bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological control of rangeland weeds in Australia
Authors: Julien M. H.
Published: May 2006

Weeds of Australian rangelands have been the target for biological control since 1914. There have been several spectacular successes, e.g. prickly pear cactus (Opuntia spp.), with extraordinary ecological and commercial benefits. There have also been projects where no positive outcome has occurred, e.g. prickly acacia [Acacia nilotica (L.) Willd. ex Delile ssp. indica (Benth.) Brenan], parkinsonia (Parkinsonia aculeata L.), and creeping lantana [Lantana montevidensis (Spreng.) Briq.]. Numerous other projects are currently underway and require continuing support to achieve the stated aims. There is considerable potential to increase investment in biological control of rangeland weeds to improve outcomes of current projects and to implement new projects. There is promise of excellent benefits to cost ratios based on past performance. However, there is a worrying trend of loss of capacity in Australia to conduct biological control. Since resources will always be limited, it is important that the weeds that have the greatest impact on ecosystem function and commercial production are identified and targeted for management. Biological control should be part of the management strategies for those priority weeds when conflict over weediness v. commercial value can be resolved in favour of biological control, and when it is considered that biological control could offer benefits.
Assessment of current weed control methods relevant to the management of the biodiversity of Australian rangelands
Authors: Vitelli J. S. , Pitt J. L.
Published: May 2006

The Australian rangelands contain extensive and often dense populations of a wide variety of weed species. An array of techniques is available for effectively controlling many of these. To achieve long-term weed control, weeds should be targeted objectively and the dependence on the use of single treatments such as herbicides and machinery reduced, with greater adoption of integrated methods. The combination of methods will differ if the primary objective within the rangelands is to restore and maintain biodiversity or to improve forage production for domestic and native animals. Revegetation of sites and exclusion of herbivores from weed treated areas is important in establishing species that will compete with invasive weeds. Due to rangelands being sparsely populated, the necessary equipment, skills and finances to use appropriate control options on extensive weed infestations are often lacking, with landholders requiring the assistance of local, state and federal authorities to assist in managing weeds.
Weeds of Australian rangelands
Authors: Martin Tara G. , Campbell Shane , Grounds Simone
Published: May 2006

Despite recognition that non-native plant species represent a substantial risk to natural systems, there is currently no compilation of weeds that impact on the biodiversity of the rangelands within Australia. Using published and expert knowledge, this paper presents a list of 622 non-native naturalised species known to occur within the rangelands. Of these, 160 species (26%) are considered a current threat to rangeland biodiversity. Most of these plant species have been deliberately introduced for forage or other commercial use (e.g. nursery trade). Among growth forms, shrubs and perennial grasses comprise over 50% of species that pose the greatest risk to rangeland biodiversity. We identify regions within the rangelands containing both high biodiversity values and a high proportion of weeds and recommend these areas as priorities for weed management. Finally, we examine the resources available for weed detection and identification since detecting weeds in the early stages of invasion is the most cost effective method of reducing further impact.
Accumulation of small murine minor satellite transcripts leads to impaired centromeric architecture and function
Authors: Bouzinba-Segard Haniaa , Guais Adeline , Francastel Claire
Published: May 2006

RNAs have been implicated in the assembly and stabilization of large-scale chromatin structures including centromeric architecture; unidentified RNAs are integral components of human pericentric heterochromatin and are required for localization of the heterochromatin protein HP1 to centromeric regions. Because satellite repeats in centromeric regions are known to be transcribed, we assessed a role for noncoding centromeric RNAs in the structure and function of the centromere. We identified minor satellite transcripts of 120 nt in murine cells that localize to centromeres and accumulate upon stress or differentiation. Forced accumulation of 120-nt transcripts leads to defects in chromosome segregation and sister-chromatid cohesion, changes in hallmark centromeric epigenetic markers, and mislocalization of centromere-associated proteins essential for centromere function. These findings suggest that small centromeric RNAs may represent one of many pathways that regulate heterochromatin assembly in mammals, possibly through tethering of kinetochore- and heterochromatin-associated proteins.
Imaging breast adipose and fibroglandular tissue molecular signatures by using hybrid MRI-guided near-infrared spectral tomography
Authors: Brooksby Ben , Pogue Brian W. , Jiang Shudong , Dehghani Hamid , Srinivasan Subhadra , Kogel Christine , Tosteson Tor D. , Weaver John , Poplack Steven P. , Paulsen Keith D.
Published: May 2006

Magnetic resonance (MR)-guided near-infrared spectral tomography was developed and used to image adipose and fibroglandular breast tissue of 11 normal female subjects, recruited under an institutional review board-approved protocol. Images of hemoglobin, oxygen saturation, water fraction, and subcellular scattering were reconstructed and show that fibroglandular fractions of both blood and water are higher than in adipose tissue. Variation in adipose and fibroglandular tissue composition between individuals was not significantly different across the scattered and dense breast categories. Combined MR and near-infrared tomography provides fundamental molecular information about these tissue types with resolution governed by MR T1 images.
Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor
Authors: van der Sloot Almer M. , Tur Vicente , Szegezdi Eva , Mullally Margaret M. , Cool Robbert H. , Samali Afshin , Serrano Luis , Quax Wim J.
Published: May 2006

