bluuebunny/crossref_metadata_2025 huggingface dataset:
Bi-correlation clustering algorithm for determining a set of co-regulated genes
Authors: Bhattacharya Anindya , De Rajat K.
Published: September 2009

Motivation: Biclustering has been emerged as a powerful tool for identification of a group of co-expressed genes under a subset of experimental conditions (measurements) present in a gene expression dataset. Several biclustering algorithms have been proposed till date. In this article, we address some of the important shortcomings of these existing biclustering algorithms and propose a new correlation-based biclustering algorithm called bi-correlation clustering algorithm (BCCA).

Results: BCCA has been able to produce a diverse set of biclusters of co-regulated genes over a subset of samples where all the genes in a bicluster have a similar change of expression pattern over the subset of samples. Moreover, the genes in a bicluster have common transcription factor binding sites in the corresponding promoter sequences. The presence of common transcription factors binding sites, in the corresponding promoter sequences, is an evidence that a group of genes in a bicluster are co-regulated. Biclusters determined by BCCA also show highly enriched functional categories. Using different gene expression datasets, we demonstrate strength and superiority of BCCA over some existing biclustering algorithms.

Availability: The software for BCCA has been developed using C and Visual Basic languages, and can be executed on the Microsoft Windows platforms. The software may be downloaded as a zip file from http://www.isical.ac.in/∼rajat. Then it needs to be installed. Two word files (included in the zip file) need to be consulted before installation and execution of the software.

Contact:  rajat@isical.ac.in

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automated inference of molecular mechanisms of disease from amino acid substitutions
Authors: Li Biao , Krishnan Vidhya G. , Mort Matthew E. , Xin Fuxiao , Kamati Kishore K. , Cooper David N. , Mooney Sean D. , Radivojac Predrag
Published: September 2009

Motivation: Advances in high-throughput genotyping and next generation sequencing have generated a vast amount of human genetic variation data. Single nucleotide substitutions within protein coding regions are of particular importance owing to their potential to give rise to amino acid substitutions that affect protein structure and function which may ultimately lead to a disease state. Over the last decade, a number of computational methods have been developed to predict whether such amino acid substitutions result in an altered phenotype. Although these methods are useful in practice, and accurate for their intended purpose, they are not well suited for providing probabilistic estimates of the underlying disease mechanism.

Results: We have developed a new computational model, MutPred, that is based upon protein sequence, and which models changes of structural features and functional sites between wild-type and mutant sequences. These changes, expressed as probabilities of gain or loss of structure and function, can provide insight into the specific molecular mechanism responsible for the disease state. MutPred also builds on the established SIFT method but offers improved classification accuracy with respect to human disease mutations. Given conservative thresholds on the predicted disruption of molecular function, we propose that MutPred can generate accurate and reliable hypotheses on the molecular basis of disease for ∼11% of known inherited disease-causing mutations. We also note that the proportion of changes of functionally relevant residues in the sets of cancer-associated somatic mutations is higher than for the inherited lesions in the Human Gene Mutation Database which are instead predicted to be characterized by disruptions of protein structure.

Availability:  http://mutdb.org/mutpred

Contact:  predrag@indiana.edu; smooney@buckinstitute.org
Identifying related journals through log analysis
Authors: Lu Zhiyong , Xie Natalie , Wilbur W. John
Published: September 2009

Motivation: With the explosion of biomedical literature and the evolution of online and open access, scientists are reading more articles from a wider variety of journals. Thus, the list of core journals relevant to their research may be less obvious and may often change over time. To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data.

Availability:  http://www.ncbi.nlm.nih.gov/IRET/Journals

Contact:  luzh@ncbi.nlm.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Algorithms for optimal protein structure alignment
Authors: Poleksic Aleksandar
Published: September 2009

Motivation: Structural alignment is an important tool for understanding the evolutionary relationships between proteins. However, finding the best pairwise structural alignment is difficult, due to the infinite number of possible superpositions of two structures. Unlike the sequence alignment problem, which has a polynomial time solution, the structural alignment problem has not been even classified as solvable.

Results: We study one of the most widely used measures of protein structural similarity, defined as the number of pairs of residues in two proteins that can be superimposed under a predefined distance cutoff. We prove that, for any two proteins, this measure can be optimized for all but finitely many distance cutoffs. Our method leads to a series of algorithms for optimizing other structure similarity measures, including the measures commonly used in protein structure prediction experiments. We also present a polynomial time algorithm for finding a near-optimal superposition of two proteins. Aside from having a relatively low cost, the algorithm for near-optimal solution returns a superposition of provable quality. In other words, the difference between the score of the returned superposition and the score of an optimal superposition can be explicitly computed and used to determine whether the returned superposition is, in fact, the best superposition.

