bluuebunny/crossref_metadata_2025 huggingface dataset:
Up‐regulation of cathepsin B expression and enhanced secretion in mitochondrial DNA‐depleted osteosarcoma cells
Authors: Hamer Isabelle , Delaive Edouard , Dieu Marc , Abdel‐Sater Fadi , Mercy Ludovic , Jadot Michel , Arnould Thierry
Published: July 2008

Background information. mtDNA (mitochondrial DNA) mutations that impair oxidative phosphorylation can contribute to carcinogenesis through the increased production of reactive oxygen species and through the release of proteins involved in cell motility and invasion. On the other hand, many human cancers are associated with both the up‐regulation and the increased secretion of several proteases and heparanase. In the present study, we tried to determine whether the depletion in mtDNA could modulate the expression and/or the secretion of some lysosomal hydrolases in the 143B osteosarcoma cells, as these mtDNA‐depleted cells are characterized by a higher degree of invasiveness than the parental cells.

Results. In comparison with the parental cells, we measured a higher amount of procathepsin B in the conditioned culture medium of the 143B cells lacking mtDNA (ρ0 143B cells), as well as a rise in the specific activity of intracellular cathepsin B. In addition, we observed an activation of the transcription factor NF‐κB (nuclear factor κB) in the cells devoid of functional mitochondria. Finally, we demonstrated that the down‐regulation of the NF‐κB p65 subunit by RNA interference led to a reduction in cathepsin B expression in ρ0 143B cells.

Conclusions. The up‐regulation of cathepsin B by NF‐κB, followed by its secretion into the extracellular environment, might be partly responsible for the previously reported invasiveness of the mtDNA‐depleted 143B osteosarcoma cells.
Raman microspectrometry sulfur detection and characterization in the marine ectosymbiotic nematode Eubostrichus dianae (Desmodoridae, Stilbonematidae)
Authors: Himmel David , Maurin Leslie Candice , Gros Olivier , Mansot Jean‐Louis
Published: July 2008

Background information. Marine nematodes belonging to the Stilbonematidae (Desmodoridae) family are described as living in obligatory association with sulfur‐oxidizing chemoautotrophic ectosymbionts. The symbiotic bacteria carrying out this chemosynthesis should contain elemental sulfur in periplasmic granules as sulfur granules of chemoautotrophic endosymbionts described in various marine invertebrates.

Results. Based on TEM (transmission electron microscopy) analyses, extracellular bacteria surrounding Eubostrichus dianae possess these spherical periplasmic granules. Few investigative techniques can be used to identify elemental sulfur, S8, such as EDXS (energy dispersive X‐ray spectroscopy) and EELS (electron energy loss spectroscopy), which are associated with cryo‐fixation of the sample to avoid sulfur loss. These techniques are time consuming, expensive and require technical skills. Raman microspectrometry applied to the analysis of E. dianae allowed us to detect elemental sulfur, S8, and confirmed the location of these sulfur clusters in the bacterial coat. In the same way, Raman spectrometry was positively applied to the endosymbiotic bivalve Codakia orbicularis, suggesting that this technique can be used to characterize sulfur in ecto‐ as well as in endo‐symbiotic sulfur‐oxidizing bacteria.

Conclusions. As Raman spectrometry can be used on living organisms (without preliminary fixation) without sample damage and preserving the molecular structure of the sulfur (denatured during chemical fixation), it represents a very well‐adapted investigative tool for biologists. This technique therefore permits us to detect quickly and easily (in a few seconds and on entire living animals) the presence of sulfur compounds in the symbiotic nematode.
The Leishmania infantum cytosolic SIR2-related protein 1 (LiSIR2RP1) is an NAD+-dependent deacetylase and ADP-ribosyltransferase
Authors: Tavares Joana , Ouaissi Ali , Santarém Nuno , Sereno Denis , Vergnes Baptiste , Sampaio Paula , Cordeiro-Da-Silva Anabela
Published: July 2008

Proteins of the SIR2 (Silent Information Regulator 2) family are characterized by a conserved catalytic domain that exerts unique NAD+-dependent deacetylase activity on histones and various other cellular substrates. Previous reports from us have identified a Leishmania infantum gene encoding a cytosolic protein termed LiSIR2RP1 (Leishmania infantum SIR2-related protein 1) that belongs to the SIR2 family. Targeted disruption of one LiSIR2RP1 gene allele led to decreased amastigote virulence, in vitro as well as in vivo. In the present study, attempts were made for the first time to explore and characterize the enzymatic functions of LiSIR2RP1. The LiSIR2RP1 exhibited robust NAD+-dependent deacetylase and ADP-ribosyltransferase activities. Moreover, LiSIR2RP1 is capable of deacetylating tubulin, either in dimers or, when present, in taxol-stabilized microtubules or in promastigote and amastigote extracts. Furthermore, the immunostaining of parasites revealed a partial co-localization of α-tubulin and LiSIR2RP1 with punctate labelling, seen on the periphery of both promastigote and amastigote stages. Isolated parasite cytoskeleton reacted with antibodies showed that part of LiSIR2RP1 is associated to the cytoskeleton network of both promastigote and amastigote forms. Moreover, the Western blot analysis of the soluble and insoluble fractions of the detergent of promastigote and amastigote forms revealed the presence of α-tubulin in the insoluble fraction, and the LiSIR2RP1 distributed in both soluble and insoluble fractions of promastigotes as well as amastigotes. Collectively, the results of the present study demonstrate that LiSIR2RP1 is an NAD+-dependent deacetylase that also exerts an ADP-ribosyltransferase activity. The fact that tubulin could be among the targets of LiSIR2RP1 may have significant implications during the remodelling of the morphology of the parasite and its interaction with the host cell.
The paradoxical effects of using antiretroviral-based microbicides to control HIV epidemics
Authors: Wilson David P. , Coplan Paul M. , Wainberg Mark A. , Blower Sally M.
Published: July 2008