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potential anticancer drug that selectively induces apoptosis in a variety of cancer cells by interacting with death receptors DR4 and DR5. TRAIL can also bind to decoy receptors (DcR1, DcR2, and osteoprotegerin receptor) that cannot induce apoptosis. The occurrence of DR5-responsive tumor cells indicates that a DR5 receptor-specific TRAIL variant will permit tumor-selective therapies. By using the automatic design algorithm FOLD-X, we successfully generated DR5-selective TRAIL variants. These variants do not induce apoptosis in DR4-responsive cell lines but show a large increase in biological activity in DR5-responsive cancer cell lines. Even wild-type TRAIL-insensitive ovarian cancer cell lines could be brought into apoptosis. In addition, our results demonstrate that there is no requirement for antibody-mediated cross-linking or membrane-bound TRAIL to induce apoptosis through DR5.
Myosin-V is a mechanical ratchet
Authors: Gebhardt J. Christof M. , Clemen Anabel E.-M. , Jaud Johann , Rief Matthias
Published: May 2006

Myosin-V is a linear molecular motor that hydrolyzes ATP to move processively toward the plus end of actin filaments. Motion of this motor under low forces has been studied recently in various single-molecule assays. In this paper we show that myosin-V reacts to high forces as a mechanical ratchet. High backward loads can induce rapid and processive backward steps along the actin filament. This motion is completely independent of ATP binding and hydrolysis. In contrast, forward forces cannot induce ATP-independent forward steps. We can explain this pronounced mechanical asymmetry by a model in which the strength of actin binding of a motor head is modulated by the lever arm conformation. Knowledge of the complete force–velocity dependence of molecular motors is important to understand their function in the cellular environment.
A metabolic network in the evolutionary context: Multiscale structure and modularity
Authors: Spirin Victor , Gelfand Mikhail S. , Mironov Andrey A. , Mirny Leonid A.
Published: May 2006

The enormous complexity of biological networks has led to the suggestion that networks are built of modules that perform particular functions and are “reused” in evolution in a manner similar to reusable domains in protein structures or modules of electronic circuits. Analysis of known biological networks has revealed several modules, many of which have transparent biological functions. However, it remains to be shown that identified structural modules constitute evolutionary building blocks, independent and easily interchangeable units. An alternative possibility is that evolutionary modules do not match structural modules. To investigate the structure of evolutionary modules and their relationship to functional ones, we integrated a metabolic network with evolutionary associations between genes inferred from comparative genomics. The resulting metabolic–genomic network places metabolic pathways into evolutionary and genomic context, thereby revealing previously unknown components and modules. We analyzed the integrated metabolic–genomic network on three levels: macro-, meso-, and microscale. The macroscale level demonstrates strong associations between neighboring enzymes and between enzymes that are distant on the network but belong to the same linear pathway. At the mesoscale level, we identified evolutionary metabolic modules and compared them with traditional metabolic pathways. Although, in some cases, there is almost exact correspondence, some pathways are split into independent modules. On the microscale level, we observed high association of enzyme subunits and weak association of isoenzymes independently catalyzing the same reaction. This study shows that evolutionary modules, rather than pathways, may be thought of as regulatory and functional units in bacterial genomes.
Bacteriorhodopsin (bR) as an electronic conduction medium: Current transport through bR-containing monolayers
Authors: Jin Yongdong , Friedman Noga , Sheves Mordechai , He Tao , Cahen David
Published: May 2006

Studying electron transport (ET) through proteins is hampered by achieving reproducible experimental configurations, particularly electronic contacts to the proteins. The transmembrane protein bacteriorhodopsin (bR), a natural light-activated proton pump in purple membranes of
Halobacterium salinarum
, is well studied for biomolecular electronics because of its sturdiness over a wide range of conditions. To date, related studies of dry bR systems focused on photovoltage generation and photoconduction with multilayers, rather than on the ET ability of bR, which is understandable because ET across 5-nm-thick, apparently insulating membranes is not obvious. Here we show that electronic current passes through bR-containing artificial lipid bilayers in solid “electrode–bilayer–electrode” structures and that the current through the protein is more than four orders of magnitude higher than would be estimated for direct tunneling through 5-nm, water-free peptides. We find that ET occurs only if retinal or a close analogue is present in the protein. As long as the retinal can isomerize after light absorption, there is a photo-ET effect. The contribution of light-driven proton pumping to the steady-state photocurrents is negligible. Possible implications in view of the suggested early evolutionary origin of halobacteria are noted.
Mouse telocentric sequences reveal a high rate of homogenization and possible role in Robertsonian translocation
Authors: Kalitsis Paul , Griffiths Belinda , Choo K. H. Andy
Published: May 2006