Contact:  poleksic@cs.uni.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Iyengar Yoga versus Enhanced Usual Care on Blood Pressure in Patients with Prehypertension to Stage I Hypertension: a Randomized Controlled Trial
Authors: Cohen Debbie L. , Bloedon LeAnne T. , Rothman Rand L. , Farrar John T. , Galantino Mary Lou , Volger Sheri , Mayor Christine , Szapary Phillipe O. , Townsend Raymond R.
Published: September 2009

The prevalence of prehypertension and Stage 1 hypertension continues to increase despite being amenable to non‐pharmacologic interventions. Iyengar yoga (IY) has been purported to reduce blood pressure (BP) though evidence from randomized trials is lacking. We conducted a randomized controlled trial to assess the effects of 12 weeks of IY versus enhanced usual care (EUC) (based on individual dietary adjustment) on 24‐h ambulatory BP in yoga‐naïve adults with untreated prehypertension or Stage 1 hypertension. In total, 26 and 31 subjects in the IY and EUC arms, respectively, completed the study. There were no differences in BP between the groups at 6 and 12 weeks. In the EUC group, 24‐h systolic BP (SBP), diastolic BP (DBP) and mean arterial pressure (MAP) significantly decreased by 5, 3 and 3 mmHg, respectively, from baseline at 6 weeks (P < .05), but were no longer significant at 12 weeks. In the IY group, 24 h SBP was reduced by 6 mmHg at 12 weeks compared to baseline (P = .05). 24 h DBP (P < .01) and MAP (P < .05) decreased significantly each by 5 mmHg. No differences were observed in catecholamine or cortisol metabolism to explain the decrease in BP in the IY group at 12 weeks. Twelve weeks of IY produces clinically meaningful improvements in 24 h SBP and DBP. Larger studies are needed to establish the long term efficacy, acceptability, utility and potential mechanisms of IY to control BP.
Electroacupuncture Treatment Normalized Sleep Disturbance in Morphine Withdrawal Rats
Authors: Li Yi-Jing , Zhong Fei , Yu Peng , Han Ji-Sheng , Cui Cai-Lian , Wu Liu-Zhen
Published: September 2009

Sleep disturbance is considered as an important symptom of acute and protracted opiate withdrawal. Current results suggest that sleep disturbance may be taken as a predictor of relapse. Appropriate sleep enhancement therapy will be in favor of the retention in treatment for opiate addicts. Our previous studies have shown that electroacupuncture (EA) is effective in suppressing morphine withdrawal syndrome. The aim of the present study is to investigate the effect of 2 and 100 Hz EA on the sleep disturbance during morphine withdrawal. Rats were made dependent on morphine by repeated morphine injections (escalating doses of 5–80 mg kg−1, subcutaneously, twice a day) for 5 days. EA of 2 or 100 Hz was given twice a day for 3 days, starting at 48 h after the last morphine injection. Electroencephalogram and electromyogram were monitored at the end of the first and the last EA treatments, respectively. Results showed that non‐rapid eye movement (NREM) sleep, REM sleep and total sleep time decreased dramatically, while the sleep latency prolonged significantly during acute morphine withdrawal. Both 2 and 100 Hz EA produced a significant increase in NREM sleep, REM sleep and total sleep time. It was suggested that EA could be a potential treatment for sleep disturbance during morphine withdrawal.
Exploring spatial non-stationarity of fisheries survey data using geographically weighted regression (GWR): an example from the Northwest Atlantic
Authors: Windle Matthew J. S. , Rose George A. , Devillers Rodolphe , Fortin Marie-Josée
Published: September 2009

Windle, M. J. S., Rose, G. A., Devillers, R., and Fortin, M-J. 2010. Exploring spatial non-stationarity of fisheries survey data using geographically weighted regression (GWR): an example from the Northwest Atlantic. – ICES Journal of Marine Science, 67: 145–154. Analyses of fisheries data have traditionally been performed under the implicit assumption that ecological relationships do not vary within management areas (i.e. assuming spatially stationary processes). We question this assumption using a local modelling technique, geographically weighted regression (GWR), not previously used in fisheries analyses. Outputs of GWR are compared with those of global logistic regression and generalized additive models (GAMs) in predicting the distribution of northern cod off Newfoundland, Canada, based on environmental (temperature and distance from shore) and biological factors (snow crab and northern shrimp) from 2001. Results from the GWR models explained significantly more variability than the global logistic and GAM regressions, as shown by goodness-of-fit tests and a reduction in the spatial autocorrelation of model residuals. GWR results revealed spatial regions in the relationships between cod and explanatory variables and that the significance and direction of these relationships varied locally. A k-means cluster analysis based on GWR t-values was used to delineate distinct zones of species–environment relationships. The advantages and limitations of GWR are discussed in terms of potential application to fisheries ecology.
Balancing protection and release of DNA: tools to address a bottleneck of non-viral gene delivery
Authors: Grigsby Christopher L. , Leong Kam W.
Published: September 2009

