bluuebunny/crossref_metadata_2025 huggingface dataset:
Survey of the productivity, composition and estimated inputs of fixed nitrogen by pastures in central-western New South Wales
Authors: Bowman A. M. , Smith W. , Peoples M. B. , Brockwell J.
Published: January 2005

Total productivity and legume nitrogen fixation (N2 fixation) in dryland pastures were examined in a 2 year study (1999–2001) on 118 farms in central-western New South Wales. Pasture exclosure cages, placed at 217 on-farm sites, were harvested on 7 occasions and the foliage hand-sorted according to species in order to measure shoot dry matter (DM). The separated legume shoot material collected in spring 1999 (52 different legume samples) and 2000 (76 different legume samples) from a subset of representative pastures (41 cages on 28 different farms in 1999, 32 cages on 25 different farms in 2000) was also analysed for concentration of nitrogen (%N) and 15N natural abundance. These data were subsequently used to calculate the proportion of the legume shoot N derived from atmospheric N (%Ndfa), comparative measures of the relative efficiency of N2 fixation (kg N fixed/t DM accumulated) and the amounts of shoot N fixed (kg N/ha). The survey encompassed 8 common pasture types, and 5 others that were less common, ranging from native perennial grass pastures with little legume content to lucerne (Medicago sativa L.) pastures with and without companion clovers. Fifteen legume species were found in the pastures, some only occasionally. Lucerne and white clover (Trifolium repens L.) were the only perennials. Mean spring estimates of %Ndfa were similar in 1999 and 2000 for lucerne (72 and 81%, respectively), rose clover (T. hirtum All., 82 and 77%) and annual medics (Medicago spp., 89 and 86%). For the remaining 12 legume species, measures of %Ndfa ranged from 64 to 95% and averaged 83%. Shoot %N contents were greater for lucerne than for the other 14 legumes and this was reflected in the comparative measures of N2 fixation which ranged from 14.5 kg N/t DM for rose clover to 25.7 kg N/t DM for lucerne in 2000. The most productive pasture type comprised lucerne plus balansa clover [T. michelianum Savi var. balansae (Boiss.) Azn.], white clover or arrowleaf clover (T. vesiculosum Savi), but all pasture types that contained lucerne were highly productive. Spring was the most productive season and summer the least. Lucerne was overwhelmingly the most productive legume and was responsible for >83% of the fixed N in those pastures that contained both lucerne and other legumes. Lucerne productivity was approximately uniform throughout the year whereas, for other pastures, especially those based on rose clover or subterranean clover (T. subterraneum L.), there were sharp peaks in spring and little or no dry matter production over summer. The presence of lucerne in pastures significantly (P<0.05) reduced broadleaf weeds. It was concluded that, where there are requirements in central-western New South Wales agriculture for uniform forage production throughout the year and a high input of fixed N, lucerne is substantially superior to other species.
Effect of cutting regime on the agronomic performance of two contrasting lines of Melilotus albus
Authors: Evans P. M. , Trigg P. J. , Kearney G. A. , Byron A. H.
Published: January 2005

Two lines of Melilotus albus (Medik) of different maturity and morphological characteristics were subjected to 6 cutting regimes ranging from a single cut in March (2002) to 6 cuts between mid-October (2001) and March (2002). The yield of the late maturing, tall line, H11743 (B) was more than 13 t/ha of dry matter for the season, which was achieved with either 1 or 2 cuts. Dry matter production decreased as the number of cuts increased, with production reduced to 6 t/ha when it was cut every month between October and March inclusive. The early maturing, more prostrate genotype, Adela (E) was similarly affected by cutting regime; however, its production was lower, ranging between 4 and 6 t/ha for the season. Seed yields were not seriously affected in H11743 when it was cut until December, before allowing the plants to grow until maturity. Continuing to cut into January and February severely decreased seed yields. Seed yields for Adela were lower but followed a similar pattern to H11743. When Adela was cut every month from October until January or later it produced very little seed. Seedling regeneration closely followed seed yields, being highest (4000 seedlings/m2) with 2 cuts and being adequate (more than 2000 seedlings/m2) for both lines when the last cut was in December. Seed softened gradually over time after maturity in February, and from the end of August onwards the residual hard seed remained relatively stable at around 10% with no differences in seed softening rates between the 2 lines.
The results suggest that if persistence is to be achieved, defoliation of annual Melilotus albus will have to be stopped around January or the grazing pressure will have to be substantially reduced to allow seed set and regeneration. The late maturing genotype produced more dry matter and regenerated better than the early type, regardless of cutting regime.
Time of sowing and fungicides affect blackleg (Leptosphaeria maculans) severity and yield in canola
Authors: Khangura R. K. , Barbetti M. J.
Published: January 2005