The telomere and centromere are two specialized structures of eukaryotic chromosomes that are essential for chromosome stability and segregation. These structures are usually characterized by large tracts of tandemly repeated DNA. In mouse, the two structures are often located in close proximity to form telocentric chromosomes. To date, no detailed sequence information is available across the mouse telocentric regions. The antagonistic mechanisms for the stable maintenance of the mouse telocentric karyotype and the occurrence of whole-arm Robertsonian translocations remain enigmatic. We have identified large-insert fosmid clones that span the telomere and centromere of several mouse chromosome ends. Sequence analysis shows that the distance between the telomeric T
2
AG
3
and centromeric minor satellite repeats range from 1.8 to 11 kb. The telocentric regions of different mouse chromosomes comprise a contiguous linear order of T
2
AG
3
repeats, a highly conserved truncated long interspersed nucleotide element 1 repeat, and varying amounts of a recently discovered telocentric tandem repeat that shares considerable identity with, and is inverted relative to, the centromeric minor satellite DNA. The telocentric domain as a whole exhibits the same polarity and a high sequence identity of >99% between nonhomologous chromosomes. This organization reflects a mechanism of frequent recombinational exchange between nonhomologous chromosomes that should promote the stable evolutionary maintenance of a telocentric karyotype. It also provides a possible mechanism for occasional inverted mispairing and recombination between the oppositely oriented TLC and minor satellite repeats to result in Robertsonian translocations.
Suppression of the DNA repair defects of BRCA2-deficient cells with heterologous protein fusions
Authors: Saeki Hiroshi , Siaud Nicolas , Christ Nicole , Wiegant Wouter W. , van Buul Paul P. W. , Han Mingguang , Zdzienicka Małgorzata Z. , Stark Jeremy M. , Jasin Maria
Published: May 2006

The BRCA2 tumor suppressor plays an important role in the repair of DNA damage by homologous recombination, also termed homology-directed repair (HDR). Human BRCA2 is 3,418 aa and is composed of several domains. The central part of the protein contains multiple copies of a motif that binds the Rad51 recombinase (the BRC repeat), and the C terminus contains domains that have structural similarity to domains in the ssDNA-binding protein replication protein A (RPA). To gain insight into the role of BRCA2 in the repair of DNA damage, we fused a single (BRC3, BRC4) or multiple BRC motifs to the large RPA subunit. Expression of any of these protein fusions in
Brca2
mutant cells substantially improved HDR while suppressing mutagenic repair. A fusion containing a Rad52 ssDNA-binding domain also was active in HDR. Mutations that reduced ssDNA or Rad51 binding impaired the ability of the fusion proteins to function in HDR. The high level of spontaneous chromosomal aberrations in
Brca2
mutant cells was largely suppressed by the BRC-RPA fusion proteins, supporting the notion that the primary role of BRCA2 in maintaining genomic integrity is in HDR, specifically to deliver Rad51 to ssDNA. The fusion proteins also restored Rad51 focus formation and cellular survival in response to DNA damaging agents. Because as little as 2% of BRCA2 fused to RPA is sufficient to suppress cellular defects found in
Brca2
-mutant mammalian cells, these results provide insight into the recently discovered diversity of BRCA2 domain structures in different organisms.
Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments
Authors: Van Mooy Benjamin A. S. , Rocap Gabrielle , Fredricks Helen F. , Evans Colleen T. , Devol Allan H.
Published: May 2006

There is growing evidence that dissolved phosphorus can regulate planktonic production in the oceans’ subtropical gyres, yet there is little quantitative information about the biochemical fate of phosphorus in planktonic communities. We observed in the North Pacific Subtropical Gyre (NPSG) that the synthesis of membrane lipids accounted for 18–28% of the phosphate (PO
4
3−
) taken up by the total planktonic community. Paradoxically,
Prochlorococcus
, the cyanobacterium that dominates NPSG phytoplankton, primarily synthesizes sulfoquinovosyldiacylglycerol (SQDG), a lipid that contains sulfur and sugar instead of phosphate. In axenic cultures of
Prochlorococcus
, it was observed that <1% of the total PO
4
3−
uptake was incorporated into membrane lipids. Liquid chromatography/mass spectrometry of planktonic lipids in the NPSG confirmed that SQDG was the dominant membrane lipid. Furthermore, the analyses of SQDG synthesis genes from the Sargasso Sea environmental genome showed that the use of sulfolipids in subtropical gyres was confined primarily to picocyanobacteria; no sequences related to known heterotrophic bacterial SQDG lineages were found. This biochemical adaptation by
Prochlorococcus
must be a significant benefit to these organisms, which compete against phospholipid-rich heterotrophic bacteria for PO
4
3−
. Thus, evolution of this “sulfur-for-phosphorus” strategy set the stage for the success of picocyanobacteria in oligotrophic environments and may have been a major event in Earth’s early history when the relative availability of sulfate and PO
4
3−
were significantly different from today’s ocean.
Extending the effects of spike-timing-dependent plasticity to behavioral timescales
Authors: Drew Patrick J. , Abbott L. F.
Published: May 2006

Activity-dependent modification of synaptic strengths due to spike-timing-dependent plasticity (STDP) is sensitive to correlations between pre- and postsynaptic firing over timescales of tens of milliseconds. Temporal associations typically encountered in behavioral tasks involve times on the order of seconds. To relate the learning of such temporal associations to STDP, we must account for this large discrepancy in timescales. We show that the gap between synaptic and behavioral timescales can be bridged if the stimuli being associated generate sustained responses that vary appropriately in time. Synapses between neurons that fire this way can be modified by STDP in a manner that depends on the temporal ordering of events separated by several seconds even though the underlying plasticity has a much smaller temporal window.
Scaling the metabolic balance of the oceans
Authors: López-Urrutia Ángel , San Martin Elena , Harris Roger P. , Irigoien Xabier
Published: May 2006

