bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated nutrient management for resource-poor farming systems: A case study of adaptive research and technology dissemination in Uganda
Authors: Wortmann Charles S. , Ssali Henry
Published: October 2009

Resource-poor farmers often have diverse but small quantities of materials available that might be used to manage soil fertility. Opportunity costs of money are very high and farmers often opt to invest their scarce financial resources elsewhere rather than in fertilizer. This paper presents an approach to adaptive research and technology dissemination that was applied in Uganda and is applicable for improvement of integrated nutrient management (INM) in resource-poor farming systems. While little information may be available from research conducted in a particular agroecological zone (AEZ), information on INM components from diverse sources may be applicable for major crops in that AEZ. This information must be compiled and subjected to agronomic and economic analysis. A conceptual framework, e.g., in the form of a tentative decision guide, is then constructed, with consideration of interactions among nutrient sources, given the farmers' situations. Researchers estimate the most likely rates of application and substitution ratios, and then judge their confidence in the estimates. Priority actions are then identified for research and extension. When confident of their estimates, researchers formulate recommendations for promotion through extension means. If confidence is lacking, on-farm verification trials or other research may be needed. The approach is illustrated by work done for one AEZ in Uganda for maize and dry bean production, but is intended for application to other resource-poor farming systems in eastern Africa.
Species interactions and community ecology in low external-input agriculture
Authors: Gliessman Stephen R.
Published: October 2009

Low external-input agriculture seeks to optimize interactions between species that permit processes at the ecological community level to shift inputs away from nonrenewable or synthetic sources. This goal can be reached through the study of the ecological basis of an array of plant-plant and plant-insect interactions, especially in intercropping systems where particular plant mixtures are of benefit to the entire crop community. These polyculture systems can be managed for nutrient cycling efficiency and pest and disease regulation using knowledge of multi-trophic level interactions and application of recent developments in mutualism and competition theory. A mechanistic model of additive and removal reactions on the environment is proposed as a means of studying species interactions.
Scampanata at the widows' windows: a case-study of sound and ritual insult in cinquecento Florence
Authors: COLLERAN KATE
Published: October 2009

This article presents the tale of a serial flirt, punished for making a noisy, lewd nuisance of himself outside a widows' residence in Florence in 1553. Close study of this vivid episode uncovers some of the sonic strategies of ritual insult and abuse available to early modern city-dwellers, and is also an opportunity to explore the connections between aurality and spatiality in late Renaissance Florence.
Industry, political alliances and the regulation of urban space in Los Angeles
Authors: HISE GREG
Published: October 2009

The formation of industrial districts and the role that development played in shaping the pattern of American cities has become a standard for urban history. This has not been the case for Los Angeles. Despite its centrality for a metropolitan economy that has led California for a century and that today leads the nation in manufacturing employment, scholars and pundits have overlooked production in favour of consumption. Little is known about how firms, business associations and city officials created space for industry during the late nineteenth century when manufacturers' locational decisions contributed to spatial concentration in the city's core. A case study of the Cudahy Packing Company reveals why such sites were favoured, how a sectoral-specific district emerged and the processes through which Angelenos transformed a Yankee pueblo into an industrial city. Two factors, the local state's enablement of manufacturing via policy and regulation and the use of industrialization as an immigrant removal strategy, emerge as significant. Neither has been prominent in the literature on the growth of Los Angeles while the latter, the linking of race-ethnicity with land use, has been less prominent in prior studies of industrial districts.
Religious Practices among Indian Hindus: Does that Influence Their Political Choices?
Authors: KUMAR SANJAY
Published: October 2009

The article focuses on the issue of patterns of religious engagement among Indian Hindus during last decade. It tries to look at both the issue of private religion practiced in the form of offering puja at home and public religion seen in terms of participation in Katha, Satsang, Bhajan-Kirtan etc. by Indian Hindus. Sizeable numbers of Indian Hindus offer puja every day; sizeable numbers of them are also engaged in public religious activities. This is more prevalent among the urban, educated, upper-caste, upper-class Hindus compared to their counterpart. Along with factors, which influence religious practices, is gender. Hindu women are more religious compared to the Hindu men. Similarly, upper-caste Hindus practice religious activities more regularly compared to other Hindus. There is hardly any change in patterns of engagement in religious activities among Hindus over the last five years. The levels of engagement in religious activities also have an impact on voting behavior. The higher the engagement in religious activities, the greater is the support for the BJP and vice versa. Between the 2004 and 2009 Lok Sabha elections, there had been a decline in the vote share of BJP due to its declining popularity amongst all the Hindu voters, but the decline in the support for the BJP is much sharper amongst highly religious Hindus compared to those who are not so religious. Along with other factors, this may be one of the important factors that led to the defeat of BJP in the 2009 Lok Sabha elections. The article draws evidence from the National Election Study 2004 and 2009 conducted by the Centre for the Study of Developing Societies during these two elections.
Analysis, gene cloning and expression of two α-amylases from Bacillus cereus
Authors: Lin-lin Zhang , Qi Wang , Rong-xi Li , Yong-jun Wang , Ru-hong Mei
Published: October 2009