Engineering polymeric gene-delivery vectors to release an intact DNA payload at the optimal time and subcellular compartment remains a formidable challenge. An ideal vector would provide total protection of complexed DNA from degradation prior to releasing it efficiently near or within the nucleus of a target cell. While optimization of polymer properties, such as molecular weight and charge density, has proved largely inadequate in addressing this challenge, applying polymeric carriers that respond to temperature, light, pH and redox environment to trigger a switch from a tight, protective complex to a more relaxed interaction favouring release at the appropriate time and place has shown promise. Currently, a paucity of gene carriers able to satisfy the contrary requirements of adequate DNA protection and efficient release contributes to the slow progression of non-viral gene therapy towards clinical translation. This review highlights the promising carrier designs that may achieve an optimal balance of DNA protection and release. It also discusses the imaging techniques and three-dimensionalin vitromodels that can help study these two barriers in the non-viral gene transfer process. Ultimately, efficacious non-viral gene therapy will depend on the combination of intelligent material design, innovative imaging techniques and sophisticatedin vitromodel systems to facilitate the rational design of polymeric gene-delivery vectors.
Quantum metabolism explains the allometric scaling of metabolic rates
Authors: Demetrius Lloyd , Tuszynski J. A.
Published: September 2009

A general model explaining the origin of allometric laws of physiology is proposed based on coupled energy-transducing oscillator networks embedded in a physical
d
-dimensional space (
d
= 1, 2, 3). This approach integrates Mitchell's theory of chemi-osmosis with the Debye model of the thermal properties of solids. We derive a scaling rule that relates the energy generated by redox reactions in cells, the dimensionality of the physical space and the mean cycle time. Two major regimes are found corresponding to classical and quantum behaviour. The classical behaviour leads to allometric isometry while the quantum regime leads to scaling laws relating metabolic rate and body size that cover a broad range of exponents that depend on dimensionality and specific parameter values. The regimes are consistent with a range of behaviours encountered in micelles, plants and animals and provide a conceptual framework for a theory of the metabolic function of living systems.
A novel method of solution for the fluid-loaded plate
Authors: Ashton A. C. L. , Fokas A. S.
Published: September 2009

We study the equations governing a fluid-loaded plate. We first reformulate these equations as a system of two equations, one of which is an explicit non-local equation for the wave height and the velocity potential on the free surface. We then concentrate on the linearized equations and show that the problems formulated either on the full or the half-line can be solved by employing the unified approach to boundary value problems introduced by one of the authors in the late 1990s. The problem on the full line was analysed by Crighton & Oswell (Crighton & Oswell 1991
Phil. Trans. R. Soc. Lond. A
335
, 557–592 (doi:10.1098/rsta.1991.0060)) using a combination of Laplace and Fourier transforms. The new approach avoids the technical difficulty of the
a priori
assumption that the amplitude of the plate is in
L

d
t

1
(
R
+
) and furthermore yields a simpler solution representation that immediately implies that the problem is well-posed. For the problem on the half-line, a similar analysis yields a solution representation, which, however, involves two unknown functions. The main difficulty with the half-line problem is the characterization of these two functions. By employing the so-called global relation, we show that the two functions can be obtained via the solution of a complex-valued integral equation of the convolution type. This equation can be solved in a closed form using the Laplace transform. By prescribing the initial data
η
0
to be in
H
〈5〉
5
(
R
+
), or equivalently four times continuously differentiable with sufficient decay at infinity, we show that the solution depends continuously on the initial data, and, hence, the problem is well-posed.
Superadiabatic transitions in quantum molecular dynamics
Authors: Betz Volker , Goddard Benjamin D. , Teufel Stefan
Published: September 2009

We study the dynamics of a molecule’s nuclear wave function near an avoided crossing of two electronic energy levels for one nuclear degree of freedom. We derive the general form of the Schrödinger equation in the
n
th superadiabatic representation for all

. Using these results, we obtain closed formulas for the time development of the component of the wave function in an initially unoccupied energy subspace when a wave packet travels through the transition region. In the optimal superadiabatic representation, which we define, this component builds up monotonically. Finally, we give an explicit formula for the transition wave function away from the avoided crossing, which is in excellent agreement with high-precision numerical calculations.
Spatial swarm segregation and reproductive isolation between the molecular forms ofAnopheles gambiae
Authors: Diabaté Abdoulaye , Dao Adama , Yaro Alpha S. , Adamou Abdoulaye , Gonzalez Rodrigo , Manoukis Nicholas C. , Traoré Sékou F. , Gwadz Robert W. , Lehmann Tovi
Published: September 2009