Oceanic communities are sources or sinks of CO
2
, depending on the balance between primary production and community respiration. The prediction of how global climate change will modify this metabolic balance of the oceans is limited by the lack of a comprehensive underlying theory. Here, we show that the balance between production and respiration is profoundly affected by environmental temperature. We extend the general metabolic theory of ecology to the production and respiration of oceanic communities and show that ecosystem rates can be reliably scaled from theoretical knowledge of organism physiology and measurement of population abundance. Our theory predicts that the differential temperature-dependence of respiration and photosynthesis at the organism level determines the response of the metabolic balance of the epipelagic ocean to changes in ambient temperature, a prediction that we support with empirical data over the global ocean. Furthermore, our model predicts that there will be a negative feedback of ocean communities to climate warming because they will capture less CO
2
with a future increase in ocean temperature. This feedback of marine biota will further aggravate the anthropogenic effects on global warming.
Plasmodium falciparum
ensures its amino acid supply with multiple acquisition pathways and redundant proteolytic enzyme systems
Authors: Liu Jun , Istvan Eva S. , Gluzman Ilya Y. , Gross Julia , Goldberg Daniel E.
Published: May 2006

Degradation of host hemoglobin by the human malaria parasite
Plasmodium falciparum
is a massive metabolic process. What role this degradation plays and whether it is essential for parasite survival have not been established, nor have the roles of the various degradative enzymes been clearly defined. We report that
P. falciparum
can grow in medium containing a single amino acid (isoleucine, the only amino acid missing from human hemoglobin). In this medium, growth of hemoglobin-degrading enzyme gene knockout lines (missing falcipain-2 and plasmepsins alone or in combination) is impaired. Blockade of plasmepsins with the potent inhibitor pepstatin A has a minimal effect on WT parasite growth but kills falcipain-2 knockout parasites at low concentrations and is even more potent on falcipain-2, plasmepsin I and IV triple knockout parasites. We conclude that: (
i
) hemoglobin degradation is necessary for parasite survival; (
ii
) hemoglobin degradation is sufficient to supply most of the parasite’s amino acid requirements; (
iii
) external amino acid acquisition and hemoglobin digestion are partially redundant nutrient pathways; (
iv
) hemoglobin degradation uses dual protease families with overlapping function; and (
v
) hemoglobin-degrading plasmepsins are not promising drug targets.
Mitochondrial genome of
Trichoplax adhaerens
supports Placozoa as the basal lower metazoan phylum
Authors: Dellaporta Stephen L. , Xu Anthony , Sagasser Sven , Jakob Wolfgang , Moreno Maria A. , Buss Leo W. , Schierwater Bernd
Published: May 2006

Mitochondrial genomes of multicellular animals are typically 15- to 24-kb circular molecules that encode a nearly identical set of 12–14 proteins for oxidative phosphorylation and 24–25 structural RNAs (16S rRNA, 12S rRNA, and tRNAs). These genomes lack significant intragenic spacers and are generally without introns. Here, we report the complete mitochondrial genome sequence of the placozoan
Trichoplax adhaerens
, a metazoan with the simplest known body plan of any animal, possessing no organs, no basal membrane, and only four different somatic cell types. Our analysis shows that the
Trichoplax
mitochondrion contains the largest known metazoan mtDNA genome at 43,079 bp, more than twice the size of the typical metazoan mtDNA. The mitochondrion’s size is due to numerous intragenic spacers, several introns and ORFs of unknown function, and protein-coding regions that are generally larger than those found in other animals. Not only does the
Trichoplax
mtDNA have characteristics of the mitochondrial genomes of known metazoan outgroups, such as chytrid fungi and choanoflagellates, but, more importantly, it shares derived features unique to the Metazoa. Phylogenetic analyses of mitochondrial proteins provide strong support for the placement of the phylum Placozoa at the root of the Metazoa.
Butyrylcholinesterase attenuates amyloid fibril formation
in vitro
Authors: Diamant Sophia , Podoly Erez , Friedler Assaf , Ligumsky Hagai , Livnah Oded , Soreq Hermona
Published: May 2006

In Alzheimer’s disease, both acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) colocalize with brain fibrils of amyloid-β (Aβ) peptides, and synaptic AChE-S facilitates fibril formation by association with insoluble Aβ fibrils. Here, we report that human BChE and BSP41, a synthetic peptide derived from the BChE C terminus, inversely associate with the soluble Aβ conformers and delay the onset and decrease the rate of Aβ fibril formation
in vitro
, at a 1:100 BChE/Aβ molar ratio and in a dose-dependent manner. The corresponding AChE synthetic peptide (ASP)40 peptide, derived from the homologous C terminus of synaptic human (h)AChE-S, failed to significantly affect Aβ fibril formation, attributing the role of enhancing this process to an AChE domain other than the C terminus. Circular dichroism and molecular modeling confirmed that both ASP40 and BChE synthetic peptide (BSP)41 are amphipathic α-helices. However, ASP40 shows symmetric amphipathicity, whereas BSP41 presented an aromatic tryptophan residue in the polar side of the C terminus. That this aromatic residue is causally involved in the attenuating effect of BChE was further supported by mutagenesis experiments in which (W8R) BSP41 showed suppressed capacity to attenuate fibril formation. In Alzheimer’s disease, BChE may have thus acquired an inverse role to that of AChE by adopting imperfect amphipathic characteristics of its C terminus.
Bases of biocontrol: Sequence predicts synthesis and mode of action of agrocin 84, the Trojan Horse antibiotic that controls crown gall
Authors: Kim Jung-Gun , Park Byoung Keun , Kim Sung-Uk , Choi Doil , Nahm Baek Hie , Moon Jae Sun , Reader John S. , Farrand Stephen K. , Hwang Ingyu
Published: May 2006