Three different times of sowing in conjunction with various fungicide treatments were evaluated for the management of blackleg in canola (Brassica napus L.) variety Karoo. The trials were conducted at 4 different locations in Western Australia: East Chapman, Merredin, Wongan Hills and Mt Barker, representing a range of environmental conditions. The first time of sowing was at the break of the season followed by 2 subsequent sowings about 3 and 6 weeks later. Blackleg severity was significantly reduced by 14% when sowing was delayed until the end of June or early July, however, there were yield penalties due to the shortened growing season. Yield losses from blackleg were 16, 38 and 34% for mid-May, early to mid-June and end June to early July sown crops, respectively. All the fungicide treatments substantially reduced blackleg severity and increased yields at all the locations except for East Chapman (low rainfall site). The maximum protection fungicide treatment (Jockey seed dressing at 6.6 g a.i./kg seed + Impact in-furrow at 100 g a.i./ha + 3 foliar applications of flusilazole at 100 g a.i/ha) improved seed yield by 47, 56, 46 and 16% at Merredin, Wongan Hills and Mt Barker and East Chapman, respectively, compared with the nil treatment. Averaged over time of sowing and locations, the treatments of Jockey and Impact reduced disease severities by 20 and 25% and increased seed yields by 19 and 24%, respectively. There is potential for some other fungicide treatments, such as seed dressing with Jockey in combination with foliar application of either flusilazole or prochloraz, for the control of blackleg.
These investigations suggest that damage from blackleg, in some areas during some seasons, could be minimised by sowing canola crops as early as possible before the onset of maturation of pseudothecia thus avoiding major ascospore showers at the seedling stage of maximum susceptibility. However, in case of a late break of season, fungicide protection may be essential to minimise losses from blackleg, particularly if sowing moderately susceptible cultivars under moderate to high disease pressure situations.
Interactions between meat ants (Iridomyrmex spadius) and bellyache bush (Jatropha gossypiifolia)
Authors: Bebawi F. F. , Campbell S. D.
Published: January 2005

Understanding the dispersal of weed species is important for the development of effective control strategies. In this study, a series of experiments was conducted to clarify the role that meat ants (Iridomyrmex spadius) play in dispersing bellyache bush (Jatropha gossypiifolia), an exotic shrub currently invading the rangelands of northern Australia. The nutrient composition of food [lipids (fatty acids), fat and soluble carbohydrates] provided by bellyache bush seed components [caruncle, exotegmen and seed (without caruncle and exotegmen)] was identified. Seed components were rich in lipids, particularly palmitic, oleic, stearic, linoleic and eicosenic acids. Oleic and palmitic were most abundant in the caruncle (30% each), linoleic in the seed (61%) and palmitic in the exotegmen (36%). Over all seed components, fat concentration was relatively high (6.3%) compared with soluble carbohydrates (2.3%). The impact of feeding was then determined by comparing germination and viability of intact, non-carunculate (caruncle manually removed) and ant-discarded bellyache bush seeds. Feeding by meat ants significantly increased seed germinability, whilst having no adverse affects on viability. The quantity of seeds dispersed and the seasonal pattern of dispersal was recorded by collecting seed from the middens of randomly selected meat ant nests on a monthly basis. On average, 12 330 ± 603 seeds were retrieved from the middens of individual meat ant nests over 12 months, with highest numbers recorded between February and June (>1200 seeds/ant nest). The effect of this dispersal was determined through comparisons of plant densities within core infestations of bellyache bush, meat ant nest middens and pastures located directly adjacent to core infestations and that were being invaded primarily through localised ballistic dispersal. The density of bellyache bush plants growing from the seed reserves within middens averaged 79 plants/m2, just 18% less than that within core infestations. Seedling survival (1 year) and growth within core infestation and meat ant sites was also quantified. The middens of meat ant nests provided an environment conducive to higher seedling survival and faster growth rates than occurred within core infestations. Mutualistic interaction between bellyache bush and meat ants is likely to build local ‘infestation pressure’ that may be conducive to range extension in years of exceptionally wet seasons. Management of seed dispersal by meat ants may reduce that risk.
Heparan 2-O-sulfotransferase,hst-2, is essential for normal cell migration inCaenorhabditis elegans
Authors: Kinnunen Tarja , Huang Zebo , Townsend Joanne , Gatdula Michelle M. , Brown Jillian R. , Esko Jeffrey D. , Turnbull Jeremy E.
Published: January 2005

The importance of heparan sulfate proteoglycans has been highlighted by a number of human genetic disorders associated with mutations in genes encoding for heparan sulfate proteoglycan protein cores or biosynthetic enzymes required for heparan sulfate (HS) assembly. To study the functional role of HS inCaenorhabditis elegansdevelopment cosmid sequence C34F6.4 was identified as theC. elegansortholog of vertebrate heparan 2-O-sulfotransferase (HS2ST) and the gene namedhst-2. HS2ST activity is present inC. elegansand is completely absent in a deletion mutant ofhst-2,ok595, and specifically reduced byhst-2RNA interference. Expression ofhst-2in CHO cells deficient in HS2ST rescues enzyme activity and binding of FGF2 to cell surface HS.hst-2expression is found in the hypodermis, muscle, distal tip cells (DTCs), and in neurons. A null mutation inhst-2causes cell migration defects. This work demonstrates sulfotransferase activity inC. elegansand indicates that specific 2-O-sulfate modifications are critical for normal HS functions in controlling cell migration.
Intercellular transfer of P-glycoprotein mediates acquired multidrug resistance in tumor cells
Authors: Levchenko Andre , Mehta Bipin M. , Niu Xinle , Kang Grace , Villafania Liliana , Way Denise , Polycarpe Dolores , Sadelain Michel , Larson Steven M.
Published: January 2005