Anopheles gambiae, the major malaria vector in Africa, can be divided into two subgroups based on genetic and ecological criteria. These two subgroups, termed the M and S molecular forms, are believed to be incipient species. Although they display differences in the ecological niches they occupy in the field, they are often sympatric and readily hybridize in the laboratory to produce viable and fertile offspring. Evidence for assortative mating in the field was recently reported, but the underlying mechanisms awaited discovery. We studied swarming behaviour of the molecular forms and investigated the role of swarm segregation in mediating assortative mating. Molecular identification of 1145 males collected from 68 swarms in Donéguébougou, Mali, over 2 years revealed a strict pattern of spatial segregation, resulting in almost exclusively monotypic swarms with respect to molecular form. We found evidence of clustering of swarms composed of individuals of a single molecular form within the village. Tethered M and S females were introduced into natural swarms of the M form to verify the existence of possible mate recognition operating within-swarm. Both M and S females were inseminated regardless of their form under these conditions, suggesting no within-mate recognition. We argue that our results provide evidence that swarm spatial segregation strongly contributes to reproductive isolation between the molecular forms in Mali. However this does not exclude the possibility of additional mate recognition operating across the range distribution of the forms. We discuss the importance of spatial segregation in the context of possible geographic variation in mechanisms of reproductive isolation.
The first well-preserved Early Cretaceous brachiosaurid dinosaur in Asia
Authors: You Hai-Lu , Li Da-Qing
Published: September 2009

A new genus and species of brachiosaurid sauropods,
Qiaowanlong kangxii
gen. et sp. nov., is reported, representing the first well-preserved Early Cretaceous brachiosaurid in Asia and expanding the distribution of brachiosaurids undoubtedly into the Asian continent. The new taxon was recovered from the late Early Cretaceous Xinminpu Group of Yujingzi Basin in northwestern Gansu Province, China, and is represented by a series of eight mid-cervical vertebrae, a right pelvic girdle and some unidentified bones. The existence of deeply excavated cervical neural spines and a rising transition in the neural spine height among mid-cervical vertebrae clearly show the affinity of
Qiaowanlong
as a member of brachiosaurids. Among brachiosaurids,
Qiaowanlong
shares a derived feature with the North American Early Cretaceous brachiosaurid
Sauroposeidon
: the lack of cranial centrodiapophyseal lamina. However,
Qiaowanlong
is unique in possessing a suite of features, such as a low central length/cotyle height ratio, bifurcated cervical neural spines and a much reduced ischium. The discovery of
Qiaowanlong
and other new material indicates a diverse and abundant sauropod assemblage in China during the Early Cretaceous.
Protecting aquatic organisms from chemicals: the harsh realities
Authors: Sumpter John P.
Published: September 2009

Tens of thousands of man-made chemicals are in everyday use in developed countries. A high proportion of these, or their transformation products, probably reach the aquatic environment. A considerable amount is known about the environmental concentrations of some of these chemicals (such as metals), especially the regulated ones, but little or nothing is known about the majority. In densely populated countries, most or all rivers will receive both diffuse (e.g. agricultural runoff) and point source (e.g. sewage treatment plant effluent) inputs, and hence be contaminated with complex, ill-defined mixtures of chemicals. Most freshwater organisms will be exposed, to varying degrees, to this contamination. The number of species exposed is in the thousands, and quite possibly tens of thousands. Little is known about whether or not these species are adversely affected by the chemicals present in their environment. Often it is not even known what species are present, let alone whether they are affected by the chemicals present. In a few high-profile cases (e.g. tributyl tin causing imposex in molluscs and oestrogens ‘feminizing’ male fish), chemicals have undoubtedly adversely affected aquatic species, occasionally leading to population crashes. Whether or not other chemicals are affecting less visible species (such as most invertebrates) is largely unknown. It is possible that only very few chemicals in the freshwater environment are adversely affecting wildlife, but it is equally possible that some effects of chemicals are, as yet, undiscovered (and may remain so). Nor it is clear which chemicals may pose the greatest risk to aquatic organisms. All these uncertainties leave much to chance, yet designing a regulatory system that would better protect aquatic organisms from chemicals is difficult. A more flexible and intelligent strategy may improve the current situation. Finally, the risk due to chemicals is put into context with the many other threats, such as alien species and new diseases that undoubtedly can pose significant risks to aquatic ecosystems.
Modern approaches to the analysis of disinfection by-products in drinking water
Authors: Weinberg Howard S.
Published: September 2009

The discovery and study of disinfection by-products (DBPs) of health and regulatory concern in drinking water have often been hampered by the lack of appropriate analytical methods, but, with the new tools and expertise now available to the drinking water industry, there is an opportunity to plug a major gap in our knowledge of the nature and identity of these chemicals. The challenge is that less than half of the halogenated by-products resulting from the chlorination of drinking water have been identified, and even less is known about those produced in waters treated with ozone, chloramines or chlorine dioxide. For the DBPs that have been identified, very little or no occurrence data exist for the unregulated chemicals to document how often a particular DBP is formed and in what quantity. The elucidation of the nature and identity of these by-products is hindered by two complicating factors. The first is the inherent aqueous solubility of many of these compounds, which renders their efficient extraction from water difficult to achieve. The second is the lack of established identity of specific potential by-products, which complicates targeted analytical approaches. This paper reviews existing and new methodologies that attempt to overcome some of these challenges.
Environmental fate of phenolic endocrine disruptors: field and laboratory studies
Authors: Giger Walter , Gabriel Frédéric L. P. , Jonkers Niels , Wettstein Felix E. , Kohler Hans-Peter E.
Published: September 2009