Agrobacterium radiobacter
K84, used worldwide to biocontrol crown gall disease caused by
Agrobacterium tumefaciens
, produces an antiagrobacterial compound called agrocin 84. We report the nucleotide sequence of pAgK84, a 44.42-kb plasmid coding for production of this disubstituted adenine nucleotide antibiotic. pAgK84 encodes 36 ORFs, 17 of which (
agn
) code for synthesis of or immunity to agrocin 84. Two genes,
agnB2
and
agnA
, encode aminoacyl tRNA synthetase homologues. We have shown that the toxic moiety of agrocin 84 inhibits cellular leucyl-tRNA synthetases and AgnB2, which confers immunity to the antibiotic, is a resistant form of this enzyme. AgnA, a truncated homologue of asparaginyl tRNA synthetase could catalyze the phosphoramidate bond between a precursor of the methyl pentanamide side group and the nucleotide. We propose previously undescribed chemistry, catalyzed by AgnB1, to generate the precursor necessary for this phosphoramidate linkage. AgnC7 is related to ribonucleotide reductases and could generate the 3′-deoxyarabinose moiety of the nucleoside. Bioinformatics suggest that
agnC3
,
agnC4
, and
agnC6
contribute to maturation of the methyl pentanamide, whereas
agnC2
may produce the glucofuranose side group bound to the adenine ring. AgnG is related to bacterial exporters. An
agnG
mutant accumulated agrocin 84 intracellularly but did not export the antibiotic. pAgK84 is transmissible and encodes genes for conjugative DNA processing but lacks a type IV secretion system, suggesting that pAgK84 transfers by mobilization. By sequence analysis, the deletion engineered into pAgK1026 removed the
oriT
and essential
tra
genes, confirming the enhanced environmental safety of this modified form of pAgK84.
Adenine and 2-aminopurine: Paradigms of modern theoretical photochemistry
Authors: Serrano-Andrés Luis , Merchán Manuela , Borin Antonio C.
Published: May 2006

Distinct photophysical behavior of nucleobase adenine and its constitutional isomer, 2-aminopurine, has been studied by using quantum chemical methods, in particular an accurate
ab initio
multiconfigurational second-order perturbation theory. After light irradiation, the efficient, ultrafast energy dissipation observed for nonfluorescent 9H-adenine is explained here by the nonradiative internal conversion process taking place along a barrierless reaction path from the initially populated
1
(ππ*
L
a
) excited state toward a low-lying conical intersection (CI) connected with the ground state. In contrast, the strong fluorescence recorded for 2-aminopurine at 4.0 eV with large decay lifetime is interpreted by the presence of a minimum in the
1
(ππ*
L
a
) hypersurface lying below the lowest CI and the subsequent potential energy barrier required to reach the funnel to the ground state. Secondary deactivation channels were found in the two systems related to additional CIs involving the
1
(ππ*
L
b
) and
1
(
n
π*) states. Although in 9H-adenine a population switch between both states is proposed, in 7H-adenine this may be perturbed by a relatively larger barrier to access the
1
(
n
π*) state, and, therefore, the
1
(ππ*
L
b
) state becomes responsible for the weak fluorescence measured in aqueous adenine at ≈4.5 eV. In contrast to previous models that explained fluorescence quenching in adenine, unlike in 2-aminopurine, on the basis of the vibronic coupling of the nearby
1
(ππ*) and
1
(
n
π*) states, the present results indicate that the
1
(
n
π*) state does not contribute to the leading photophysical event and establish the prevalence of a model based on the CI concept in modern photochemistry.
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Authors: Li Weizhong , Godzik Adam
Published: May 2006

Motivation: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282–283, Bioinformatics, 18, 77–82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.

Availability:  

Contact:  liwz@sdsc.edu
Metatool 5.0: fast and flexible elementary modes analysis
Authors: Kamp Axel von , Schuster Stefan
Published: May 2006

Summary: Elementary modes analysis is a powerful tool in the constraint-based modeling of metabolic networks. In recent years, new approaches to calculating elementary modes in biochemical reaction networks have been developed. As a consequence, the program Metatool, which is one of the first programs dedicated to this purpose, has been reimplemented in order to make use of these new approaches. The performance of Metatool has been significantly increased and the new version 5.0 can now be run inside the GNU octave or Matlab environments to allow more flexible usage and integration with other tools.

Availability: The script files and compiled shared libraries can be downloaded from the Metatool website at . Metatool consists of script files (m-files) for GNU octave as well as Matlab and shared libraries. The scripts are licensed under the GNU Public License and the use of the shared libraries is free for academic users and testing purposes. Commercial use of Metatool requires a special contract.