Bacillus cereus can produce α-amylase, which has important industrial production value and can endure high temperatures. The enzymatic characteristics of two α-amylases from B. cereus (B905 and B904) were studied. The results showed that both preserved their activity at 90–100°C. Their thermal stability and enzymatic activity did not depend on Ca2+. However, their protein molecular weights were obviously different. The structural genes of amy905 and amy904 were cloned successfully using the polymerase chain reaction (PCR) and expressed in Escherichia coli. The amy904 and amy905 genes were 1362 bp and 1761 bp long and their protein molecular weights were about 55 kDa and 68 kDa, respectively.
Identification of resistance to corn-borer of transgenic maize inbred lines and hybrids with GFM Cry1A gene
Authors: Ying Yuan , Xiao-Hui Li , Xiang-Mei Kong , Zhi-Lei Jiang , Chun-Jing Lin , Cong-Cong Li , Na Liu , Chuan-Bo Sun , De-Pu Liu
Published: October 2009

Six transgenic maize lines with the fully modified gene GFM Cry1A were obtained and polymerase chain reaction (PCR) analysis of their T5 generation plants indicated that foreign genes could be stably inherited. Three hybrids (Simi25Bt, Tongdan24Bt and Jidan209Bt) were created using the transgenic lines and combined with regular maize inbred lines. The results of resistance identification of the transgenic inbred lines and hybrids showed that the difference of resistance among transgenic lines was very significant; there also existed a difference among individuals of the same line and among the three hybrids. Compared with the control inbred line (CK), the average of four transgenic inbred lines in the number of tunnels per stalk, larval tunnel length per plant and length of surviving larvae were decreased by 70%, 80% and 70%, respectively. Enzyme-linked immunosorbent assay (ELISA) testing showed that the average of Bt Cry1A protein expression level for six transgenic inbred lines was 0.16% total protein and the highest expression level was 0.19%. At maturity, compared with the control variety (CK), the larval tunnel length per plant of the three hybrids (Simi25Bt, Tongdan24Bt and Jidan209Bt) was decreased by 39.97%, 36.20% and 53.83%, respectively, which was a decrease of 43.36% on average. The investigation of agronomic characters showed that there was no significant difference between the improved hybrids and the control in plant height, ear length, row number per ear, kernel number per row and 100-kernels weight. It is thought that the GFM Cry1A gene can be applied to improve resistance to corn-borer, and maize inbred lines with the Bt gene can be directly applied to conventional maize breeding.
Spatio-temporal expression analysis of two kinds of chemical communication-related proteins in the worker bee Apis cerana cerana Fabricius (Hymenoptera: Apidae)
Authors: Hong-Liang Li , Ya-Li Zhang , Hai-Yan Wang , Qi-Kang Gao , Jia-An Cheng
Published: October 2009

The spatio-temporal expressed profiles of two kinds of chemical communication-related protein genes, the odorant-binding protein of Ac-ASP2 and chemosensory protein of Ac-ASP3, were identified by real-time polymerase chain reaction (PCR). Results obtained using the 2−ΔΔCt method showed that Ac-ASP2 was a gene coding antenna-specific protein that did not express in larvae and pupae, but had discontinuous high abundance periods at 1, 9, 15, 27 and 30 days. The expressing abundance at such periods was at least ten times higher than that at other periods. From the distribution of Ac-ASP3 mRNA observed in different tissues, the transcript levels seemed to be higher in the wings, abdomen and thorax (of order ~106), and lower in the legs, antennae and head (of order ~105). From highest to lowest, the original copy number was found in the various body parts in the following order: wings, abdomen, thorax, legs, antenna, and head. The results suggest that Ac-ASP3 has an intimate relation with the chemosensory behaviour of wings and abdomen in Apis cerana cerana.
Cloning and tissue expression of the adiponectin gene in geese
Authors: Guo-Qing Xu , Dao-Qing Gong , Dong-Sheng Chu , Biao Dong , He Meng
Published: October 2009

Three pairs of primers were designed for amplification of the adiponectin gene in geese (Anser demeatica) based on the published sequences of chicken, duck and other adiponectin homologues. The complete 1062 bp sequence of the adiponectin gene in geese, obtained by polymerase chain reaction (PCR) amplification and splicing, contained two exons and one intron. The coding sequence was 738 bp long and included codes for 245 amino acids (GenBank Accession No. EU370686). The coding sequence and the corresponding protein of goose adiponectin shared the highest homology with ducks, 94.85% and 95.51%, respectively; homology with chicken adiponectin was next highest, while the lowest homology was to be found with mammals. The predicted molecular weight (MW) and isoelectric point (pI) were 26,603.3 Da and pH 5.19, respectively, which were highly similar to those of species considered above. Reverse transcription-PCR revealed that goose adiponectin mRNA was highly expressed in skeletal muscle, fatty tissue, heart and stomach muscles. Medium levels of expression were detected in the small intestine, stomach glandular tissue, kidney and lung, while it was only weakly expressed in the liver, spleen, ovaries and diencephalon.
Cloning of carnation GA 20-oxidase and the construction of a plant RNAi vector
Authors: Liang Jin , Yun Liu , Zhen-Yuan Sun , Tian-Hong Li
Published: October 2009