Vaginal microbicides, designed to prevent HIV infection in women, are one of the most promising biomedical interventions. Clinical trials of second-generation microbicides have begun; if shown to be effective, they could be licensed within 5–10 years. Because these microbicides contain antiretrovirals (ARVs), they could be highly effective. However, there is concern that, if used by HIV-positive women, ARV resistance may evolve. By analyzing a mathematical model, we find that adherence could have both beneficial and detrimental effects on trial outcomes. Most importantly, we show that planned trial designs could mask resistance risks and therefore enable high-risk microbicides to pass clinical testing. We then parameterize a transmission model using epidemiological, clinical, and behavioral data to predict the consequences of wide-scale usage of high-risk microbicides in a heterosexual population. Surprisingly, we show that reducing a participant's risk of resistance during a trial could lead to unexpectedly high rates of resistance afterward when microbicides are used in public health interventions. We also find that, paradoxically, although microbicides will be used by women to protect themselves against infection, they could provide greater benefit to men. More infections in men than in women will be prevented if there is a high probability that ARVs are systemically absorbed, microbicides are less than ∼50% effective, and/or adherence is less than ∼60%. Men will always benefit more than women in terms of infections prevented per resistant case; but this advantage decreases as the relative fitness of drug-resistant strains increases. Interventions that use ARV-based microbicides could have surprising consequences.
Directed assembly of cell-laden microgels for fabrication of 3D tissue constructs
Authors: Du Yanan , Lo Edward , Ali Shamsher , Khademhosseini Ali
Published: July 2008

We present a bottom-up approach to direct the assembly of cell-laden microgels to generate tissue constructs with tunable microarchitecture and complexity. This assembly process is driven by the tendency of multiphase liquid–liquid systems to minimize the surface area and the resulting surface free energy between the phases. We demonstrate that shape-controlled microgels spontaneously assemble within multiphase reactor systems into predetermined geometric configurations. Furthermore, we characterize the parameters that influence the assembly process, such as external energy input, surface tension, and microgel dimensions. Finally, we show that multicomponent cell-laden constructs could be generated by assembling microgel building blocks and performing a secondary cross-linking reaction. This bottom-up approach for the directed assembly of cell-laden microgels provides a powerful and highly scalable approach to form biomimetic 3D tissue constructs and opens a paradigm for directing the assembly of mesoscale materials.
Pairwise-additive hydrophobic effect for alkanes in water
Authors: Wu Jianzhong , Prausnitz John M.
Published: July 2008

Pairwise additivity of the hydrophobic effect is indicated by reliable experimental Henry's constants for a large number of linear and branched low-molecular-weight alkanes in water. Pairwise additivity suggests that the hydrophobic effect is primarily a local phenomenon and that the hydrophobic interaction may be represented by a semiempirical force field. By representing the hydrophobic potential between two methane molecules as a linear function of the overlap volume of the hydration layers, we find that the contact value of the hydrophobic potential (−0.72 kcal/mol) is smaller than that from quantum mechanics simulations (−2.8 kcal/mol) but is close to that from classical molecular dynamics (−0.5∼−0.9 kcal/mol).
Golgi α-mannosidase II cleaves two sugars sequentially in the same catalytic site
Authors: Shah Niket , Kuntz Douglas A. , Rose David R.
Published: July 2008

Golgi α-mannosidase II (GMII) is a key glycosyl hydrolase in the N-linked glycosylation pathway. It catalyzes the removal of two different mannosyl linkages of GlcNAcMan
5
GlcNAc
2
, which is the committed step in complex
N
-glycan synthesis. Inhibition of this enzyme has shown promise in certain cancers in both laboratory and clinical settings. Here we present the high-resolution crystal structure of a nucleophile mutant of
Drosophila melanogaster
GMII (dGMII) bound to its natural oligosaccharide substrate and an oligosaccharide precursor as well as the structure of the unliganded mutant. These structures allow us to identify three sugar-binding subsites within the larger active site cleft. Our results allow for the formulation of the complete catalytic process of dGMII, which involves a specific order of bond cleavage, and a major substrate rearrangement in the active site. This process is likely conserved for all GMII enzymes—but not in the structurally related lysosomal mannosidase—and will form the basis for the design of specific inhibitors against GMII.
Continental diatom biodiversity in stream benthos declines as more nutrients become limiting
Authors: Passy Sophia I.
Published: July 2008