The overexpression of P-glycoprotein (P-gp) causes resistance to chemotherapy in many tumor types. Here, we report intercellular transfer of functional P-gp from P-gp-positive to P-gp-negative cells
in vitro
and
in vivo
. The expression of acquired P-gp is transient in isolated cells but persists in the presence of P-gp-positive cells or under the selective pressure of colchicine. The intercellular transfer of functional P-gp occurs between different tumor cell types and results in increased drug resistance both
in vitro
and
in vivo
. Most importantly, the acquired resistance permits tumor cells to survive potentially toxic drug concentrations long enough to develop intrinsic P-gp-mediated resistance. P-gp transfer also occurs to putative components of tumor stroma, such as fibroblasts, raising the possibility that multidrug resistance could be conferred by resistant tumor cells to critical stromal elements within the tumor mass. This is the first report, to our knowledge, that a protein transferred between cells retains its function and confers a complex biologic property upon the recipient cell. These findings have important implications for proteomic analyses in tumor samples and resistance to cancer therapy.
Surviving heat shock: Control strategies for robustness and performance
Authors: El-Samad H. , Kurata H. , Doyle J. C. , Gross C. A. , Khammash M.
Published: January 2005

Molecular biology studies the cause-and-effect relationships among microscopic processes initiated by individual molecules within a cell and observes their macroscopic phenotypic effects on cells and organisms. These studies provide a wealth of information about the underlying networks and pathways responsible for the basic functionality and robustness of biological systems. At the same time, these studies create exciting opportunities for the development of quantitative and predictive models that connect the mechanism to its phenotype then examine various modular structures and the range of their dynamical behavior. The use of such models enables a deeper understanding of the design principles underlying biological organization and makes their reverse engineering and manipulation both possible and tractable The heat shock response presents an interesting mechanism where such an endeavor is possible. Using a model of heat shock, we extract the design motifs in the system and justify their existence in terms of various performance objectives. We also offer a modular decomposition that parallels that of traditional engineering control architectures.
Genomic instability, endoreduplication, and diminished Ig class-switch recombination in B cells lacking Nbs1
Authors: Reina-San-Martin Bernardo , Nussenzweig Michel C. , Nussenzweig André , Difilippantonio Simone
Published: January 2005

Mre11, Rad50, and Nbs1 form an evolutionarily conserved protein complex (Mre11–Rad50–Nbs1, MRN) that has been proposed to function as a DNA damage sensor. Hypomorphic mutations in Mre11 and Nbs1 result in the human ataxia–telangiectasia-like disorder and Nijmegen breakage syndrome (NBS), respectively. In contrast, complete inactivation of Mre11, Rad50, or Nbs1 leads to early embryonic lethality, suggesting that the hypomorphic mutations may fail to reveal some of the essential functions of MRN. Here, we use Cre–loxP-mediated recombination to restrict Nbs1 deletion to B lymphocytes. We find that disruption of Nbs1 results in the accumulation of high levels of spontaneous DNA damage, impaired proliferation, and chromosomal endoreduplication. Moreover, we show that Ig class-switch recombination (CSR) is diminished in Nbs1-deficient B cells. The CSR defect is B cell-intrinsic, independent of switch-region transcription, and a consequence of inefficient recombination at the DNA level. Our findings reveal that Nbs1 is critical for efficient Ig CSR and maintenance of the integrity of chromosomal structure and number.
Extracellular deoxyribonuclease made by group A
Streptococcus
assists pathogenesis by enhancing evasion of the innate immune response
Authors: Sumby Paul , Barbian Kent D. , Gardner Donald J. , Whitney Adeline R. , Welty Diane M. , Long R. Daniel , Bailey John R. , Parnell Michael J. , Hoe Nancy P. , Adams Gerald G. , DeLeo Frank R. , Musser James M.
Published: January 2005

Many pathogenic bacteria produce extracellular DNase, but the benefit of this enzymatic activity is not understood. For example, all strains of the human bacterial pathogen group A
Streptococcus
(GAS) produce at least one extracellular DNase, and most strains make several distinct enzymes. Despite six decades of study, it is not known whether production of DNase by GAS enhances virulence. To test the hypothesis that extracellular DNase is required for normal progression of GAS infection, we generated seven isogenic mutant strains in which the three chromosomal- and prophage-encoded DNases made by a contemporary serotype M1 GAS strain were inactivated. Compared to the wild-type parental strain, the isogenic triple-mutant strain was significantly less virulent in two mouse models of invasive infection. The triple-mutant strain was cleared from the skin injection site significantly faster than the wild-type strain. Preferential clearance of the mutant strain was related to the differential extracellular killing of the mutant and wild-type strains, possibly through degradation of neutrophil extracellular traps, innate immune structures composed of chromatin and granule proteins. The triple-mutant strain was also significantly compromised in its ability to cause experimental pharyngeal disease in cynomolgus macaques. Comparative analysis of the seven DNase mutant strains strongly suggested that the prophage-encoded SdaD2 enzyme is the major DNase that contributes to virulence in this clone. We conclude that extracellular DNase activity made by GAS contributes to disease progression, thereby resolving a long-standing question in bacterial pathogenesis research.
Predicting the risk of extinction from shared ecological characteristics
Authors: Kotiaho Janne S. , Kaitala Veijo , Komonen Atte , Päivinen Jussi
Published: January 2005