A pair of degenerate primers was designed based on a conserved domain of GA 20-oxidase reported in other plants. The full-length (1179 bp) carnation (Dianthus caryophyllus L. cv. Master) GA 20-oxidase cDNA (named Dc20ox) was cloned by reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). BLAST analysis revealed that the deduced amino acid sequence had high homology (66–75%) with the GA 20-oxidase sequences from other plants. An RNAi vector (pART400) was constructed from a 400 bp fragment representing a highly conserved region of GA 20-oxidase.
Identification and structure analysis of three tilapia species using microsatellite markers
Authors: Hong-Mei Song , Jun-Jie Bai , Ying-Chun Quan , Sheng-Jie Li
Published: October 2009

Seventeen special loci were selected from 77 microsatellite markers to distinguish three varieties of tilapias, including the six differential loci UNH636, UNH117, UNH172, UNH738, UNH878 and UNH896 in Oreochromis aureus; five differential loci UNH913, UNH907, UNH222, UNH980 and UNH880 in O. niloticus; and six differential loci of UNH876, UNH899, UNH853, UNH932, UNH933 and UNH773 in O. mossambicus. Any one of the 17 loci could amplify particular bands to distinguish one tilapia from the other two. The genetic structure of O. aureus, O. niloticus and O. mossambicus stocks and their phylogenetic relationships were also analysed using these 17 loci. In total 142 alleles were detected, and the average number of alleles per locus was 8.35. Additionally, a clustering analysis was performed based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using the unweighted pair group method using arithmetic average (UPGMA). The results showed that the mean value of observed heterozygosity was 0.0941, 0.5490 and 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230 and 0.1965, and the polymorphism information content was 0.0869, 0.7149 and 0.1643, in O. aureus, O. niloticus and O. mossambicus, respectively. The UPGMA tree demonstrated that O. aureus was more closely related to O. mossambicus than to O. niloticus.
Influence of BCG dose and age of inoculated mice on immunoprotection against tuberculosis and expression of IFN-γ/IL-4
Authors: Hui-Jun Guo , Bao-Quan Li , Jia-Qian Chai , Wei-Shan Chang , Chun-Yang Wang , Hong-Mei Li
Published: October 2009

BalB/C neonate mice and adult BalB/C mice were vaccinated using BCG (Bacille Calmette–Guerin). The pathogenic growth characteristics of BCG inin vitroculture on spleen cells (SPC) were observed and changes in induced expression of IFN (interferon)-γ and IL (interleukin)-4 in SPC were detected using the ELISPOT assay. The results showed that a low dose of BCG (2×103cfu) exerted 100% immunoprotection on 7-day-old neonate mice and a high dose of BCG (4×104cfu) exerted 75% immunoprotection. A low dose of BCG (2×103cfu) exerted 67% immunoprotection on 35-day-old mice. It is also shown that Th1-type cell immunity dominated by IFN-γ was enhanced significantly in the neonate mice injected with a low dose of BCG (2×103cfu), and Th2-type cell immunity dominated by IL-4 was depressed at the same time. IFN-γ and IL-4 induced by a high dosage of BCG (4×104cfu) in neonate mice were both increased. IFN-γ and IL-4 induced by a low dose of BCG (2×103cfu) in 35-day-old mice were also increased. The results indicate that there exists a marked correlation between immunoprotection by BCG in mice and both the immunizing dose and age of the immune animals, which might be relevant to the changes induced by BCG on Th1- and Th2-type cell immunity.
Optimism, Self-Efficacy, and Perceived Stress as Predictors of Self-Reported Health Symptoms in College Students
Authors: Schulz Heiko , Vögele Claus , Meyer Björn
Published: October 2009

Abstract. Studies provide support for the notion of increased vulnerability to upper respiratory track infections (URIs) with exposure to psychological stress, but only few have examined whether optimism and self-efficacy might moderate this relationship. The purpose of the present study was to examine (a) the influence of academic exam stress on susceptibility to URIs and (b) the extent to which these personality characteristics buffer against stress-related vulnerability to URIs. Using a repeated-measures design, URI infection status was measured in a sample of 80 college students with self-reports both during an exam period and outside such a period. Results suggested that optimism may protect from the adverse influence of heightened stress and that pessimistic, low self-efficacious participants may be at elevated risk for the development of URIs at times of increased stress.
Modeling storms improves estimates of long‐term shoreline change
Authors: Frazer L. Neil , Anderson Tiffany R. , Fletcher Charles H.
Published: October 2009

Large storms make it difficult to extract the long‐term trend of erosion or accretion from shoreline position data. Here we make storms part of the shoreline change model by means of a storm function. The data determine storm amplitudes and the rate at which the shoreline recovers from storms. Historical shoreline data are temporally sparse, and inclusion of all storms in one model over‐fits the data, but a probability‐weighted average model shows effects from all storms, illustrating how model averaging incorporates information from good models that might otherwise have been discarded as un‐parsimonious. Data from Cotton Patch Hill, DE, yield a long‐term shoreline loss rate of 0.49 ± 0.01 m/yr, about 16% less than published estimates. A minimum loss rate of 0.34 ± 0.01 m/yr is given by a model containing the 1929, 1962 and 1992 storms.
Uncertainty in the estimation of potential evapotranspiration under climate change
Authors: Kingston Daniel G. , Todd Martin C. , Taylor Richard G. , Thompson Julian R. , Arnell Nigel W.
Published: October 2009