Biodiversity of both terrestrial ecosystems and lacustrine phytoplankton increases with niche dimensionality, which can be determined by the number of limiting resources (NLR) in the environment. In the present continental study, I tested whether niche dimensionality and, with this species, richness scale positively with NLR in running waters. Diatom richness in 2,426 benthic and 383 planktonic communities from 760 and 127 distinct localities, respectively, was examined as a function of NLR, including basic cations, silica, iron, ammonia, nitrate, and dissolved phosphorus. The patterns found in the two communities were opposite: as more resources became limiting, diatom richness declined in the benthos but increased in the phytoplankton. The divergence of benthic from both planktonic and terrestrial communities is attributed to the complex spatial organization of the benthos, generating strong internal resource gradients. Differential stress tolerance among benthic diatoms allows substantial overgrowth, which greatly reduces nutrient transport to the biofilm base and can be supported only by high ambient resource levels. Therefore, niche dimensionality in the benthos increases with the number of resources at high supply. These findings provide a mechanistic explanation of the well documented phenomenon of increased species richness after fertilization in freshwater as opposed to terrestrial ecosystems. Clearly, however, new theoretical approaches, retaining resource availability as an environmental constraint but incorporating a trade-off between tolerance and spatial positioning, are necessary to address coexistence in one of the major producer communities in streams, the algae.
Acc
homoeoloci and the evolution of wheat genomes
Authors: Chalupska D. , Lee H. Y. , Faris J. D. , Evrard A. , Chalhoub B. , Haselkorn R. , Gornicki P.
Published: July 2008

The DNA sequences of wheat
Acc-1
and
Acc-2
loci, encoding the plastid and cytosolic forms of the enzyme acetyl-CoA carboxylase, were analyzed with a view to understanding the evolution of these genes and the origin of the three genomes in modern hexaploid wheat.
Acc-1
and
Acc-2
loci from each of the wheats
Triticum urartu
(A genome),
Aegilops tauschii
(D genome),
Triticum turgidum
(AB genome), and
Triticum aestivum
(ABD genome), as well as two
Acc-2
-related pseudogenes from
T. urartu
were sequenced. The 2.3–2.4 Mya divergence time calculated here for the three homoeologous chromosomes, on the basis of coding and intron sequences of the
Acc-1
genes, is at the low end of other estimates. Our clock was calibrated by using 60 Mya for the divergence between wheat and maize. On the same time scale, wheat and barley diverged 11.6 Mya, based on sequences of
Acc
and other genes. The regions flanking the
Acc
genes are not conserved among the A, B, and D genomes. They are conserved when comparing homoeologous genomes of diploid, tetraploid, and hexaploid wheats. Substitution rates in intergenic regions consisting primarily of repetitive sequences vary substantially along the loci and on average are 3.5-fold higher than the
Acc
intron substitution rates. The composition of the
Acc
homoeoloci suggests haplotype divergence exceeding in some cases 0.5 Mya. Such variation might result in a significant overestimate of the time since tetraploid wheat formation, which occurred no more than 0.5 Mya.
The Prodi government of 2006 and 2007: A retrospective look
Authors: Paolucci Caterina , Newell James L.
Published: July 2008

Now that the fifteenth legislature has come to an end, it is appropriate to assess the performance of the government whose fall was responsible for this event, as well as the coalition's significance for the trajectory of Italian politics generally. The four articles that follow this one together initiate the task, exploring performance from an institutional and policy-making point of view. This article suggests four criteria for evaluating the performance of any government and offers a brief initial ‘summary report’ in terms of them – paying special attention to implementation of the programme and to communications. Bearing in mind the structural conditions in which it had to work, the government had some notable achievements to its credit, but these same conditions undermined it by opening up an unbridgeable gap between performance and popular perceptions of performance.
The Prodi government's proposed citizenship reform, and the debate on immigration and its impact in Italy
Authors: Bigot Giulia , Fella Stefano
Published: July 2008

Within a few months of the second Prodi government taking office in 2006, the Interior Minister, Giuliano Amato, reignited the ongoing debate on immigration, social integration, nationality and citizenship in Italy by launching the government's proposed reform of the law on citizenship. This article examines the implications of the reform and the debate it has provoked among the political parties in Italy in the context of the broader political discussion that has developed in Italy since the 1990s regarding immigration control, social integration and multiculturalism. The article sheds light on the way in which themes such as ‘multiculturalism’, ‘integration’ and ‘citizenship’ are conceptualised by political actors in Italy, and the way in which discussion of these themes relates to the broader political strategies and trajectories followed by these actors.
Myosin-10 and actin filaments are essential for mitotic spindle function
Authors: Woolner Sarah , O'Brien Lori L. , Wiese Christiane , Bement William M.
Published: July 2008

Mitotic spindles are microtubule-based structures responsible for chromosome partitioning during cell division. Although the roles of microtubules and microtubule-based motors in mitotic spindles are well established, whether or not actin filaments (F-actin) and F-actin–based motors (myosins) are required components of mitotic spindles has long been controversial. Based on the demonstration that myosin-10 (Myo10) is important for assembly of meiotic spindles, we assessed the role of this unconventional myosin, as well as F-actin, in mitotic spindles. We find that Myo10 localizes to mitotic spindle poles and is essential for proper spindle anchoring, normal spindle length, spindle pole integrity, and progression through metaphase. Furthermore, we show that F-actin localizes to mitotic spindles in dynamic cables that surround the spindle and extend between the spindle and the cortex. Remarkably, although proper anchoring depends on both F-actin and Myo10, the requirement for Myo10 in spindle pole integrity is F-actin independent, whereas F-actin and Myo10 actually play antagonistic roles in maintenance of spindle length.
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
Authors: Fejes Anthony P. , Robertson Gordon , Bilenky Mikhail , Varhol Richard , Bainbridge Matthew , Jones Steven J. M.
Published: July 2008

Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads.