Alkylphenolic compounds derived from microbial degradation of non-ionic surfactants became a major focus of environmental research in the early 1980s. More toxic than the parent compounds and weakly oestrogenic, certain metabolites of nonylphenol polyethoxylate (NP
n
EO) surfactants, especially nonylphenol (NP), raised sustained concern over the risk they pose to the environment and triggered legal measures as well as partly voluntary actions by the manufacturing industry. Continuous progress in the development of analytical techniques is crucial to understand how these alkylphenolic compounds behave in wastewater treatment, the aquatic environment and in laboratory experiments. Measured concentrations and mass flows of phenolic endocrine disruptors, particularly nonylphenolic compounds, bisphenol A and parabens in municipal wastewater effluents and in the Glatt River, Switzerland, show that rain events leading to discharges of untreated wastewater into rivers have a great impact on the riverine mass flows of contaminants. Biotransformation experiments in our laboratory with nonylphenoxyacetic acid and individual NP isomers enabled the elucidation of degradation pathways of these compounds. The finding that nonylphenoxyacetic acid is metabolized via NP further underscores the role of NP as the most relevant metabolite in the degradation of NP
n
EO. Several
Sphingomonadaceae
bacterial strains were found to degrade
α
-quaternary 4-NP isomers by an
ipso
-substitution mechanism, and to use only the aromatic part of the molecule. These reactions turned out to be isomer specific, meaning that rate and extent of transformation depend on constitution, and possibly also on the absolute configuration of the alkyl side chain of a specific isomer. The observation that NP isomers with distinct oestrogenic activities are differentially degraded has significant implications for risk assessment.
Plant SMU-1 and SMU-2 Homologues Regulate Pre-mRNA Splicing and Multiple Aspects of Development
Authors: Chung Taijoon , Wang Dongfang , Kim Cheol-Soo , Yadegari Ramin , Larkins Brian A.
Published: September 2009

In eukaryotes, alternative splicing of pre-mRNAs contributes significantly to the proper expression of the genome. However, the functions of many auxiliary spliceosomal proteins are still unknown. Here, we functionally characterized plant homologues of nematode suppressors of mec-8 and unc-52 (smu). We compared transcript profiles of maize (Zea mays) smu2 endosperm with those of wild-type plants and identified pre-mRNA splicing events that depend on the maize SMU2 protein. Consistent with a conserved role of plant SMU-2 homologues, Arabidopsis (Arabidopsis thaliana) smu2 mutants also show altered splicing of similar target pre-mRNAs. The Atsmu2 mutants occasionally show developmental phenotypes, including abnormal cotyledon numbers and higher seed weights. We identified AtSMU1 as one of the SMU2-interacting proteins, and Atsmu1 mutations cause similar developmental phenotypes with higher penetrance than Atsmu2. The AtSMU2 and AtSMU1 proteins are localized to the nucleus and highly prevalent in actively dividing tissues. Taken together, our data indicated that the plant SMU-1 and SMU-2 homologues appear to be involved in splicing of specific pre-mRNAs that affect multiple aspects of development.
Expressing the Diphtheria Toxin A Subunit from theHAP2(GCS1) Promoter Blocks Sperm Maturation and Produces Single Sperm-Like Cells Capable of Fertilization
Authors: Frank Aubrey C. , Johnson Mark A.
Published: September 2009

After meiosis, the male germline of flowering plants undergoes two mitoses, producing two sperm that are carried within a pollen tube to an ovule. One sperm fuses with the egg to form the zygote and the other fuses with the central cell to form the primary endosperm. The mechanisms that control male germline development and gene expression, and ensure that sperm properly fuse with female gametes are just beginning to be understood. Expression of the potent translation inhibitor, diphtheria toxin A subunit, from the Arabidopsis (Arabidopsis thaliana) HAP2(GCS1) promoter blocked sperm development before the final cell division, resulting in pollen tubes that carried a single sperm-like cell rather than two sperm. These pollen tubes targeted ovules and fertilized either the egg or the central cell, producing seeds with either endosperm or an embryo, but not both. Endosperm-only seeds significantly outnumbered embryo-only seeds, suggesting that single sperm-like cells preferentially fuse with the central cell. These experiments show that de novo translation is required for completion of sperm development, that the HAP2(GCS1) promoter is very tightly controlled, and that disruption of gene expression can result in male germ cells with a bias for gamete fusion.
MedicagoN2-Fixing Symbiosomes Acquire the Endocytic Identity Marker Rab7 but Delay the Acquisition of Vacuolar Identity
Authors: Limpens Erik , Ivanov Sergey , van Esse Wilma , Voets Guido , Fedorova Elena , Bisseling Ton
Published: September 2009