Contact:  kamp@minet.uni-jena.de
ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data
Authors: van Wieringen Wessel N. , Belien Jeroen A. M. , Vosse Sjoerd J. , Achame Eskeatnaf M. , Ylstra Bauke
Published: May 2006

Summary: We describe a tool, called ACE-it (Array CGH Expression integration tool). ACE-it links the chromosomal position of the gene dosage measured by array CGH to the genes measured by the expression array. ACE-it uses this link to statistically test whether gene dosage affects RNA expression.

Availability: ACE-it is freely available at

Contact:  b.ylstra@vumc.nl

Supplementary Information: Programs, the manual and supplementary information are available on the website.
Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes
Authors: Skibbe David S. , Wang Xiujuan , Zhao Xuefeng , Borsuk Lisa A. , Nettleton Dan , Schnable Patrick S.
Published: May 2006

Motivation: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been developed. Results: Data from each of three scan intensities (low, medium, high) were analyzed separately using multiple scan and linear regression approaches to identify and compare the sets of genes that exhibit statistically significant differential expression. In the multiple scan approach only one-third of the differentially expressed genes were shared among the three intensities, and each scan intensity identified unique sets of differentially expressed genes. The set of differentially expressed genes from any one scan amounted to <70% of the total number of genes identified in at least one scan. The average signal intensity of genes that exhibited statistically significant changes in expression was highest for the low-intensity scan and lowest for the high-intensity scan, suggesting that low-intensity scans may be best for detecting expression differences in high-signal genes, while high-intensity scans may be best for detecting expression differences in low-signal genes. Comparison of the differentially expressed genes identified in the multiple scan and linear regression approaches revealed that the multiple scan approach effectively identifies a subset of statistically significant genes that linear regression approach is unable to identify. Quantitative RT–PCR (qRT–PCR) tests demonstrated that statistically significant differences identified at all three scan intensities can be verified.

Availability: The data presented can be viewed at under GEO accession no. GSE3017.

Contact: schnable@iastate.edu

Supplementary information: Data from these experiments can be viewed at
Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli
Authors: Rodríguez J. Vidal , Kaandorp Jaap A. , Dobrzyński Maciej , Blom Joke G.
Published: May 2006

Motivation: Many biochemical networks involve reactions localized on the cell membrane. This can give rise to spatial gradients of the concentration of cytosolic species. Moreover, the number of membrane molecules can be small and stochastic effects can become relevant. Pathways usually consist of a complex interaction network and are characterized by a large set of parameters. The inclusion of spatial and stochastic effects is a major challenge in developing quantitative and dynamic models of pathways.

Results: We have developed a particle-based spatial stochastic method (GMP) to simulate biochemical networks in space, including fluctuations from the diffusion of particles and reactions. Gradients emerging from membrane reactions can be resolved. As case studies for the GMP method we used a simple gene expression system and the phosphoenolpyruvate:glucose phosphotransferase system pathway.

Availability: The source code for the GMP method is available at

Contact:  jrodrigu@science.uva.nl
Antioxidant Activity of Iranian Echium amoenum Fisch & C.A. Mey Flower Decoction in Humans: A cross‐sectional Before/After Clinical Trial
Authors: Ranjbar Akram , Khorami Sara , Safarabadi Mehdi , Shahmoradi Amene , Malekirad Ali Akbar , Vakilian Katyon , Mandegary Ali , Abdollahi Mohammad
Published: May 2006

Medicinal plants are recognized as sources of natural antioxidants that can protect from biological system oxidative stress. The present cross‐sectional before/after clinical trial was carried out to investigate the antioxidant properties of the decoction of the flowers of Echium amoenum Fisch & C.A. Mey in humans. A group of 38 healthy subjects was invited to use the E. amoenum (7 mg kg−1) twice daily for 14 days. Blood samples before and after entering the study were measured for lipid peroxidation level (LPO), total antioxidant capacity (TAC) and total thiol (SH) molecules. A significant reduction of blood LPO (24.65 ± 11.3 versus 19.05 ± 9.7, P = 0.029) was observed after 14 days of E. amoenum consumption. Blood TAC (1.46 ± 0.51 versus 1.70 ± 0.36, P = 0.018) and total thiol molecules (0.49 ± 0.11 versus 0.56 ± 0.12, P = 0.001) increased after 14 days of E. amoenum consumption. In conclusion, this antioxidative stress potential of E. amoenum may be due to its bioactive antioxidant components, especially rosmarinic acid and flavonoids. In recent years the importance of oxidative stress in the pathophysiology of many human disorders has been confirmed, thus use of this plant as a dietary supplement is highly recommended.
RPA, a Class II ARFGAP Protein, Activates ARF1 and U5 and Plays a Role in Root Hair Development in Arabidopsis
Authors: Song Xiu-Fen , Yang Chun-Ying , Liu Jie , Yang Wei-Cai
Published: May 2006