Availability: The FindPeaks 3.1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks Source files for FindPeaks 3.1 are available for academic use.

Contact:  afejes@bcgsc.ca
Potential Benefits on Impairment of Endothelial Function after a High‐Fat Meal of 4 Weeks of Flavonoid Supplementation
Authors: Barringer T. A. , Hatcher L. , Sasser H. C.
Published: July 2008

Studies with foods high in flavonoids have demonstrated improvement in endothelial function. We investigated whether 4 weeks of flavonoid supplementation would prevent an adverse impact on endothelial function of a high‐fat meal. Endothelial function was measured by reactive hyperemia peripheral arterial tonometry (RH‐PAT). The RH‐PAT index was measured both before and 3 h after a high‐fat meal, in 23 healthy volunteers. Subjects were randomized in a double‐blind, cross‐over design to 4 weeks of daily supplementation with OPC‐3, or a matching placebo. RH‐PAT index before and after the high‐fat meal was measured at the beginning and end of each 4‐week treatment phase. The high‐fat meal caused a decline in endothelial function at baseline in the placebo (_10.71%, P = .006) and flavonoid [_9.97% (P = .077)] groups, and there was no difference in decline between arms (P = .906). The high‐fat meal produced a decline after 4 weeks of placebo [_12.37% (P = .005)], but no decline after 4 weeks of flavonoid supplement [_3.16% (P = .663)], and the difference between the two responses was highly significant (P < .0001). Within‐group comparisons revealed no difference in endothelial function decline in the placebo arm between baseline and 4 weeks [_10.71% versus _12.37% (P = .758)]. In the flavonoid supplement arm, the difference in endothelial function decline between baseline and 4 weeks was _9.97% versus _3.16%, but did not reach statistical significance (P = .451). These results suggest that the flavonoid supplement used in this study mitigates the impairment of endothelial function caused by a high‐fat meal. Whether certain subpopulations derive greater or lesser benefit remains unclear.
Seeking Help for Disaster Services After a Flood
Authors: Stimpson Jim P. , Wilson Fernando A. , Jeffries Shawn K.
Published: July 2008

Objectives:This article describes how the frequency of exposure to a flood is associated with the probability of seeking help from agencies (eg, Federal Emergency Management Agency, Red Cross) that provide disaster-related services. The article also describes the population characteristics for the people who are most likely to seek help for disaster services.

Methods:Prospective cohort data from 1735 respondents of the Iowa Health Poll were used. Multivariate logistic regression was used to model the odds of seeking help from any agency for flood-related problems.

Results:Overall, most people, regardless of flood exposure, did not seek help from disaster service agencies. Disaster services were sought by 23% of respondents who experienced 1 flood, 31% who have experienced 2 floods, and 26% who have experienced 3 or more floods. Multivariate adjusted odds of seeking help were associated with number of flood experiences (odds ratio [OR] 1.58), white race (OR 0.24), economic hardship (OR 1.43), urban residence (OR 0.43), and social support (OR 0.55).

Conclusions:On average, the probability of seeking disaster relief services increases with the number of flood experiences. Racial/ethnic minorities, rural residents, economically challenged individuals, and people with low levels of perceived social support may be more likely than people without these characteristics to seek services. (Disaster Med Public Health Preparedness. 2008;2:139–141)
Seven in Absentia Proteins Affect Plant Growth and Nodulation inMedicago truncatula
Authors: Den Herder Griet , De Keyser Annick , De Rycke Riet , Rombauts Stephane , Van de Velde Willem , Clemente María R. , Verplancke Christa , Mergaert Peter , Kondorosi Eva , Holsters Marcelle , Goormachtig Sofie
Published: July 2008

Protein ubiquitination is a posttranslational regulatory process essential for plant growth and interaction with the environment. E3 ligases, to which the seven in absentia (SINA) proteins belong, determine the specificity by selecting the target proteins for ubiquitination. SINA proteins are found in animals as well as in plants, and a small gene family with highly related members has been identified in the genome of rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), Medicago truncatula, and poplar (Populus trichocarpa). To acquire insight into the function of SINA proteins in nodulation, a dominant negative form of the Arabidopsis SINAT5 was ectopically expressed in the model legume M. truncatula. After rhizobial inoculation of the 35S:SINAT5DN transgenic plants, fewer nodules were formed than in control plants, and most nodules remained small and white, a sign of impaired symbiosis. Defects in rhizobial infection and symbiosome formation were observed by extensive microscopic analysis. Besides the nodulation phenotype, transgenic plants were affected in shoot growth, leaf size, and lateral root number. This work illustrates a function for SINA E3 ligases in a broad spectrum of plant developmental processes, including nodulation.
Viroid-Induced Symptoms inNicotiana benthamianaPlants Are Dependent on RDR6 Activity
Authors: Gómez Gustavo , Martínez Germán , Pallás Vicente
Published: July 2008