Rhizobium bacteria form N2-fixing organelles, called symbiosomes, inside the cells of legume root nodules. The bacteria are generally thought to enter the cells via an endocytosis-like process. To examine this, we studied the identity of symbiosomes in relation to the endocytic pathway. We show that in Medicago truncatula, the small GTPases Rab5 and Rab7 are endosomal membrane identity markers, marking different (partly overlapping) endosome populations. Although symbiosome formation is considered to be an endocytosis-like process, symbiosomes do not acquire Rab5 at any stage during their development, nor do they accept the trans-Golgi network identity marker SYP4, presumed to mark early endosomes in plants. By contrast, the endosomal marker Rab7 does occur on symbiosomes from an early stage of development when they have stopped dividing up to the senescence stage. However, the symbiosomes do not acquire vacuolar SNAREs (SYP22 and VTI11) until the onset of their senescence. By contrast, symbiosomes acquire the plasma membrane SNARE SYP132 from the start of symbiosome formation throughout their development. Therefore, symbiosomes appear to be locked in a unique SYP132- and Rab7-positive endosome stage and the delay in acquiring (lytic) vacuolar identity (e.g., vacuolar SNAREs) most likely ensures their survival and maintenance as individual units.
The Arabidopsis Nitrate Transporter NRT1.7, Expressed in Phloem, Is Responsible for Source-to-Sink Remobilization of Nitrate
Authors: Fan Shu-Chun , Lin Choun-Sea , Hsu Po-Kai , Lin Shan-Hua , Tsay Yi-Fang
Published: September 2009

Several quantitative trait locus analyses have suggested that grain yield and nitrogen use efficiency are well correlated with nitrate storage capacity and efficient remobilization. This study of the Arabidopsis thaliana nitrate transporter NRT1.7 provides new insights into nitrate remobilization. Immunoblots, quantitative RT-PCR, β-glucuronidase reporter analysis, and immunolocalization indicated that NRT1.7 is expressed in the phloem of the leaf minor vein and that its expression levels increase coincidentally with the source strength of the leaf. In nrt1.7 mutants, more nitrate was present in the older leaves, less 15NO3  − spotted on old leaves was remobilized into N-demanding tissues, and less nitrate was detected in the phloem exudates of old leaves. These data indicate that NRT1.7 is responsible for phloem loading of nitrate in the source leaf to allow nitrate transport out of older leaves and into younger leaves. Interestingly, nrt1.7 mutants showed growth retardation when external nitrogen was depleted. We conclude that (1) nitrate itself, in addition to organic forms of nitrogen, is remobilized, (2) nitrate remobilization is important to sustain vigorous growth during nitrogen deficiency, and (3) source-to-sink remobilization of nitrate is mediated by phloem.
A Transporter at the Node Responsible for Intervascular Transfer of Silicon in Rice
Authors: Yamaji Naoki , Ma Jian Feng
Published: September 2009

The concentration of essential mineral nutrients in the edible portion of plants such as grains may affect the nutritional value of these foods, while concentrations of toxic minerals in the plant are matter of food safety. Minerals taken up by the roots from soils are normally redirected at plant nodes before they are finally transported into developing seeds. However, the molecular mechanisms involved in this process have not been identified so far. Herein, we report on a transporter (Lsi6) responsible for the redirection of a plant nutrient at the node. Lsi6 is a silicon transporter in rice (Oryza sativa), and its expression in node I below the panicles is greatly enhanced when the panicle is completely emerged. Lsi6 is mainly localized at the xylem transfer cells located at the outer boundary region of the enlarged large vascular bundles in node I. Knockout of Lsi6 decreased Si accumulation in the panicles but increased Si accumulation in the flag leaf. These results suggest that Lsi6 is a transporter involved in intervascular transfer (i.e., transfer of silicon from the large vascular bundles coming from the roots to the diffuse vascular bundles connected to the panicles). These findings will be useful for selectively enhancing the accumulation of essential nutrients and reducing toxic minerals in the edible portion of cereals.
Phase behaviour and thermoelastic properties of perdeuterated ammonia hydrate and ice polymorphs from 0 to 2 GPa
Authors: Fortes A. D. , Wood I. G. , Vočadlo L. , Knight K. S. , Marshall W. G. , Tucker M. G. , Fernandez-Alonso F.
Published: September 2009

The results are described of a series of neutron powder diffraction experiments over the pressure and temperature ranges 0 <P< 2 GPa, 150 <T< 240 K, which were carried out with the objective of determining the phase behaviour and thermoelastic properties of perdeuterated ammonia dihydrate (ND3·2D2O). In addition to the low-pressure cubic crystalline phase, ADH I, two closely related monoclinic polymorphs of ammonia dihydrate have been identified, which commonly occur as a composite in the range 450–550 MPa at 175 K; these are labelled ADH IIaand IIb, and each has unit-cell volumeV≃ 310 Å3and number of formula units per unit cellZ= 4. It has been determined that this composite dissociates to a mixture of ammonia monohydrate (ND3·D2O) phase II (AMH II) and ice II when warmed to ∼190 K at 550 MPa, which in turn partially melts to ice II + liquid atT= 196 K; AMH II has a large orthorhombic unit cell (V≃ 890 Å3,Z= 16). Above 600 MPa, an orthorhombic polymorph of ammonia dihydrate (withV≃ 530 Å3,Z= 8), which has been referred to previously as ADH IV, persists to pressures greater than 2 GPa and appears to be the liquidus phase over this whole pressure range. This phase has been observed co-existing with ice II, ice VI and AMH II. The most plausible synthesis of the high-pressure phase behaviour is described here. This model explains the reported observations, and provides measurements of the densities, thermal expansion, bulk moduli and crystal growth kinetics of the high-pressure ammonia dihydrate, ammonia monohydrate and ice polymorphs.
AMPLIMODES: symmetry-mode analysis on the Bilbao Crystallographic Server
Authors: Orobengoa Danel , Capillas Cesar , Aroyo Mois I. , Perez-Mato J. Manuel
Published: September 2009