The polar growth of plant cells depends on the secretion of a large amount of membrane and cell wall materials at the growing tip to sustain rapid growth. Small GTP-binding proteins, such as Rho-related GTPases from plants and ADP-ribosylation factors (ARFs), have been shown to play important roles in polar growth via regulating intracellular membrane trafficking. To investigate the role of membrane trafficking in plant development, a Dissociation insertion line that disrupted a putative ARF GTPase-activating protein (ARFGAP) gene, AT2G35210, was identified in Arabidopsis (Arabidopsis thaliana). Phenotypic analysis showed that the mutant seedlings developed isotropically expanded, short, and branched root hairs. Pollen germination in vitro indicated that the pollen tube growth rate was slightly affected in the mutant. AT2G35210 is specifically expressed in roots, pollen grains, and pollen tubes; therefore, it is designated as ROOT AND POLLEN ARFGAP (RPA). RPA encodes a protein with an N-terminal ARFGAP domain. Subcellular localization experiments showed that RPA is localized at the Golgi complexes via its 79 C-terminal amino acids. We further showed that RPA possesses ARF GTPase-activating activity and specifically activates Arabidopsis ARF1 and ARF1-like protein U5 in vitro. Furthermore, RPA complemented Saccharomyces cerevisiaeglo3Δ gcs1Δ double mutant, which suggested that RPA functions as an ARFGAP during vesicle transport between the Golgi and the endoplasmic reticulum. Together, we demonstrated that RPA plays a role in root hair and pollen tube growth, most likely through the regulation of Arabidopsis ARF1 and ARF1-like protein U5 activity.
A Conserved Mechanism Controls Translation of Rubisco Large Subunit in Different Photosynthetic Organisms
Authors: Cohen Idan , Sapir Yair , Shapira Michal
Published: May 2006

We previously proposed a mechanism for control of Rubisco expression and assembly during oxidative stress in Chlamydomonas reinhardtii. The N terminus of the large subunit (LSU) comprises an RNA recognition motif (RRM) that is normally buried in the protein, but becomes exposed under oxidizing conditions when the glutathione pool shifts toward its oxidized form. Thus, de novo translation and assembly of Rubisco LSU stop with similar kinetics and the unpaired small subunit (SSU) is rapidly degraded. Here we show that the structure of the N-terminal domain is highly conserved throughout evolution, despite its relatively low sequence similarity. Furthermore, Rubisco from a broad evolutionary range of photosynthetic organisms binds RNA under oxidizing conditions, with dissociation constant values in the nanomolar range. In line with these observations, oxidative stress indeed causes a translational arrest in land plants as well as in Rhodospirillum rubrum, a purple bacterium that lacks the SSU. We highlight an evolutionary conserved element located within α-helix B, which is located in the center of the RRM and is also involved in the intramolecular interactions between two LSU chains. Thus, assembly masks the N terminus of the LSU hiding the RRM. When assembly is interrupted due to structural changes that occur under oxidizing conditions or in the absence of a dedicated chaperone, the N-terminal domain can become exposed, leading to the translational arrest of Rubisco LSU. Taken together, these results support a model by which LSU translation is governed by its dimerization. In the case that regulation of type I and type II Rubisco is conserved, the SSU does not appear to be directly involved in LSU translation.
Trichomes of Tobacco Excrete Zinc as Zinc-Substituted Calcium Carbonate and Other Zinc-Containing Compounds
Authors: Sarret Géraldine , Harada Emiko , Choi Yong-Eui , Isaure Marie-Pierre , Geoffroy Nicolas , Fakra Sirine , Marcus Matthew A. , Birschwilks Mandy , Clemens Stephan , Manceau Alain
Published: May 2006

Tobacco (Nicotiana tabacum L. cv Xanthi) plants were exposed to toxic levels of zinc (Zn). Zn exposure resulted in toxicity signs in plants, and these damages were partly reduced by a calcium (Ca) supplement. Confocal imaging of intracellular Zn using Zinquin showed that Zn was preferentially accumulated in trichomes. Exposure to Zn and Zn + Ca increased the trichome density and induced the production of Ca/Zn mineral grains on the head cells of trichomes. These grains were aggregates of submicrometer-sized crystals and poorly crystalline material and contained Ca as major element, along with subordinate amounts of Zn, manganese, potassium, chlorine, phosphorus, silicon, and magnesium. Micro x-ray diffraction revealed that the large majority of the grains were composed essentially of metal-substituted calcite (CaCO3). CaCO3 polymorphs (aragonite and vaterite) and CaC2O4 (Ca oxalate) mono- and dihydrate also were identified, either as an admixture to calcite or in separate grains. Some grains did not diffract, although they contained Ca, suggesting the presence of amorphous form of Ca. The presence of Zn-substituted calcite was confirmed by Zn K-edge micro-extended x-ray absorption fine structure spectroscopy. Zn bound to organic compounds and Zn-containing silica and phosphate were also identified by this technique. The proportion of Zn-substituted calcite relative to the other species increased with Ca exposure. The production of Zn-containing biogenic calcite and other Zn compounds through the trichomes is a novel mechanism involved in Zn detoxification. This study illustrates the potential of laterally resolved x-ray synchrotron radiation techniques to study biomineralization and metal homeostasis processes in plants.
PINOID Positively Regulates Auxin Efflux inArabidopsisRoot Hair Cells and Tobacco Cells
Authors: Lee Sang Ho , Cho Hyung-Taeg
Published: May 2006