Viroids are small self-replicating RNAs that infect plants. How these noncoding pathogenic RNAs interact with hosts to induce disease symptoms is a long-standing unanswered question. Recent experimental data have led to the suggestive proposal of a pathogenic model based on the RNA silencing mechanism. However, evidence of a direct relation between key components of the RNA silencing pathway and symptom expression in infected plants remains elusive. To address this issue, we used a symptomatic transgenic line of Nicotiana benthamiana that expresses and processes dimeric forms of Hop stunt viroid (HSVd). These plants were analyzed under different growing temperature conditions and were used as stocks in grafting assays with the rdr6i-Nb line, in which the RNA-dependent RNA polymerase 6 (RDR6) is constitutively silenced. Here, we show that the symptom expression in N. benthamiana plants is independent of HSVd accumulation levels but dependent on an active state of the viroid-specific RNA silencing pathway. The scion of rdr6i-Nb plants remained asymptomatic when grafted onto symptomatic plants, despite an accumulation of a high level of mature forms of HSVd, indicating the requirement of RDR6 for viroid-induced symptom production. In addition, the RDR6 requirement for symptom expression was also observed in wild-type N. benthamiana plants mechanically infected with HSVd. These results provide biological evidence of the involvement of the viroid-specific RNA silencing pathway in the symptom expression associated with viroid pathogenesis.
Proteome-Wide Characterization of Seed Aging in Arabidopsis: A Comparison between Artificial and Natural Aging Protocols
Authors: Rajjou Loïc , Lovigny Yoann , Groot Steven P.C. , Belghazi Maya , Job Claudette , Job Dominique
Published: July 2008

A variety of mechanisms have been proposed to account for the extension of life span in seeds (seed longevity). In this work, we used Arabidopsis (Arabidopsis thaliana) seeds as a model and carried out differential proteomics to investigate this trait, which is of both ecological and agricultural importance. In our system based on a controlled deterioration treatment (CDT), we compared seed samples treated for different periods of time up to 7 d. Germination tests showed a progressive decrease of germination vigor depending on the duration of CDT. Proteomic analyses revealed that this loss in seed vigor can be accounted for by protein changes in the dry seeds and by an inability of the low-vigor seeds to display a normal proteome during germination. Furthermore, CDT strongly increased the extent of protein oxidation (carbonylation), which might induce a loss of functional properties of seed proteins and enzymes and/or enhance their susceptibility toward proteolysis. These results revealed essential mechanisms for seed vigor, such as translational capacity, mobilization of seed storage reserves, and detoxification efficiency. Finally, this work shows that similar molecular events accompany artificial and natural seed aging.
Integration of Carbon and Nitrogen Metabolism with Energy Production Is Crucial to Light Acclimation in the CyanobacteriumSynechocystis
Authors: Singh Abhay K. , Elvitigala Thanura , Bhattacharyya-Pakrasi Maitrayee , Aurora Rajeev , Ghosh Bijoy , Pakrasi Himadri B.
Published: July 2008

Light drives the production of chemical energy and reducing equivalents in photosynthetic organisms required for the assimilation of essential nutrients. This process also generates strong oxidants and reductants that can be damaging to the cellular processes, especially during absorption of excess excitation energy. Cyanobacteria, like other oxygenic photosynthetic organisms, respond to increases in the excitation energy, such as during exposure of cells to high light (HL) by the reduction of antenna size and photosystem content. However, the mechanism of how Synechocystis sp. PCC 6803, a cyanobacterium, maintains redox homeostasis and coordinates various metabolic processes under HL stress remains poorly understood. In this study, we have utilized time series transcriptome data to elucidate the global responses of Synechocystis to HL. Identification of differentially regulated genes involved in the regulation, protection, and maintenance of redox homeostasis has offered important insights into the optimized response of Synechocystis to HL. Our results indicate a comprehensive integrated homeostatic interaction between energy production (photosynthesis) and energy consumption (assimilation of carbon and nitrogen). In addition, measurements of physiological parameters under different growth conditions showed that integration between the two processes is not a consequence of limitations in the external carbon and nitrogen levels available to the cells. We have also discovered the existence of a novel glycosylation pathway, to date known as an important nutrient sensor only in eukaryotes. Up-regulation of a gene encoding the rate-limiting enzyme in the hexosamine pathway suggests a regulatory role for protein glycosylation in Synechocystis under HL.
Conifers, Angiosperm Trees, and Lianas: Growth, Whole-Plant Water and Nitrogen Use Efficiency, and Stable Isotope Composition (δ
13C and δ
18O) of Seedlings Grown in a Tropical Environment
Authors: Cernusak Lucas A. , Winter Klaus , Aranda Jorge , Turner Benjamin L.
Published: July 2008