AMPLIMODESis a computer program available on the Bilbao Crystallographic Server that can perform a symmetry-mode analysis of any distorted structure of displacive type. The analysis consists in decomposing the symmetry-breaking distortion present in the distorted structure into contributions from different symmetry-adapted modes. Given the high- and the low-symmetry structures,AMPLIMODESdetermines the atomic displacements that relate them, defines a basis of symmetry-adapted modes, and calculates the amplitudes and polarization vectors of the distortion modes of different symmetry frozen in the structure. The program uses a mode parameterization that is as close as possible to the crystallographic conventions, expressing all quantities for the asymmetric unit of the low-symmetry structure. Distorted structures are often related to their higher-symmetry counterparts by temperature- and/or pressure-driven phase transitions, ferroic phase transitions being a particular example. The automatic symmetry-mode analysis performed byAMPLIMODEScan be very useful for establishing the driving mechanisms of such structural phase transitions or the fundamental instabilities at the origin of the distorted phases.
Round robin on Rietveld quantitative phase analysis of Portland cements
Authors: León-Reina L. , De la Torre A. G. , Porras-Vázquez J. M. , Cruz M. , Ordonez L. M. , Alcobé X. , Gispert-Guirado F. , Larrañaga-Varga A. , Paul M. , Fuellmann T. , Schmidt R. , Aranda M. A. G.
Published: September 2009

Interlaboratory studies on the precision and accuracy of Rietveld quantitative phase analysis (R-QPA) of mixtures of crystalline phases have already been carried out. However, cement-related materials are samples of variable complexity, ranging from three phases in white Portland clinkers to more than eight phases in grey cements, that need to be specifically investigated. Here, the results are reported from a round robin on the R-QPA of cement-related materials from laboratories with experience in this type of analysis. The aim of the work was to evaluate the levels of precision and accuracy associated with Portland clinkers and cements. Two sets of samples have been investigated, artificial mixtures and commercial samples. Artificial mixtures were prepared by mixing (weighing) synthesized single-crystalline phases in the appropriate proportions: (i) white clinker (Ca3SiO5, Ca2SiO4and Ca3Al2O6) and (ii) grey cement (Ca3SiO5, Ca2SiO4, Ca3Al2O6, Ca4Al2Fe2O10, CaCO3and CaSO4·2H2O). These two samples were used to assess the accuracy and uncertainty of the procedure, as an expected mineralogical phase fraction, the `true mineralogical percentage', is available under the assumption of negligible non-diffracting contents. In order to assess the validity and limitations of the Rietveld-based approach for cement materials, three commercial samples were measured: (i) white Portland clinker, (ii) grey Portland clinker and (iii) a type-I grey Portland cement. The samples studied have been chosen in order to cover most of the different typologies of binders. Reproducibilities and general uncertainty values, with a level of confidence of 95%, are reported and discussed.
A simple technique to convert sitting-drop vapor diffusion into hanging-drop vapor diffusion by solidifying the reservoir solution with agarose
Authors: Whon Tae Woong , Lee Yong-Hwan , An Dong-Shan , Song Hyun Kyu , Kim Song-Gun
Published: September 2009

A simple protocol to convert sitting-drop vapor-diffusion plating into a hanging-drop vapor-diffusion experiment in protein crystallization is reported. After making a sitting-drop plate, agarose solution was added to solidify the reservoir solution, and the plates were incubated upside down. Crystallization experiments with hen egg white lysozyme, thaumatin and glucose isomerase showed that the `upside-down sitting-drop' method could produce single crystals with all the benefits of the hanging-drop crystallization method.
Nonstoichiometry, amorphicity and microstructural evolution during phase transformations of photocatalytic titania powders
Authors: Lim Suo Hon , Ritter Clemens , Ping Yang , Schreyer Martin , White Timothy J.
Published: September 2009