Intercellular transport of auxin is mediated by influx and efflux carriers in the plasma membrane and subjected to developmental and environmental regulation. Here, using the auxin-sensitive Arabidopsis thaliana root hair cell system and the tobacco (Nicotiana tabacum) suspension cell system, we demonstrate that the protein kinase PINOID (PID) positively regulates auxin efflux. Overexpression of PID (PIDox) or the auxin efflux carrier component PINFORMED3 (PIN3, PIN3ox), specifically in the root hair cell, greatly suppressed root hair growth. In both PIDox and PIN3ox transformants, root hair growth was nearly restored to wild-type levels by the addition of auxin, protein kinase inhibitors, or auxin efflux inhibitors. Localization of PID or PIN3 at the cell boundary was disrupted by brefeldin A and staurosporine. A mutation in the kinase domain abrogated the ability of PID to localize at the cell boundary and to inhibit root hair growth. These results suggest that PIDox- or PIN3ox-enhanced auxin efflux results in a shortage of intracellular auxin and a subsequent inhibition of root hair growth. In an auxin efflux assay using transgenic tobacco suspension cells, PIDox or PIN3ox also enhanced auxin efflux. Collectively, these results suggest that PID positively regulates cellular auxin efflux, most likely by modulating the trafficking of PIN and/or some other molecular partners involved in auxin efflux.
A Novel Organization of ACT Domains in Allosteric Enzymes Revealed by the Crystal Structure of Arabidopsis Aspartate Kinase
Authors: Mas-Droux Corine , Curien Gilles , Robert-Genthon Mylène , Laurencin Mathieu , Ferrer Jean-Luc , Dumas Renaud
Published: May 2006

Asp kinase catalyzes the first step of the Asp-derived essential amino acid pathway in plants and microorganisms. Depending on the source organism, this enzyme contains up to four regulatory ACT domains and exhibits several isoforms under the control of a great variety of allosteric effectors. We report here the dimeric structure of a Lys and S-adenosylmethionine–sensitive Asp kinase isoform from Arabidopsis thaliana in complex with its two inhibitors. This work reveals the structure of an Asp kinase and an enzyme containing two ACT domains cocrystallized with its effectors. Only one ACT domain (ACT1) is implicated in effector binding. A loop involved in the binding of Lys and S-adenosylmethionine provides an explanation for the synergistic inhibition by these effectors. The presence of S-adenosylmethionine in the regulatory domain indicates that ACT domains are also able to bind nucleotides. The organization of ACT domains in the present structure is different from that observed in Thr deaminase and in the regulatory subunit of acetohydroxyacid synthase III.
NMR solution structure and backbone dynamics of domain III of the E protein of tick‐borne Langat flavivirus suggests a potential site for molecular recognition
Authors: Mukherjee Munia , Dutta Kaushik , White Mark A. , Cowburn David , Fox Robert O.
Published: May 2006

Flaviviruses cause many human diseases, including dengue fever, yellow fever, West Nile viral encephalitis, and hemorrhagic fevers, and are transmitted to their vertebrate hosts by infected mosquitoes and ticks. Domain III of the envelope protein (E‐D3) is considered to be the primary viral determinant involved in the virus–host‐cell receptor interaction, and thus represents an excellent target for antiviral drug development. Langat (LGT) virus is a naturally attenuated BSL‐2 TBE virus and is a model for the pathogenic BSL‐3 and BSL‐4 viruses in the serogroup. We have determined the solution structure of LGT‐E‐D3 using heteronuclear NMR spectroscopy. The backbone dynamics of LGT‐E‐D3 have been investigated using 15N relaxation measurements. A detailed analysis of the solution structure and dynamics of LGT‐E‐D3 suggests potential residues that could form a surface for molecular recognition, and thereby represent a target site for antiviral therapeutics design.
Solution structure of HndAc: A thioredoxin‐like domain involved in the NADP‐reducing hydrogenase complex
Authors: Nouailler Matthieu , Morelli Xavier , Bornet Olivier , Chetrit Bernard , Dermoun Zorah , Guerlesquin Françoise
Published: May 2006

The NADP‐reducing hydrogenase complex from Desulfovibrio fructosovorans is a heterotetramer encoded by the hndABCD operon. Sequence analysis indicates that the HndC subunit (52 kDa) corresponds to the NADP‐reducing unit, and the HndD subunit (63.5 kDa) is homologous to Clostridium pasteurianum hydrogenase. The role of HndA and HndB subunits (18.8 kDa and 13.8 kDa, respectively) in the complex remains unknown. The HndA subunit belongs to the [2Fe‐2S] ferredoxin family typified by C. pasteurianum ferredoxin. HndA is organized into two independent structural domains, and we report in the present work the NMR structure of its C‐terminal domain, HndAc. HndAc has a thioredoxin‐like fold consisting in four β‐strands and two relatively long helices. The [2Fe‐2S] cluster is located near the surface of the protein and bound to four cysteine residues particularly well conserved in this class of proteins. Electron exchange between the HndD N‐terminal [2Fe‐2S] domain (HndDN) and HndAc has been previously evidenced, and in the present studies we have mapped the binding site of the HndDN domain on HndAc. A structural analysis of HndB indicates that it is a FeS subunit with 41% similarity with HndAc and it contains a possible thioredoxin‐like fold. Our data let us propose that HndAc and HndB can form a heterodimeric intermediate in the electron transfer between the hydrogenase (HndD) active site and the NADP reduction site in HndC.