Seedlings of several species of gymnosperm trees, angiosperm trees, and angiosperm lianas were grown under tropical field conditions in the Republic of Panama; physiological processes controlling plant C and water fluxes were assessed across this functionally diverse range of species. Relative growth rate, r, was primarily controlled by the ratio of leaf area to plant mass, of which specific leaf area was a key component. Instantaneous photosynthesis, when expressed on a leaf-mass basis, explained 69% of variation in r (P < 0.0001, n = 94). Mean r of angiosperms was significantly higher than that of the gymnosperms; within angiosperms, mean r of lianas was higher than that of trees. Whole-plant nitrogen use efficiency was also significantly higher in angiosperm than in gymnosperm species, and was primarily controlled by the rate of photosynthesis for a given amount of leaf nitrogen. Whole-plant water use efficiency, TEc, varied significantly among species, and was primarily controlled by c  i/c  a, the ratio of intercellular to ambient CO2 partial pressures during photosynthesis. Instantaneous measurements of c  i/c  a explained 51% of variation in TEc (P < 0.0001, n = 94). Whole-plant 13C discrimination also varied significantly as a function of c  i/c  a (R  2 = 0.57, P < 0.0001, n = 94), and was, accordingly, a good predictor of TEc. The 18O enrichment of stem dry matter was primarily controlled by the predicted 18O enrichment of evaporative sites within leaves (R  2 = 0.61, P < 0.0001, n = 94), with some residual variation explained by mean transpiration rate. Measurements of carbon and oxygen stable isotope ratios could provide a useful means of parameterizing physiological models of tropical forest trees.
Mutations in SUPPRESSOR OF VARIEGATION1, a Factor Required for Normal Chloroplast Translation, Suppress var2-Mediated Leaf Variegation in Arabidopsis
Authors: Yu Fei , Liu Xiayan , Alsheikh Muath , Park Sungsoon , Rodermel Steve
Published: July 2008

The Arabidopsis thaliana yellow variegated2 (var2) mutant is variegated due to lack of a chloroplast FtsH-like metalloprotease (FtsH2/VAR2). We have generated suppressors of var2 variegation to gain insight into factors and pathways that interact with VAR2 during chloroplast biogenesis. Here, we describe two such suppressors. Suppression of variegation in the first line, TAG-FN, was caused by disruption of the nuclear gene (SUPPRESSOR OF VARIEGATION1 [SVR1]) for a chloroplast-localized homolog of pseudouridine (Ψ) synthase, which isomerizes uridine to Ψ in noncoding RNAs. svr1 single mutants were epistatic to var2, and they displayed a phenotypic syndrome that included defects in chloroplast rRNA processing, reduced chloroplast translation, reduced chloroplast protein accumulation, and elevated chloroplast mRNA levels. In the second line (TAG-IE), suppression of variegation was caused by a lesion in SVR2, the gene for the ClpR1 subunit of the chloroplast ClpP/R protease. Like svr1, svr2 was epistatic to var2, and clpR1 mutants had a phenotype that resembled svr1. We propose that an impairment of chloroplast translation in TAG-FN and TAG-IE decreased the demand for VAR2 activity during chloroplast biogenesis and that this resulted in the suppression of var2 variegation. Consistent with this hypothesis, var2 variegation was repressed by chemical inhibitors of chloroplast translation. In planta mutagenesis revealed that SVR1 not only played a role in uridine isomerization but that its physical presence was necessary for proper chloroplast rRNA processing. Our data indicate that defects in chloroplast rRNA processing are a common, but not universal, molecular phenotype associated with suppression of var2 variegation.
Badh2, Encoding Betaine Aldehyde Dehydrogenase, Inhibits the Biosynthesis of 2-Acetyl-1-Pyrroline, a Major Component in Rice Fragrance
Authors: Chen Saihua , Yang Yi , Shi Weiwei , Ji Qing , He Fei , Zhang Ziding , Cheng Zhukuan , Liu Xiangnong , Xu Mingliang
Published: July 2008

In rice (Oryza sativa), the presence of a dominant Badh2 allele encoding betaine aldehyde dehydrogenase (BADH2) inhibits the synthesis of 2-acetyl-1-pyrroline (2AP), a potent flavor component in rice fragrance. By contrast, its two recessive alleles, badh2-E2 and badh2-E7, induce 2AP formation. Badh2 was found to be transcribed in all tissues tested except for roots, and the transcript was detected at higher abundance in young, healthy leaves than in other tissues. Multiple Badh2 transcript lengths were detected, and the complete, full-length Badh2 transcript was much less abundant than partial Badh2 transcripts. 2AP levels were significantly reduced in cauliflower mosaic virus 35S-driven transgenic lines expressing the complete, but not the partial, Badh2 coding sequences. In accordance, the intact, full-length BADH2 protein (503 residues) appeared exclusively in nonfragrant transgenic lines and rice varieties. These results indicate that the full-length BADH2 protein encoded by Badh2 renders rice nonfragrant by inhibiting 2AP biosynthesis. The BADH2 enzyme was predicted to contain three domains: NAD binding, substrate binding, and oligomerization domains. BADH2 was distributed throughout the cytoplasm, where it is predicted to catalyze the oxidization of betaine aldehyde, 4-aminobutyraldehyde (AB-ald), and 3-aminopropionaldehyde. The presence of null badh2 alleles resulted in AB-ald accumulation and enhanced 2AP biosynthesis. In summary, these data support the hypothesis that BADH2 inhibits 2AP biosynthesis by exhausting AB-ald, a presumed 2AP precursor.
Tomato Protein Kinase 1b Mediates Signaling of Plant Responses to Necrotrophic Fungi and Insect Herbivory
Authors: AbuQamar Synan , Chai Mao-Feng , Luo Hongli , Song Fengming , Mengiste Tesfaye
Published: July 2008