21st century climate change is projected to result in an intensification of the global hydrological cycle, but there is substantial uncertainty in how this will impact freshwater availability. A relatively overlooked aspect of this uncertainty pertains to how different methods of estimating potential evapotranspiration (PET) respond to changing climate. Here we investigate the global response of six different PET methods to a 2°C rise in global mean temperature. All methods suggest an increase in PET associated with a warming climate. However, differences in PET climate change signal of over 100% are found between methods. Analysis of a precipitation/PET aridity index and regional water surplus indicates that for certain regions and GCMs, choice of PET method can actually determine the direction of projections of future water resources. As such, method dependence of the PET climate change signal is an important source of uncertainty in projections of future freshwater availability.
Airflow induced by pumping tests in unconfined aquifer with a low‐permeability cap
Authors: Jiao Jiu Jimmy , Guo Haipeng
Published: October 2009

Most analytical and numerical models developed to analyze pumping test data focus on saturated flow below the water table. Traditionally the soil above the initial water table prior to pumping has been thought to have little influence on the test results and has usually been ignored. It is hypothesized that, if the unsaturated zone is capped by low‐permeability soil, airflow in the unsaturated zone may be developed during pumping and may have impact on the drawdown in the aquifer. A transient, three‐dimensional and variably saturated flow model is employed to simulate the pumping‐induced air and groundwater flows in both the saturated zone and unsaturated zone with a low‐permeability layer. The results demonstrate that negative pressure in the unsaturated zone can be generated by pumping. The negative pressure begins to appear as the drawdown rate increases to a maximum, approaches a peak before the drawdown rate becomes zero, and then gradually disappears. Drawdown obtained from the capped aquifer is much greater because the water in the pores in the unsaturated zone is sucked by the negative pressure and the gravity drainage from the pores is hampered. Consequently, the drawdown versus time curve does not conform to the traditional S‐shaped curve for an unconfined aquifer but is similar to that of a confined aquifer. If the airflow caused by the low‐permeability cap is ignored, the error in estimated drawdown could be over 80% for the specific parameters and aquifer configuration used in the study. The possible errors in parameter estimation when airflow is ignored are explored. Overall, the hydraulic conductivity of the aquifer can be overestimated and the specific yield of the aquifer underestimated if airflow is ignored. The estimation error for specific yield tends to be greater than that in hydraulic conductivity.
Are coral-dwelling crabs monophyletic? A phylogeny of the Trapezioidea (Crustacea : Decapoda : Brachyura)
Authors: Lai Joelle C. Y. , Ahyong Shane T. , Jeng M.-S. , Ng Peter K. L.
Published: October 2009

Many brachyuran crab genera are known to be obligate symbionts on scleractinian corals in shallow tropical seas (e.g. Cymo, Tanaocheles, Domecia, Tetralia, Tetraloides and Trapezia). Most are currently placed in several families and superfamilies, the most prominent being the Trapezioidea, containing Domeciidae, Tetraliidae and Trapeziidae. The distinctness of the domeciids has long been recognised in Domecinae, and finally Domeciidae. Tetraliidae, however, has only recently been recognised when the classical coral obligate family Trapeziidae was split into two families, Trapeziidae sensu stricto and Tetraliidae. Recognition of Tetraliidae, however, has been controversial, and some workers have suggested that it should be regarded as a synonym of Trapeziidae, principally on the basis of carapace morphology and larval features. Using two gene markers, we evaluate the status of Trapezioidea and, in particular, that of Tetraliidae. Our analyses support the distinction between Tetraliidae and Trapeziidae and suggest that crabs have independently colonised hard corals several times.
Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals
Authors: Lefèvre Christophe M. , Sharp Julie A. , Nicholas Kevin R.
Published: October 2009

Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of β-casein occurred in the monotreme lineage, as opposed to more ancient duplications of α-casein in the eutherian lineage, while marsupials possess only single copies of α- and β-caseins. Despite this variability, the close proximity of the main α- and β-casein genes in an inverted tail–tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages.
Analysis of SINE and LINE repeat content of Y chromosomes in the platypus, Ornithorhynchus anatinus
Authors: Kortschak R. Daniel , Tsend-Ayush Enkhjargal , Grützner Frank
Published: October 2009

Monotremes feature an extraordinary sex-chromosome system that consists of five X and five Y chromosomes in males. These sex chromosomes share homology with bird sex chromosomes but no homology with the therian X. The genome of a female platypus was recently completed, providing unique insights into sequence and gene content of autosomes and X chromosomes, but no Y-specific sequence has so far been analysed. Here we report the isolation, sequencing and analysis of ~700 kb of sequence of the non-recombining regions of Y2, Y3 and Y5, which revealed differences in base composition and repeat content between autosomes and sex chromosomes, and within the sex chromosomes themselves. This provides the first insights into repeat content of Y chromosomes in platypus, which overall show similar patterns of repeat composition to Y chromosomes in other species. Interestingly, we also observed differences between the various Y chromosomes, and in combination with timing and activity patterns we provide an approach that can be used to examine the evolutionary history of the platypus sex-chromosome chain.
Annotation confidence score for genome annotation: a genome comparison approach
Authors: Yang Youngik , Gilbert Donald , Kim Sun
Published: October 2009