The performance of photocatalytic titania powders is regulated, in part, by nonstoichiometry and the proportions of the crystalline and amorphous components. These variables can be quantitatively established by Rietveld analysis of diffraction data when internal standards are used to fix absolutely the crystallochemical parameters during quantitative phase analysis and to correct for mass absorption. Here, fixed-wavelength neutron and multiple-wavelength X-ray powder diffraction are used to assess phase development in alkoxide-derived titania gel as a function of temperature. In this manner, it is shown that the amorphous gel is progressively replaced by anatase for temperatures ≤ 773 K, and that during the reconstructive transition to rutile (773–873 K) aperiodicity increases as anatase is broken down to clusters of TiO6octahedra, with a fraction (∼10 wt%) of this short-range order persisting to 1273 K. Microabsorption correlates with X-ray energy, leading to systematic aberrations in the Rietveld scale factors connected to microstructural evolution which accompanies phase development during heat treatment. These changes are consistent with encapsulation of anatase and rutile by ubiquitous non-diffracting materials. The appearance of significant quantities of an intervening disordered phase during the dimorph transformation is supportive of recent kinetic models; however, its impact on catalytic activity remains to be determined.
SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules
Authors: Bardhan Jaydeep , Park Sanghyun , Makowski Lee
Published: September 2009

This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program calledSoftWAXS. The accuracy and efficiency ofSoftWAXSare analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute–solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.
Why Rice yellow mottle virus, a rapidly evolving RNA plant virus, is not efficient at breaking rymv1‐2 resistance
Authors: POULICARD NILS , PINEL‐GALZI AGNES , HEBRARD EUGENIE , FARGETTE DENIS
Published: September 2009

Rice yellow mottle virus (RYMV) reaches a high virus content in rice, is genetically highly variable and evolves rapidly. Nevertheless, only a small proportion of isolates overcome rymv1‐2 rice resistance by mutations in the VPg (viral protein genome‐linked). The accumulation rates of wild‐type (WT) and resistance‐breaking (RB) genotypes of the E‐ and T‐pathotypes of RYMV, with average and low virulence, respectively, were assessed. By quantitative reverse transcriptase‐polymerase chain reaction, it was shown that: (i) in resistant plants, both WT genotypes reached a level of 105–107 viral copies per milligram of fresh leaf; (ii) the accumulation of RB genotypes was variable, but was always much higher than the WT, with an RB/WT accumulation ratio of up to 106; (iii) in susceptible plants, the RB genotypes were counter‐selected to a similar level. In competition experiments, there was a straightforward exclusion of WT by RB genotypes in resistant hosts. The mutation rate in VPg was more than 1 × 10−3 mutations per site per year. Overall, a steady supply of highly adaptive RB genotypes was expected in resistant plants. However, the use of the few possible mutational pathways to virulence is tightly regulated by pathotype‐specific genetic constraints: codon usage, mutational bias and sign epistasis. In addition, genetic drift may restrict the fixation of RB mutants. Altogether, both genetic and demographic constraints contribute to the low ability of RYMV to break rymv1‐2 resistance.
Differences in woody vegetation are unrelated to use by African elephants (Loxodonta africana) in Mkhuze Game Reserve, South Africa
Authors: White Angela M. , Goodman Peter S.
Published: September 2009

The reintroduction of African elephants into fenced game reserves throughout South Africa has presented managers with several challenges. Although elephants are a natural part of southern African ecosystems, their confinement to fenced protected areas in South Africa has exacerbated their potential to impact their habitats negatively. However, many studies investigating the impact of elephants have failed to control for the effects of other browsers on the vegetative community. In this study, we used location data on an elephant herd to delineate high‐use and low‐use areas. This paired design allowed us to minimize confounding factors that could explain differences in the structure, diversity and utilization of woody species. We found little evidence to suggest elephant‐mediated change in, or selection for, the structure or diversity of woody species; however, our results suggest that elephants may be altering the composition of species by preferentially using areas with higher canopy diversity and by enhancing sapling recruitment. Although stripping of bark was higher in high‐use areas, there was no evidence of differential mortality of tree species. Therefore, in our study area, and over the current time scale, elephants are having a negligible impact on the vegetative community.
Impact of habitat disturbance in the wetland forests of East Usambara, Tanzania
Authors: Senzota Ramadhani , Mbago Frank
Published: September 2009

We evaluated habitat characteristics of East Usambara wetland forests. The abundance and species composition in the tree, shrub and herbaceous layers were enumerated in two sets of nested plots, one set in a natural wetland forest and the second in a wetland forest that had been disturbed by small‐scale gold mining activities. Each set had thirty‐six 1 m × 1 m plots for herbs, inside nine 5 m × 5 m plots for shrubs, in three 20 m × 20 m plots for trees. The habitat profile of herbaceous – shrub – tree layers was found to be sharply different from one obtained in previous studies at the surrounding nonwetland forests as were species composition and abundance. Unlike in the nonwetland forests, the herbaceous layer was thick, the shrub layer very thin and the woody species density and richness much lower. Disturbance significantly reduced woody cover and changed species composition in the herbaceous layer. Recovery of the woody vegetation was low. Wetland forests in the East Usambaras form a small fraction of the total area, but they are a unique biodiversity repository, they appear to be an important carbon dioxide sink and to reserve and purify water. They are sensitive to disturbance and need protection.