Understanding the ultimate causes of population declines and extinction is vital in our quest to stop the currently rampant biodiversity loss. Comparison of ecological characteristics between threatened and nonthreatened species may reveal these ultimate causes. Here, we report an analysis of ecological characteristics of 23 threatened and 72 nonthreatened butterfly species. Our analysis reveals that threatened butterflies are characterized by narrow niche breadth, restricted resource distribution, poor dispersal ability, and short flight period. Based on the characteristics, we constructed an ecological extinction risk rank and predicted which of the currently nonthreatened species are at the highest risk of extinction. Our analysis reveals that two species currently classified as nonthreatened are, in fact, at high risk of extinction, and that the status of a further five species should be reconsidered.
Skp2 inhibits FOXO1 in tumor suppression through ubiquitin-mediated degradation
Authors: Huang Haojie , Regan Kevin M. , Wang Fang , Wang Diping , Smith David I , van Deursen Jan M. A. , Tindall Donald J.
Published: January 2005

Forkhead transcription factors FOXO1 (FKHR), FOXO3a (FKHRL1), and FOXO4 (AFX) play a pivotal role in tumor suppression by inducing growth arrest and apoptosis. Loss of function of these factors due to phosphorylation and proteasomal degradation has been implicated in cell transformation and malignancy. However, the ubiquitin ligase necessary for the ubiquitination of the FOXO factors and the relevance of this regulation to tumorigenesis have not been characterized. Here we demonstrate that Skp2, an oncogenic subunit of the Skp1/Cul1/F-box protein ubiquitin complex, interacts with, ubiquitinates, and promotes the degradation of FOXO1. This effect of Skp2 requires Akt-specific phosphorylation of FOXO1 at Ser-256. Moreover, expression of Skp2 inhibits transactivation of FOXO1 and abolishes the inhibitory effect of FOXO1 on cell proliferation and survival. Furthermore, expression of the FOXO1 protein is lost in a mouse lymphoma model, where Skp2 is overexpressed. These data suggest that the Skp2-promoted proteolysis of FOXO1 plays a key role in tumorigenesis.
Short-lived chlorine-36 in a Ca- and Al-rich inclusion from the Ningqiang carbonaceous chondrite
Authors: Lin Yangting , Guan Yunbin , Leshin Laurie A. , Ouyang Ziyuan , Wang Daode
Published: January 2005

Excesses of sulfur-36 in sodalite, a chlorine-rich mineral, in a calcium- and aluminum-rich inclusion from the Ningqiang carbonaceous chondrite linearly correlate with chorine/sulfur ratios, providing direct evidence for the presence of short-lived chlorine-36 (with a half-life of 0.3 million years) in the early solar system. The best inferred (
36
Cl/
35
Cl)
o
ratios of the sodalite are ≈5 × 10
-6
. Different from other short-lived radionuclides, chlorine-36 was introduced into the inclusion by solid-gas reaction during secondary alteration. The alteration reaction probably took place at least 1.5 million years after the first formation of the inclusion, based on the correlated study of the
26
Al-
26
Mg systems of the relict primary minerals and the alteration assemblages, from which we inferred an initial ratio of (
36
Cl/
35
Cl)
o
> 1.6 × 10
-4
at the time when calcium- and aluminum-rich inclusions formed. This discovery supports a supernova origin of short-lived nuclides [Cameron, A. G. W., Hoeflich, P., Myers, P. C. & Clayton, D. D. (1995)
Astrophys. J.
447, L53; Wasserburg, G. J., Gallino, R. & Busso, M. (1998)
Astrophys. J.
500, L189–L193], but presents a serious challenge for local irradiation models [Shu, F. H., Shang, H., Glassgold, A. E. & Lee, T. (1997)
Science
277, 1475–1479; Gounelle, M., Shu, F. H., Shang, H., Glassgold, A. E., Rehm, K. E. & Lee, T. (2001)
Astrophys. J.
548, 1051–1070]. Furthermore, the short-lived
36
Cl may serve as a unique fine-scale chronometer for volatile-rock interaction in the early solar system because of its close association with aqueous and/or anhydrous alteration processes.
Enthalpy of helix–coil transition: Missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues
Authors: Richardson John M. , Lopez Maria M. , Makhatadze George I.
Published: January 2005

It is known that different amino acid residues have effects on the thermodynamic stability of an α-helix. The underlying mechanism for the thermodynamic helical propensity is not well understood. The major accepted hypothesis is the difference in the side-chain configurational entropy loss upon helix formation. However, the changes in the side-chain configurational entropy explain only part of the thermodynamic helical propensity, thus implying that there must be a difference in the enthalpy of helix–coil transition for different residues. This work provides an experimental test to this hypothesis. Direct calorimetric measurements of folding of a model host peptide in which the helix formation is induced by metal binding is applied to a wide range of residue types, both naturally occurring and nonnatural, at the guest site. Based on the calorimetric results for 12 peptides, it was found that indeed there is a difference in the enthalpy of helix–coil transition for different amino acid residues, and simple empirical rules that define these differences are presented. The obtained difference in the enthalpies of helix–coil transition complement the differences in configurational entropies and provide the complete thermodynamic characterization of the helix-forming tendencies.
Commensurability and stability in nonperiodic systems
Authors: Fasano Y. , De Seta M. , Menghini M. , Pastoriza H. , de la Cruz F.
Published: January 2005