Motivation: The massively parallel sequencing technology can be used by small research labs to generate genome sequences of their research interest. However, annotation of genomes still relies on the manual process, which becomes a serious bottleneck to the high-throughput genome projects. Recently, automatic annotation methods are increasingly more accurate, but there are several issues. One important challenge in using automatic annotation methods is to distinguish annotation quality of ORFs or genes. The availability of such annotation quality of genes can reduce the human labor cost dramatically since manual inspection can focus only on genes with low-annotation quality scores.

Results: In this article, we propose a novel annotation quality or confidence scoring scheme, called Annotation Confidence Score (ACS), using a genome comparison approach. The scoring scheme is computed by combining sequence and textual annotation similarity using a modified version of a logistic curve. The most important feature of the proposed scoring scheme is to generate a score that reflects the excellence in annotation quality of genes by automatically adjusting the number of genomes used to compute the score and their phylogenetic distance. Extensive experiments with bacterial genomes showed that the proposed scoring scheme generated scores for annotation quality according to the quality of annotation regardless of the number of reference genomes and their phylogenetic distance.

Availability:  http://microbial.informatics.indiana.edu/acs.

Contact:  sumkim2@indiana.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Curious Case of Charles Darwin and Homeopathy
Authors: Ullman Dana
Published: October 2009

In 1849, Charles Darwin was so ill that he was unable to work one out of every 3 days, and after having various troubling symptoms for 2–12 years, he wrote to a friend that he was ‘going the way of all flesh’. He sought treatment from Dr James Manby Gully, a medical doctor who used water cure and homeopathic medicines. Despite being highly skeptical of these treatments, he experienced a dramatic improvement in his health, though some of his digestive and skin symptoms returned various times in his life. He grew to appreciate water cure, but remained skeptical of homeopathy, even though his own experiments on insectivore plants using what can be described as homeopathic doses of ammonia salts surprised and shocked him with their significant biological effect. Darwin even expressed concern that he should publish these results. Two of Darwin′s sons were as incredulous as he was, but their observations confirmed the results of his experiments. Darwin was also known to have read a book on evolution written by a homeopathic physician that Darwin described as similar to his own but ‘goes much deeper.’
Diaphragmatic Breathing Reduces Exercise‐Induced Oxidative Stress
Authors: Martarelli Daniele , Cocchioni Mario , Scuri Stefania , Pompei Pierluigi
Published: October 2009

Diaphragmatic breathing is relaxing and therapeutic, reduces stress, and is a fundamental procedure of Pranayama Yoga, Zen, transcendental meditation and other meditation practices. Analysis of oxidative stress levels in people who meditate indicated that meditation correlates with lower oxidative stress levels, lower cortisol levels and higher melatonin levels. It is known that cortisol inhibits enzymes responsible for the antioxidant activity of cells and that melatonin is a strong antioxidant; therefore, in this study, we investigated the effects of diaphragmatic breathing on exercise‐induced oxidative stress and the putative role of cortisol and melatonin hormones in this stress pathway. We monitored 16 athletes during an exhaustive training session. After the exercise, athletes were divided in two equivalent groups of eight subjects. Subjects of the studied group spent 1 h relaxing performing diaphragmatic breathing and concentrating on their breath in a quiet place. The other eight subjects, representing the control group, spent the same time sitting in an equivalent quite place. Results demonstrate that relaxation induced by diaphragmatic breathing increases the antioxidant defense status in athletes after exhaustive exercise. These effects correlate with the concomitant decrease in cortisol and the increase in melatonin. The consequence is a lower level of oxidative stress, which suggests that an appropriate diaphragmatic breathing could protect athletes from long‐term adverse effects of free radicals.
The Herb Medicine Formula “Chong Lou Fu Fang” Increases the Cytotoxicity of Chemotherapeutic Agents and Down‐Regulates the Expression of Chemotherapeutic Agent Resistance‐Related Genes in Human Gastric Cancer Cells In Vitro
Authors: Liu Yongping , Ling Yang , Hu Wenjing , Xie Li , Yu Lixia , Qian Xiaoping , Zhang Binxia , Liu Baorui
Published: October 2009

