‐ming , Xu Ming‐gang , Di Hongjie 
Published: July 2007

SummaryThe abundance and composition of soil ammonia‐oxidizing bacteria (AOB) and ammonia‐oxidizing archaea (AOA) were investigated by using quantitative real‐time polymerase chain reaction, cloning and sequencing approaches based on amoA genes. The soil, classified as agri‐udic ferrosols with pH (H2O) ranging from 3.7 to 6.0, was sampled in summer and winter from long‐term field experimental plots which had received 16 years continuous fertilization treatments, including fallow (CK0), control without fertilizers (CK) and those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK, PK, NPK and NPK plus organic manure (OM). Population sizes of AOB and AOA changed greatly in response to the different fertilization treatments. The NPK + OM treatment had the highest copy numbers of AOB and AOA amoA genes among the treatments that received mineral fertilizers, whereas the lowest copy numbers were recorded in the N treatment. Ammonia‐oxidizing archaea were more abundant than AOB in all the corresponding treatments, with AOA to AOB ratios ranging from 1.02 to 12.36. Significant positive correlations were observed among the population sizes of AOB and AOA, soil pH and potential nitrification rates, indicating that both AOB and AOA played an important role in ammonia oxidation in the soil. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from different treatments were affiliated with Nitrosospira or Nitrosospira‐like species and grouped into cluster 3, and little difference in AOB community composition was recorded among different treatments. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). Cluster M dominated exclusively in the N, NP, NK and PK treatments, indicating a pronounced difference in the community composition of AOA in response to the long‐term fertilization treatments. These findings could be fundamental to improve our understanding of the importance of both AOB and AOA in the cycling of nitrogen and other nutrients in terrestrial ecosystems.
Ferrichrome utilization in a mesorhizobial population: microevolution of a three‐locus system
Authors: Carlton Timothy M. , Sullivan John T. , Stuart Gabriella S. , Hutt Karla , Lamont Iain L. , Ronson Clive W. 
Published: July 2007

SummaryThe ability to utilize the siderophore ferrichrome as an iron source was found to be a variable trait in a field population of mesorhizobia. To investigate the genetic basis of this variation, genes required for ferrichrome utilization (fhu genes) were characterized in Mesorhizobium strain R88B, an Fhu+ member of the population. Functional fhu genes were present at three loci. Two genes of the ferrichrome ABC transporter, fhuBD, were identified at an fhu1 locus downstream of the symbiosis island that was integrated at the phe‐tRNA gene. The fhuA gene encoding the ferrichrome outer membrane receptor was located in the fhu2 locus together with non‐functional fhuDB genes, while the fhuC gene encoding the ATPase required for ferrichrome transport was part of the fhu3 locus that included genes required to form a functional TonB complex. None of the fhu genes were present in the sequenced Mesorhizobium loti strain MAFF303099. Comparisons with MAFF303099 suggested that the fhu2 and fhu3 loci evolved through small‐scale (< 5 kb) acquisitions and deletions. Despite their independent origins, the three fhu loci were coordinately regulated in response to iron availability. Within the mesorhizobial population, the ability to utilize ferrichrome was most strongly correlated with the presence of the fhuA gene. We hypothesize that the ferrichrome transport system evolved through cycles of gene acquisition and deletion, with the positive selection pressure of an iron‐poor or siderophore‐rich environment being offset by the negative pressure of the outer membrane receptor being a target for phage.
Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway
Authors: Hansen Aviaja A. , Herbert Rodney A. , Mikkelsen Karina , Jensen Lars Liengård , Kristoffersen Tommy , Tiedje James M. , Lomstein Bente Aa. , Finster Kai W. 
Published: July 2007

SummaryThe viable and non‐viable fractions of the bacterial community in a 2347‐year‐old permafrost soil from Spitsbergen were subjected to a comprehensive investigation using culture‐independent and culture‐dependent methods. LIVE/DEAD®BacLightTM staining revealed that 26% of the total number of bacterial cells were viable. Quantitatively, aerobic microcolonies, aerobic colony‐forming units and culturable anaerobic bacteria comprised a minor fraction of the total number of viable bacteria, which underlines the necessity for alternative cultivation approaches in bacterial cryobiology. Sulfate reduction was detected at temperatures between −2°C and 29°C while methanogenesis was not detected. Bacterial diversity was high with 162 operational taxonomic units observed from 800 16S rDNA clone sequences. The 158 pure cultures isolated from the permafrost soil affiliated with 29 different bacterial genera, the majority of which have not previously been isolated from permafrost habitats. Most of the strains isolated were affiliated to the genera Cellulomonas and Arthrobacter and several of the pure cultures were closely related to bacteria reported from other cryohabitats. Characterization of viable bacterial communities in permafrost soils is important as it will enable identification of functionally important groups together with the as yet undescribed adaptations that bacteria have evolved for surviving subzero temperatures for millennia.
Anomalies of the external urethral meatus in girls with non‐neurogenic bladder sphincter dysfunction
Authors: HOEBEKE P. , VAN LAECKE E. , RAES A. , VAN GOOL J.D. , VANDE WALLE J. 
Published: July 2007

Objective To investigate in a prospective study the clinical and urodynamic characteristics associated with the correlation previously reported between non‐neuropathic bladder sphincter dysfunction and minimal meatal deformities in girls.Patients and methods From January 1995 to June 1996 all girls referred for urodynamics to investigate non‐neuropathic bladder sphincter dysfunction were examined for meatal anomalies. Two types of meatal anomalies were recognized, i.e. hypospadias, in which the urethral meatus is displaced dorsally and meatal web or covered hypospadias, in which there is a mucosal web on the dorsal side of the urethral meatus that deflects the urinary stream anteriorly. The girls presenting with minimal meatal deformities were compared with those presenting a normal meatal configuration for their history and video‐urodynamic features.Results During the study, 288 girls were referred for video‐urodynamics; 88 presented with meatal anomalies (24 hypospadias and 64 covered hypospadias) and comprised the study group; all other girls were considered as the control group. Incontinence during the day was more frequent in the study group (56%) than in the control group (34%) (P=0.003). Nocturnal enuresis was more frequent in the control group (87%) than in the study group (68%, P=0.006). Urge was more frequent in the study group (80%) than in the control group (65%, P=0.02), as was anterior deflection of the urinary stream (voiding over the toilet rim), in 48% and 4.5%, respectively (P<0.001). On video‐urodynamics, dysfunctional voiding (detrusor sphincter dyscoordination during voiding) was more frequent in the study group (59%) than in the control group (38%, P=0.009), and vaginal voiding was more frequent in the study group (40%) than in the control group (11.5%, P<0.001).Conclusion Girls presenting with meatal anomalies have more severe dysfunction, as estimated by urodynamics. Although the natural history of these anomalies and the incidence in the normal population is not known, it is thought that there is an aetiological correlation between the functional voiding disorders and the meatal anomaly. Surgical treatment to correct the anomalies is proposed.
Marriage Market, Parents’ Bargaining Powers, and Children's Nutrition and Education*
Authors: Park Cheolsung 
Published: July 2007

AbstractTest of resource pooling and test of effect of sex ratio in the marriage market on intrahousehold resource allocation are combined to test the unitary household model. The consistency condition between the two tests is derived to test the Nash household bargaining and Pareto‐efficient household models. I examine intrahousehold resource allocation to children's nutrition and education in Indonesia. For children's nutrition, the unitary household model is rejected in favour of the non‐unitary models. The results for investment in education are mixed. The decision‐making process may differ depending on the type of decision being made.