We have investigated the response of 3D Bi
2
Sr
2
CaCu
2
O
8
vortex structures to a weak perturbation induced by 2D Fe pinning structures acting on one extremity of vortex lines. The pinning patterns were nano-engineered at the sample surface by means of either a Bitter decoration of the vortex lattice or electron-beam lithography. The commensurability conditions between 2D rigid pinning potentials and 3D elastic structures with short-range positional and long-range orientational correlation have been experimentally determined. When the 2D potential is a replica of the nonperiodic vortex structure an amplification of its interaction with the vortex structure takes place. This effect is detected only for the first matching field, becoming negligible for other matching fields. On the other hand, a periodic 2D perturbation is shown to transform the nonperiodic Bragg glass-like structure into an Abrikosov crystal with an effective Debye–Waller factor.
A genomic population genetics analysis of the pathogenic enterocyte effacement island in
Escherichia coli
: The search for the unit of selection
Authors: Castillo Amanda , Eguiarte Luis E. , Souza Valeria
Published: January 2005

Comparative genomic analysis is a powerful tool for understanding the history and organization of complete genomes. The mathematical tools of population genetics combined with genomic analysis provide a powerful approach to dissect heterogeneities in genome evolution. This study presents a hierarchical analysis of the enterocyte and effacement island (35 kb), which is found in the enteropathogenic and enterohemorrhagic strains in
Escherichia coli
and in
Citrobacter rodentium
. The locus of enterocyte and effacement in
E. coli
is considered to be a clonal unit inside a clonal organism and is expected to evolve as a single unit. This analysis examines the clonal assumption by determining genetic diversity, GC content, and the substitution rates at the different functional levels of (
i
) the complete pathogenic island, (
ii
) the five operons in which the island is organized, and (
iii
) for each of the individual 41 genes that comprise the locus. We find that there is a conserved region that is composed of genes that belong to the type III secretion system and that may be products of horizontal transfer. A more diverse region is composed of genes for secreted proteins and genes that we infer to be original components of the
E. coli
genome. This genetic mosaic seems to be differentially affected by selection and mutation. Our results suggest that recombination and selection may be breaking this structure so that different elements are, at best, weakly coupled in their evolution. These observations suggest that the units of selection are not the complete island, but rather, much smaller units that comprise the island.
Nibrin functions in Ig class-switch recombination
Authors: Kracker Sven , Bergmann Yvonne , Demuth Ilja , Frappart Pierre-Olivier , Hildebrand Gabriele , Christine Rainer , Wang Zhao-Qi , Sperling Karl , Digweed Martin , Radbruch Andreas
Published: January 2005

Nijmegen breakage syndrome (NBS) is a rare autosomal recessive disorder characterized by predisposition to hematopoietic malignancy, cell-cycle checkpoint defects, and ionizing radiation sensitivity. NBS is caused by a hypomorphic mutation of the
NBS1
gene, encoding nibrin, which forms a protein complex with Mre11 and Rad50, both involved in DNA repair. Nibrin localizes to chromosomal sites of class switching, and B cells from NBS patients show an enhanced presence of microhomologies at the sites of switch recombination. Because nibrin is crucial for embryonic survival, direct demonstration by targeted deletion that nibrin functions in class switch recombination has been lacking. Here, we show by cell-type-specific conditional inactivation of
Nbn
, the murine homologue of
NBS1
, that nibrin plays a role in the repair of γ-irradiation damage, maintenance of chromosomal stability, and the recombination of Ig constant region genes in B lymphocytes.
Cell-to-cell movement of GFP during embryogenesis and early seedling development in
Arabidopsis
Authors: Kim Insoon , Cho Euna , Crawford Katrina , Hempel Frederick D. , Zambryski Patricia C.
Published: January 2005

There is increasing evidence for intercellular trafficking of macromolecules through plasmodesmata (PD) during plant development. Here we study the ability of PD to traffic proteins during embryogenesis and early seedling development in
Arabidopsis
. Transgenic lines that induce GFP expression only in meristems, MSG (meristem-specific GFP), were used to monitor GFP movement. Cell-to-cell movement of different-sized GFP reporters reveals that embryos and young seedlings traffic proteins at least 54 kDa in size. Although 27-kDa soluble GFP (1×sGFP) freely moves between cells throughout the entire embryo during all stages analyzed, 2×sGFP movement becomes more restricted as development proceeds. After germination, cells near the apical meristem in seedlings show a higher size exclusion limit (SEL), whereas the SEL becomes more restricted as surrounding tissues develop identities. Although 1×sGFP moves throughout leaf primordia, as the leaf develops only the basal part of leaf petioles, main vascular tissues, and leaf veins (not blades) allow 1×sGFP movement. Although previous studies showed that embryos allow movement of small symplastic tracers (0.5 kDa), the present data demonstrate that the embryo constitutes a single symplast that allows transport of macromolecules as well. Even 2×sGFP moves from its site of expression at the apical meristem in embryos and seedlings, yet the extent of movement is more limited than 1×sGFP. Thus, PD have distinct SELs in different subregions of the embryo and seedling. These studies support the general concept that PD in younger tissues are more dilated and less restrictive than PD in older (nonvascular) tissues.
An Eulerian path approach to local multiple alignment for DNA sequences
Authors: Zhang Yu , Waterman Michael S.
Published: January 2005