The herb medicine formula “Chong Lou Fu Fang” (CLFF) has efficacy in inhibiting the proliferation of human gastric cancer in vitro and in vivo. To explore the potentially useful combination of CLFF with chemotherapeutic agents commonly used in gastric cancer therapy, we assess the interaction between CLFF and these chemotherapeutic agents in both SGC‐7901 cell lines and BGC‐823 cell lines using a median effect analysis and apoptosis analysis, and we also investigate the influence of CLFF on chemotherapeutic agent‐associated gene expression. The synergistic analysis indicated that CLFF had a synergistic effect on the cytotoxicity of 5‐fluorouracil (5‐FU) in a relative broad dose inhibition range (20–95% fraction affected in SGC‐7901cell lines and 5–65% fraction affected in BGC‐823 cell lines), while the synergistic interaction between CLFF and oxaliplatin or docetaxel only existed in a low dose inhibition range (≤50% fraction affected in both cell lines). Combination of CLFF and chemotherapeutic agents could also induce apoptosis in a synergistic manner. After 24 h, CLFF alone or CLFF combination with chemotherapeutic agents could significantly suppress the levels of expression of chemotherapeutic agent resistance related genes in gastric cancer cells. Our findings indicate that there are useful synergistic interactions between CLFF and chemotherapeutic agents in gastric cancer cells, and the possible mechanisms might be partially due to the down‐regulation of chemotherapeutic agent resistance related genes and the synergistic apoptotic effect.
Correction for Cox
et al.
, Mechanics of atoms and fullerenes in single-walled carbon nanotubes. I. Acceptance and suction energies
Authors: Cox Barry J. , Thamwattana Ngamta , Hill James M.
Published: October 2009

Correction for ‘Mechanics of atoms and fullerenes in single-walled carbon nanotubes. I. Acceptance and suction energies’ by Barry J. Cox, Ngamta Thamwattana and James M. Hill (Proc. R. Soc. A
463
, 461–476.
(doi:
10.1098/rspa.2006.1771
)).

The following equation contains typographical errors that has no consequence for any other equation or result in the above paper.
Steady axisymmetric motion of a small bubble in a tube with flowing liquid
Authors: Feng James Q.
Published: October 2009

The steady axisymmetric behaviour of a relatively small bubble moving with a flowing liquid in a straight round tube is studied by computationally solving the nonlinear Navier–Stokes equations, using a Galerkin finite-element method with boundary-fitted mesh, for wide ranges of capillary number
C
a
and Reynolds number
R
e
. Here a bubble is considered relatively small when its volume-equivalent radius is less than that of the tube. At small values of
R
e
, the velocity of a bubble increases with bubble size for large values of
C
a
but decreases with bubble size for small values of
C
a
. At large values of
R
e
, however, a bubble of large size appears to move at a slower velocity for any given value of
C
a
. When
R
e
is large (e.g.
R
e
= 100) and
C
a
> 0.1, a bubble of radius greater than half of the tube radius moves at a velocity that seems to be independent of bubble size. The strong inertial effect at large
R
e
makes a small bubble of radius greater than a quarter of the tube radius to deform into a noticeable oblate shape as
C
a
increases from very small value, and then to be elongated into a bullet shape with further increasing
C
a
after
C
a
reaches an intermediate value. Even very small bubbles (e.g. of radius equal to one-tenth of the tube radius) can still be significantly deformed provided that the value of
C
a
is adequately large. Despite significant shape deformations that may still occur, bubbles of radius less than a quarter of that of the tube almost always move at the same velocity as that of the local liquid flow at the tube centreline (i.e. twice that of the average liquid velocity), regardless the values of
R
e
and
C
a
. This fact suggests that very small bubbles are basically carried by the local liquid flow.
Three-dimensional Green's function and its derivative for materials with general anisotropic magneto-electro-elastic coupling
Authors: Buroni Federico C. , Sáez Andrés
Published: October 2009

Explicit expressions of Green’s function and its derivative for three-dimensional infinite solids are presented in this paper. The medium is allowed to exhibit a fully magneto-electro-elastic (MEE) coupling and general anisotropic behaviour. In particular, new explicit expressions for the first-order derivative of Green’s function are proposed. The derivation combines extended Stroh formalism, Radon transform and Cauchy’s residue theory. In order to cover mathematical degenerate and non-degenerate materials in the Stroh formalism context, a multiple residue scheme is performed. Expressions are explicit in terms of Stroh’s eigenvalues, this being a feature of special interest in numerical applications such as boundary element methods. As a particular case, simplifications for MEE materials with transversely isotropic symmetry are derived. Details on the implementation and numerical stability of the proposed solutions for degenerate cases are studied.
Correction for Meese and Summers, Area summation in human vision at and above detection threshold
Authors: Meese Tim S. , Summers Robert J.
Published: October 2009

Correction for ‘Area summation in human vision at and above detection threshold’ by Tim S. Meese and Robert J. Summers (Proc. R. Soc. B
274
, 2891–2900.
(doi:
10.1098/rspb.2007.0957
)).

Several equations, detailed below, were presented incorrectly.
Correction for Moon and Stiefel, Coexisting chaotic and periodic dynamics in clock escapements
Authors: Moon Francis C. , Stiefel Preston D.
Published: October 2009

Correction for ‘Coexisting chaotic and periodic dynamics in clock escapements’ by Francis C. Moon and Preston D. Stiefel (Phil. Trans. R. Soc. A
364
, 2539–2563.
(doi:
10.1098/rsta.2006.1839
)).