The tomato protein kinase 1 (TPK1b) gene encodes a receptor-like cytoplasmic kinase localized to the plasma membrane. Pathogen infection, mechanical wounding, and oxidative stress induce expression of TPK1b, and reducing TPK1b gene expression through RNA interference (RNAi) increases tomato susceptibility to the necrotrophic fungus Botrytis cinerea and to feeding by larvae of tobacco hornworm (Manduca sexta) but not to the bacterial pathogen Pseudomonas syringae. TPK1b RNAi seedlings are also impaired in ethylene (ET) responses. Notably, susceptibility to Botrytis and insect feeding is correlated with reduced expression of the proteinase inhibitor II gene in response to Botrytis and 1-aminocyclopropane-1-carboxylic acid, the natural precursor of ET, but wild-type expression in response to mechanical wounding and methyl-jasmonate. TPK1b functions independent of JA biosynthesis and response genes required for resistance to Botrytis. TPK1b is a functional kinase with autophosphorylation and Myelin Basis Protein phosphorylation activities. Three residues in the activation segment play a critical role in the kinase activity and in vivo signaling function of TPK1b. In sum, our findings establish a signaling role for TPK1b in an ET-mediated shared defense mechanism for resistance to necrotrophic fungi and herbivorous insects.
An efficient experimental strategy for mouse embryonic stem cell differentiation and separation of a cytokeratin‐19‐positive population of insulin‐producing cells
Authors: Naujok O. , Francini F. , Jörns A. , Lenzen S.
Published: July 2008

Abstract.  Objectives: Embryonic stem cells are a potential source for insulin‐producing cells, but existing differentiation protocols are of limited efficiency. Here, the aim has been to develop a new one, which drives development of embryonic stem cells towards insulin‐producing cells rather than to neuronal cell types, and to combine this with a strategy for their separation from insulin‐negative cells. Materials and methods: The cytokeratin‐19 (CK19) promoter was used to control the expression of enhanced yellow fluorescence protein in mouse embryonic stem cells during their differentiation towards insulin‐producing cells, using a new optimized four‐stage protocol. Two cell populations, CK19+ and CK19− cells, were successfully fluorescence sorted and analysed. Results: The new method reduced neuronal progeny and suppressed differentiation into glucagon‐ and somatostatin‐producing cells. Concomitantly, β‐cell like characteristics of insulin‐producing cells were strengthened, as documented by high gene expression of the Glut2 glucose transporter and the transcription factor Pdx1. This novel protocol was combined with a cell‐sorting technique. Through the combined procedure, a fraction of glucose‐responsive insulin‐secreting CK19+ cells was obtained with 40‐fold higher insulin gene expression and 50‐fold higher insulin content than CK19− cells. CK19+ cells were immunoreactive for C‐peptide and had ultrastructural characteristics of an insulin‐secretory cell. Conclusion: Differentiated CK19+ cells reflect an endocrine precursor cell type of ductal origin, potentially suitable for insulin replacement therapy in diabetes.
Haematopoietic lineage‐committed bone marrow cells, but not cloned cultured mesenchymal stem cells, contribute to regeneration of renal tubular epithelium after HgCl2‐induced acute tubular injury
Authors: Fang T.‐C. , Otto W. R. , Rao J. , Jeffery R. , Hunt T. , Alison M. R. , Cook H. T. , Wright N. A. , Poulsom R.
Published: July 2008

Abstract.  Objective: Our previous studies have demonstrated that endogenous bone marrow cells (BMCs) contribute to renal tubular regeneration after acute tubular injury. The aim of this study was to examine which fraction of BMCs, haematopoietic lineage marrow cells (HLMCs) or mesenchymal stem cells (MSCs), are effective. Materials and methods: Six‐week‐old female mice were lethally irradiated and were transplanted with female enhanced green fluorescent protein‐positive (GFP+), plastic non‐adherent marrow cells (as a source of HLMCs) plus cloned cultured male GFP− MSCs. Four weeks later, they were assigned into two groups: control mice with vehicle treatment and mice treated with HgCl2. Tritiated thymidine was given 1 h before animal killing which occurred at intervals over 2 weeks. Kidney sections were stained for a tubular epithelial marker, cell origin indicated by GFP immunohistochemistry or Y chromosome in situ hybridization; periodic acid‐Schiff staining was performed, and samples were subjected to autoradiography. One thousand consecutive renal tubular epithelial cells per mouse, in S phase, were scored as either female (indigenous) GFP+ (HLMC‐derived) or male (MSC‐derived). Results: Haematopoietic lineage marrow cells and MSCs stably engrafted into bone marrow and spleen, but only HLMC‐derived cells, not MSCs, were found in the renal tubules and were able to undergo DNA synthesis after acute renal injury. A few MSCs were detected in the renal interstitium, but their importance needs to be further explored. Conclusion: Haematopoietic lineage marrow cells, but not cloned cultured MSCs, can play a role not only in normal wear‐and‐tear turnover of renal tubular cells, but also in repair after tubular injury.
Using soil knowledge for the evaluation of mid‐infrared diffuse reflectance spectroscopy for predicting soil physical and mechanical properties
Authors: Minasny B. , McBratney A. B. , Tranter G. , Murphy B. W.
Published: July 2008