Expensive computation in handling a large number of sequences limits the application of local multiple sequence alignment. We present an Eulerian path approach to local multiple alignment for DNA sequences. The computational time and memory usage of this approach is approximately linear to the total size of sequences analyzed; hence, it can handle thousands of sequences or millions of letters simultaneously. By constructing a De Bruijn graph, most of the conserved segments are amplified as heavy Eulerian paths in the graph, and the original patterns distributed in sequences are recovered even if they do not exist in any single sequence. This approach can accurately detect unknown conserved regions, for both short and long, conserved and degenerate patterns. We further present a Poisson heuristic to estimate the significance of a local multiple alignment. The performance of our method is demonstrated by finding Alu repeats in the human genome. We compare the results with Alus marked byrepeatmasker, where the two programs are in good agreement. Our method is robust under various conditions and superior to other methods in terms of efficiency and accuracy.
Gene flow across linguistic boundaries in Native North American populations
Authors: Hunley Keith , Long Jeffrey C.
Published: January 2005

Cultural and linguistic groups are often expected to represent genetic populations. In this article, we tested the hypothesis that the hierarchical classification of languages proposed by J. Greenberg [(1987)Language in the Americas(Stanford Univ. Press, Stanford, CA)] also represents the genetic structure of Native North American populations. The genetic data are mtDNA sequences for 17 populations gleaned from literature sources and public databases. The hypothesis was rejected. Further analysis showed that departure of the genetic structure from the linguistic classification was pervasive and not due to an outlier population or a problematic language group. Therefore, Greenberg's language groups are at best an imperfect approximation to the genetic structure of these populations. Moreover, we show that the genetic structure among these Native North American populations departs significantly from the best-fitting hierarchical models. Analysis of median joining networks for mtDNA haplotypes provides strong evidence for gene flow across linguistic boundaries. In principle, the language of a population can be replaced more rapidly than its genes because language can be transmitted both vertically from parents to children and horizontally between unrelated people. However, languages are part of a cultural complex, and there may be strong pressure to maintain a language in place whereas genes are free to flow.
Predicted hexameric structure of theAgrobacteriumVirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion
Authors: Middleton Rebecca , Sjölander Kimmen , Krishnamurthy Nandini , Foley Jonathan , Zambryski Patricia
Published: January 2005

TheAgrobacteriumT-DNA transporter belongs to a growing class of evolutionarily conserved transporters, called type IV secretion systems (T4SSs). VirB4, 789 aa, is the largest T4SS component, providing a rich source of possible structural domains. Here, we use a variety of bioinformatics methods to predict that the C-terminal domain of VirB4 (including the Walker A and B nucleotide-binding motifs) is related by divergent evolution to the cytoplasmic domain of TrwB, the coupling protein required for conjugative transfer of plasmid R388 fromEscherichia coli. This prediction is supported by detailed sequence and structure analyses showing conservation of functionally and structurally important residues between VirB4 and TrwB. The availability of a solved crystal structure for TrwB enables the construction of a comparative model for VirB4 and the prediction that, like TrwB, VirB4 forms a hexamer. These results lead to a model in which VirB4 acts as a docking site at the entrance of the T4SS channel and acts in concert with VirD4 and VirB11 to transport substrates (T-strand linked to VirD2 or proteins such as VirE2, VirE3, or VirF) through the T4SS.
Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem
Authors: Spear John R. , Walker Jeffrey J. , McCollom Thomas M. , Pace Norman R.
Published: January 2005

The geochemical energy budgets for high-temperature microbial ecosystems such as occur at Yellowstone National Park have been unclear. To address the relative contributions of different geochemistries to the energy demands of these ecosystems, we draw together three lines of inference. We studied the phylogenetic compositions of high-temperature (>70°C) communities in Yellowstone hot springs with distinct chemistries, conducted parallel chemical analyses, and carried out thermodynamic modeling. Results of extensive molecular analyses, taken with previous results, show that most microbial biomass in these systems, as reflected by rRNA gene abundance, is comprised of organisms of the kinds that derive energy for primary productivity from the oxidation of molecular hydrogen, H
2
. The apparent dominance by H
2
-metabolizing organisms indicates that H
2
is the main source of energy for primary production in the Yellowstone high-temperature ecosystem. Hydrogen concentrations in the hot springs were measured and found to range up to >300 nM, consistent with this hypothesis. Thermodynamic modeling with environmental concentrations of potential energy sources also is consistent with the proposed microaerophilic, hydrogen-based energy economy for this geothermal ecosystem, even in the presence of high concentrations of sulfide.
Whither Nationalist Urbanism? Public Life in Governor Sutiyoso's Jakarta
Authors: Kusno Abidin
Published: January 2005

This paper shows how Jakarta has been engaged in an unprecedented politics of memory since the collapse of Suharto's regime. It argues that the nationalist discourses of the city dressed in the ideology of 'nationalist urbanism' no longer appear to hold the influence that they once did in the face of the changing regime. This situation has given rise to a sense of 'looseness' at the centre, which in turn has encouraged both the government and the citizens to safeguard their space in the city by ways of remembering and forgetting the past as well as the present.
Catalytically inactive human cathepsin D triggers fibroblast invasive growth
Authors: Laurent-Matha Valérie , Maruani-Herrmann Sharon , Prébois Christine , Beaujouin Mélanie , Glondu Murielle , Noël Agnès , Alvarez-Gonzalez Marie Luz , Blacher Sylvia , Coopman Peter , Baghdiguian Stephen , Gilles Christine , Loncarek Jadranka , Freiss Gilles , Vignon Françoise , Liaudet-Coopman Emmanuelle
Published: January 2005