The following equation contains typographical errors that has no consequence for any other equation or result in the above paper.
Correction for Lévi, Implications of circadian clocks for the rhythmic delivery of cancer therapeutics
Authors: Lévi Francis , Altinok Atilla , Clairambault Jean , Goldbeter Albert
Published: October 2009

Correction for ‘Implications of circadian clocks for the rhythmic delivery of cancer therapeutics’ by Francis Lévi, Atilla Altinok, Jean Clairambault and Albert Goldbeter (Phil. Trans. R. Soc. A
366
, 3575–3598.
(doi:
10.1098/rsta.2008.0114
)).

The last sentence of the first paragraph on p. 3585 is incorrect, and should read as follows.
Differential effects of short-chain fatty acids and iron on expression of iha in Shiga-toxigenic Escherichia coli
Authors: Herold Sylvia , Paton James C. , Srimanote Potjanee , Paton Adrienne W.
Published: October 2009

Shiga-toxigenic Escherichia coli (STEC) colonizing the bowel are exposed to a variety of short-chain fatty acids (SCFAs), including acetate, propionate and butyrate, produced by gut microflora. However, the total concentrations and relative amounts of SCFAs in the lumen vary with intestinal niche. Here we report that conditions simulating SCFA concentrations present in the human gut trigger expression of the iha gene, which encodes an adherence-conferring outer-membrane protein of pathogenic E. coli. We show that growth under conditions simulating colonic, but not ileal, SCFA concentrations increases iha expression in three tested STEC strains, with the strongest expression detected in LEE-negative STEC O113:H21 strain 98NK2. Expression of iha is known to be subject to Fur-mediated iron repression in O157:H7 STEC, and the same occurs in 98NK2. However, exogenous iron did not repress iha expression in the presence of colonic SCFAs in either 98NK2 or the O157:H7 strain EDL933. Moreover, exposure to the iron chelator 2,2′-dipyridyl caused no further enhancement of iha expression over that induced by colonic SCFAs. These findings indicate that SCFAs regulate iha expression in STEC independently of iron. Increased expression of iha under colonic but not ileal SCFA conditions possibly may contribute to preferential colonization of the human colon by STEC.
Overcoming codon-usage bias in heterologous protein expression in Streptococcus gordonii
Authors: Lee Song F. , Li Yi-Jing , Halperin Scott A.
Published: October 2009

One of the limitations facing the development ofStreptococcus gordoniiinto a successful vaccine vector is the inability of this bacterium to express high levels of heterologous proteins. In the present study, we have identified 12 codons deemed as rare codons inS. gordoniiand seven other streptococcal species. tRNA genes encoding 10 of the 12 rare codons were cloned into a plasmid. The plasmid was transformed into strains ofS. gordoniiexpressing the fusion protein SpaP/S1, the anti-complement receptor 1 (CR1) single-chain variable fragment (scFv) antibody, or theToxoplasma gondiicyclophilin C18 protein. These three heterologous proteins contained high percentages of amino acids encoded by rare codons. The results showed that the production of SpaP/S1, anti-CR1 scFv and C18 increased by 2.7-, 120- and 10-fold, respectively, over the control strains. In contrast, the production of the streptococcal SpaP protein without the pertussis toxin S1 fragment was not affected by tRNA gene supplementation, indicating that the increased production of SpaP/S1 protein was due to the ability to overcome the limitation caused by rare codons required for the S1 fragment. The increase in anti-CR1 scFv production was also observed inStreptococcus mutansfollowing tRNA gene supplementation. Collectively, the findings in the present study demonstrate for the first time, to the best of our knowledge, that codon-usage bias exists inStreptococcusspp. and the limitation of heterologous protein expression caused by codon-usage bias can be overcome by tRNA supplementation.
Previously uncharacterized Salmonella enterica genes required for swarming play a role in seedling colonization
Authors: Barak Jeri D. , Gorski Lisa , Liang Anita S. , Narm Koh-Eun
Published: October 2009

Incidences of bacterial foodborne illness caused by ingestion of fresh produce are rising. Instead of this being due to incidental contamination, the animal pathogen Salmonella enterica utilizes specific molecular mechanisms to attach to and colonize plants. This work characterizes two S. enterica genes of unknown function: a putative periplasmic protein, STM0278, and a putative protein with a hydrolase in the C-terminus, STM0650. STM0278 and STM0650 are important for seedling colonization but appear to have different roles during the process of colonization. Mutants of either STM0278 or STM0650 showed reduced colonization of alfalfa seedlings at 24 h, and the STM0278 mutant also showed reduced colonization at 48 h. Both genes were expressed in planta at 4 h following inoculation of 3-day-old seedlings and at 72 h after seed inoculation. This suggests that the role of STM0650 in seedling colonization is less important later in the process or is duplicated by other mechanisms. Mutants of STM0278 and STM0650 were defective in swarming. The STM0278 mutant failed to swarm in 24 h, while swarming of the STM0650 mutant was delayed. Addition of surfactant restored swarming of the STM0278 mutant, suggesting that STM0278 is involved in surfactant or osmotic agent production or deployment. Alfalfa seed exudates as the sole nutrient source were capable of perpetuating S. enterica swarming. Sequence analysis revealed sequences homologous to STM0278 and STM0650 in plant-associated bacteria, but none in Escherichia coli. Phylogenetic analysis of STM0650 showed similar sequences from diverse classes of plant-associated bacteria. Bacteria that preferentially colonize roots, including S. enterica, may use a similar hydrolase for swarming or biofilm production on plants. Multicellular behaviours by S. enterica appear central to plant colonization. S. enterica genes involved in plant colonization and survival outside of a host are most likely among the ‘function unknown’ genes of this bacterium.
Genuine genetic redundancy in maleylacetate-reductase-encoding genes involved in degradation of haloaromatic compounds by Cupriavidus necator JMP134
Authors: Pérez-Pantoja Danilo , Donoso Raúl A. , Sánchez Miguel A. , González Bernardo
Published: October 2009