Mid‐infrared diffuse reflectance spectroscopy can provide rapid, cheap and relatively accurate predictions for a number of soil properties. Most studies have found that it is possible to estimate chemical properties that are related to surface and solid material composition. This paper focuses on prediction of physical and mechanical properties, with emphasis on the elucidation of possible mechanisms of prediction. Soil physical properties that are based on pore‐space relationships such as bulk density, water retention and hydraulic conductivity cannot be predicted well using MIR spectroscopy. Hydraulic conductivity was measured using a tension‐disc permeameter, excluding the macropore effect, but MIR spectroscopy did not give a good prediction. Properties based on the soil solid composition and surfaces such as clay content and shrink‐swell potential can be predicted reasonably well. Macro‐aggregate stability in water can be predicted reasonably as it has a strong correlation with carbon content in the soil. We found that most of the physical and mechanical properties can be related back to the fundamental soil properties such as clay content, carbon content, cation exchange capacity and bulk density. These connections have been explored previously in pedotransfer functions studies. The concept of a spectral soil inference system is reiterated: linking the spectra to basic soil properties and connecting basic soil properties to other functional soil properties via pedotransfer functions.
Distribution and community structure of ichthyoplankton from the northern and central California Current in May 2004–06
Authors: AUTH TOBY D.
Published: July 2008

The distributions, concentrations, and community structure of pelagic larval fishes collected from the central and northern California Current in the northeast Pacific Ocean during May 2004, 2005, and 2006 were analyzed to investigate inter‐annual, latitudinal, cross‐shelf, and depth‐stratified variability. The inter‐annual climate‐induced variability during the sampling period provided a unique opportunity to observe how larval fish communities adjust to rapidly changing environmental conditions. The 170 depth‐stratified samples collected from three cruises yielded 14 819 fish larvae from 56 taxa representing 23 families. Dominant larval taxa were Engraulis mordax, Citharichthys spp., Sebastes spp., and Stenobrachius leucopsarus. Larval concentrations decreased significantly in 2006 from 2004 and 2005 levels following the anomalous oceanic conditions observed in 2005 and decreased water temperature in 2006. Larvae were generally found in higher concentrations at northern (>43°N) versus southern (<43°N) stations, with larval E. mordax and Citharichthys spp. found almost exclusively in the north during all sampled years. Inter‐annual variability related to dynamic upwelling intensity was observed in cross‐shelf larval distributions, although concentrations of S. leucopsarus larvae consistently increased in the offshore direction, while larval Sebastes spp. were generally found in highest concentrations at intermediate stations along the shelf. Multivariate analyses revealed that latitude, station depth, and sea‐surface temperature were the most important factors explaining variability in larval concentrations. The present study shows that the ichthyoplankton community of the central and northern California Current changed dramatically in response to the variable environmental conditions of 2004–06.
Scale dependence in the species‐discharge relationship for fishes of the southeastern U.S.A.
Authors: MCGARVEY DANIEL J. , WARD G. MILTON
Published: July 2008

1. Species‐discharge relationships (SDR) are aquatic analogues of species‐area relationships, and are increasingly used in both basic research and conservation planning. SDR studies are often limited, however, by two shortcomings. First, they do not determine whether reported SDRs, which normally use complete drainage basins as sampling units, are scale dependent. Second, they do not account for the effects of habitat diversity within or among samples.

2. We addressed both problems by using discrete fish zones as sampling units in a SDR analysis. To do so, we first tested for longitudinal zonation in three rivers in the southeastern U.S.A. In each river, we detected successive ‘lower’, ‘middle’, and ‘upper’ fish zones, which were characterized by distinct fish assemblages with predictable habitat requirements. Because our analyses combined fish data from multiple sources, we also used rarefaction and Monte Carlo simulation to ensure that our zonation results were robust to spurious sampling effects.

3. Next, we estimated the average discharge within each zone, and plotted these estimates against the respective species richness within each zone (log10 data). This revealed a significant, linear SDR (r2 = 0.83; P < 0.01). Notably, this zonal SDR fit the empirical data better than a comparable SDR that did not discriminate among longitudinal zones. We therefore conclude that the southeastern fish SDR is scale dependent, and that accounting for within‐basin habitat diversity is an important step in explaining the high diversity of southeastern fishes.

4. We then discuss how our zonal SDR can be used to improve conservation planning. Specifically, we show how the slope of the SDR can be used to forecast potential extinction rates, and how the zonal data can be used to identify species of greatest concern.