The aspartyl-protease cathepsin D (cath-D) is overexpressed and hypersecreted by epithelial breast cancer cells and stimulates their proliferation. As tumor epithelial–fibroblast cell interactions are important events in cancer progression, we investigated whether cath-D overexpression affects also fibroblast behavior. We demonstrate a requirement of cath-D for fibroblast invasive growth using a three-dimensional (3D) coculture assay with cancer cells secreting or not pro-cath-D. Ectopic expression of cath-D in cath-D–deficient fibroblasts stimulates 3D outgrowth that is associated with a significant increase in fibroblast proliferation, survival, motility, and invasive capacity, accompanied by activation of the ras–MAPK pathway. Interestingly, all these stimulatory effects on fibroblasts are independent of cath-D proteolytic activity. Finally, we show that pro-cath-D secreted by cancer cells is captured by fibroblasts and partially mimics effects of transfected cath-D. We conclude that cath-D is crucial for fibroblast invasive outgrowth and could act as a key paracrine communicator between cancer and stromal cells, independently of its catalytic activity.
X chromosome choice occurs independently of asynchronous replication timing
Authors: Gribnau Joost , Luikenhuis Sandra , Hochedlinger Konrad , Monkhorst Kim , Jaenisch Rudolf
Published: January 2005

In mammals, dosage compensation is achieved by X chromosome inactivation in female cells. Xist is required and sufficient for X inactivation, and Xist gene deletions result in completely skewed X inactivation. In this work, we analyzed skewing of X inactivation in mice with an Xist deletion encompassing sequence 5 KB upstream of the promoter through exon 3. We found that this mutation results in primary nonrandom X inactivation in which the wild-type X chromosome is always chosen for inactivation. To understand the molecular mechanisms that affect choice, we analyzed the role of replication timing in X inactivation choice. We found that the two Xist alleles and all regions tested on the X chromosome replicate asynchronously before the start of X inactivation. However, analysis of replication timing in cell lines with skewed X inactivation showed no preference for one of the two Xist alleles to replicate early in S-phase before the onset of X inactivation, indicating that asynchronous replication timing does not play a role in skewing of X inactivation.
Ultrastructural identification of uncoated caveolin-independent early endocytic vehicles
Authors: Kirkham Matthew , Fujita Akikazu , Chadda Rahul , Nixon Susan J. , Kurzchalia Teymuras V. , Sharma Deepak K. , Pagano Richard E. , Hancock John F. , Mayor Satyajit , Parton Robert G.
Published: January 2005

Using quantitative light microscopy and a modified immunoelectron microscopic technique, we have characterized the entry pathway of the cholera toxin binding subunit (CTB) in primary embryonic fibroblasts. CTB trafficking to the Golgi complex was identical in caveolin-1null (Cav1−/−) mouse embryonic fibroblasts (MEFs) and wild-type (WT) MEFs. CTB entry in the Cav1−/− MEFs was predominantly clathrin and dynamin independent but relatively cholesterol dependent. Immunoelectron microscopy was used to quantify budded and surface-connected caveolae and to identify noncaveolar endocytic vehicles. In WT MEFs, a small fraction of the total Cav1-positive structures were shown to bud from the plasma membrane (2% per minute), and budding increased upon okadaic acid or lactosyl ceramide treatment. However, the major carriers involved in initial entry of CTB were identified as uncoated tubular or ring-shaped structures. These carriers contained GPI-anchored proteins and fluid phase markers and represented the major vehicles mediating CTB uptake in both WT and caveolae-null cells.
Clathrin- and caveolin-1–independent endocytosis
Authors: Damm Eva-Maria , Pelkmans Lucas , Kartenbeck Jürgen , Mezzacasa Anna , Kurzchalia Teymuras , Helenius Ari
Published: January 2005

Simian Virus 40 (SV40) has been shown to enter host cells by caveolar endocytosis followed by transport via caveosomes to the endoplasmic reticulum (ER). Using a caveolin-1 (cav-1)–deficient cell line (human hepatoma 7) and embryonic fibroblasts from a cav-1 knockout mouse, we found that in the absence of caveolae, but also in wild-type embryonic fibroblasts, the virus exploits an alternative, cav-1–independent pathway. Internalization was rapid (t1/2 = 20 min) and cholesterol and tyrosine kinase dependent but independent of clathrin, dynamin II, and ARF6. The viruses were internalized in small, tight-fitting vesicles and transported to membrane-bounded, pH-neutral organelles similar to caveosomes but devoid of cav-1 and -2. The viruses were next transferred by microtubule-dependent vesicular transport to the ER, a step that was required for infectivity. Our results revealed the existence of a virus-activated endocytic pathway from the plasma membrane to the ER that involves neither clathrin nor caveolae and that can be activated also in the presence of cav-1.
Viral killer toxins induce caspase-mediated apoptosis in yeast
Authors: Reiter Jochen , Herker Eva , Madeo Frank , Schmitt Manfred J.
Published: January 2005