Maleylacetate reductases (MAR) are required for biodegradation of several substituted aromatic compounds. To date, the functionality of two MAR-encoding genes (tfdF
I and tfdF
II) has been reported in Cupriavidus necator JMP134(pJP4), a known degrader of aromatic compounds. These two genes are located in tfd gene clusters involved in the turnover of 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3-CB). The C. necator JMP134 genome comprises at least three other genes that putatively encode MAR (tcpD, hqoD and hxqD), but confirmation of their functionality and their role in the catabolism of haloaromatic compounds has not been assessed. RT-PCR expression analyses of C. necator JMP134 cells exposed to 2,4-D, 3-CB, 2,4,6-trichlorophenol (2,4,6-TCP) or 4-fluorobenzoate (4-FB) showed that tfdF
I and tfdF
II are induced by haloaromatics channelled to halocatechols as intermediates. In contrast, 2,4,6-TCP only induces tcpD, and any haloaromatic compounds tested did not induce hxqD and hqoD. However, the tcpD, hxqD and hqoD gene products showed MAR activity in cell extracts and provided the MAR function for 2,4-D catabolism when heterologously expressed in MAR-lacking strains. Growth tests for mutants of the five MAR-encoding genes in strain JMP134 showed that none of these genes is essential for degradation of the tested compounds. However, the role of tfdF
I/tfdF
II and tcpD genes in the expression of MAR activity during catabolism of 2,4-D and 2,4,6-TCP, respectively, was confirmed by enzyme activity tests in mutants. These results reveal a striking example of genetic redundancy in the degradation of aromatic compounds.
The distribution pattern of proliferating cell nuclear antigen in the nuclei of Leishmania donovani
Authors: Kumar Devanand , Minocha Neha , Rajanala Kalpana , Saha Swati
Published: October 2009

DNA replication in eukaryotes is a highly conserved process marked by the licensing of multiple origins, with pre-replication complex assembly in G1 phase, followed by the onset of replication at these origins in S phase. The two strands replicate by different mechanisms, and DNA synthesis is brought about by the activity of the replicative DNA polymerases Polδand Pol ϵ. Proliferating cell nuclear antigen (PCNA) augments the processivity of these polymerases by serving as a DNA sliding clamp protein. This study reports the cloning of PCNA from the protozoanLeishmania donovani, which is the causative agent of the systemic disease visceral leishmaniasis. PCNA was demonstrated to be robustly expressed in actively proliferatingL. donovanipromastigotes. We found that the protein was present primarily in the nucleus throughout the cell cycle, and it was found in both proliferating procyclic and metacyclic promastigotes. However, levels of expression of PCNA varied through cell cycle progression, with maximum expression evident in G1 and S phases. The subnuclear pattern of expression of PCNA differed in different stages of the cell cycle; it formed distinct subnuclear foci in S phase, while it was distributed in a more diffuse pattern in G2/M phase and post-mitotic phase cells. These subnuclear foci are the sites of active DNA replication, suggesting that replication factories exist inLeishmania, as they do in higher eukaryotes, thus opening avenues for investigating otherLeishmaniaproteins that are involved in DNA replication as part of these replication factories.
Changes in context-specificity during memory reconsolidation: Selective effects of hippocampal lesions
Authors: Winocur Gordon , Frankland Paul W. , Sekeres Melanie , Fogel Stuart , Moscovitch Morris
Published: October 2009

After acquisition, memories associated with contextual fear conditioning pass through a labile phase, in which they are vulnerable to hippocampal lesions, to a more stable state, via consolidation, in which they engage extrahippocampal structures and are resistant to such disruption. The process is accompanied by changes in the form of the memory from being context-specific to context-general. However, when revived by a reminder, stable memories once again become labile and susceptible to hippocampal disruption, and memory reconsolidation is needed to stabilize them. This study addressed two questions with respect to this reconsolidation phenomenon: (1) How do reminders reinstate a hippocampally dependent memory trace? (2) As the memory changes from a stable to a labile state after a reminder, does its form remain invariant, or does it also change? Using contextual manipulations at retrieval in a test of contextual fear conditioning, we showed that when the fear-conditioning environment served as a reminder, the reinstated memory regained its context specificity and, as a result, became vulnerable again to the effects of hippocampal lesions. By comparison, exposure to a different environment during the reminder session reinstated a version of the original memory that was dependent primarily on general features of the original context and, consequently, was less affected by hippocampal lesions. These findings, which relate loss of reactivated memories after hippocampal destruction (or inactivation) to changes in memory representation, are interpreted as consistent with the transformation hypothesis of memory processing.