In yeast, apoptotic cell death can be triggered by various factors such as H2O2, cell aging, or acetic acid. Yeast caspase (Yca1p) and cellular reactive oxygen species (ROS) are key regulators of this process. Here, we show that moderate doses of three virally encoded killer toxins (K1, K28, and zygocin) induce an apoptotic yeast cell response, although all three toxins differ significantly in their primary killing mechanisms. In contrast, high toxin concentrations prevent the occurrence of an apoptotic cell response and rather cause necrotic, toxin-specific cell killing. Studies with Δyca1 and Δgsh1 deletion mutants indicate that ROS accumulation as well as the presence of yeast caspase 1 is needed for apoptosis in toxin-treated yeast cells. We conclude that in the natural environment of toxin-secreting killer yeasts, where toxin concentration is usually low, induction of apoptosis might play an important role in efficient toxin-mediated cell killing.
Limit–cycle oscillations of a heavy whirling cable subject to aerodynamic drag
Authors: Clark James David , Fraser Wynstone Barrie , Rahn Christopher David , Rajamani Arun
Published: January 2005

In this paper a simple experimental system consisting of a length of cable, fixed to the edge of a rotating disc at its upper end, and free at its lower end or with a point mass (drogue) attached there, is described. This system exhibits a rich variety of bifurcation behaviours as the length of cable, angular speed of the fixed end, mass of the drogue and elasticity of the cable is varied. Bifurcation diagrams for thequasistationaryconfigurations (cable shapes that appear stationary with respect to the rotating reference frame) are described. Linearized stability analyses of these quasistationary balloons are compared with solutions to the full time–dependent equations of motion.

It is shown that there is an exchange of stability at the turning points of the quasi–stationary bifurcation curves, and that Hopf bifurcations occur at otherwise undistinguished points of these curves. It is shown that limit–cycle oscillations of the system occur at angular speeds corresponding to points on the bifurcations curves in the neighbourhood of the Hopf bifurcation points. These oscillations have been observed experimentally.
Comparing the effects of genetic drift and fluctuating selection on genotype frequency changes in the scarlet tiger moth
Authors: O'Hara R. B.
Published: January 2005

One of the recurring arguments in evolutionary biology is whether evolution occurs principally through natural selection or through neutral processes such as genetic drift. A 60–year–long time series of changes in the genotype frequency of a colour polymorphism of the scarlet tiger moth,Callimorpha dominula, was used to compare the relative effects of genetic drift and variable natural selection. The analysis showed that most of the variation in frequency was the result of genetic drift. In addition, although selection was acting, mean fitness barely increased. This supports the ‘Red Queen's hypothesis’ that long–term improvements in fitness may not occur, because populations have to keep pace with changes in the environment.
Morphogenesis of the branching reef coralMadracis mirabilis
Authors: Kaandorp Jaap A. , Sloot Peter M. A. , Merks Roeland M. H. , Bak Rolf P. M. , Vermeij Mark J. A. , Maier Cornelia
Published: January 2005

Understanding external deciding factors in growth and morphology of reef corals is essential to elucidate the role of corals in marine ecosystems, and to explain their susceptibility to pollution and global climate change. Here, we extend on a previously presented model for simulating the growth and form of a branching coral and we compare the simulated morphologies to three–dimensional (3D) images of the coral speciesMadracis mirabilis. Simulation experiments and isotope analyses ofM. mirabilisskeletons indicate that external gradients of dissolved inorganic carbon (DIC) determine the morphogenesis of branching, phototrophic corals. In the simulations we use a first principle model of accretive growth based on local interactions between the polyps. The only species–specific information in the model is the average size of a polyp. From flow tank and simulation studies it is known that a relatively large stagnant and diffusion dominated region develops within a branching colony. We have used this information by assuming in our model that growth is entirely driven by a diffusion–limited process, where DIC supply represents the limiting factor. With such model constraints it is possible to generate morphologies that are virtually indistinguishable from the 3D images of the actual colonies.
Laying–sequence–specific variation in yolk oestrogen levels, and relationship to plasma oestrogen in female zebra finches (Taeniopygia guttata)
Authors: Williams Tony D. , Ames Caroline E. , Kiparissis Yiannis , Wynne-Edwards Katherine E.
Published: January 2005

We investigated the relationship between plasma and yolk oestrogens in laying female zebra finches (Taeniopygia guttata) by manipulating plasma oestradiol (E2) levels, via injection of oestradiol–17β, in a sequence–specific manner to maintain chronically high plasma levels for later–developing eggs (contrasting with the endogenous pattern of decreasing plasma E2 concentrations during laying). We report systematic variation in yolk oestrogen concentrations, in relation to laying sequence, similar to that widely reported for androgenic steroids. In sham–manipulated females, yolk E2 concentrationsdecreasedwith laying sequence. However, in E2–treated females plasma E2 levels were higher during the period of rapid yolk development of later–laid eggs, compared with control females. As a consequence, we reversed the laying–sequence–specific pattern of yolk E2: in E2–treated females, yolk E2 concentrationsincreasedwith laying–sequence. In general therefore, yolk E2 levels were a direct reflection of plasma E2 levels. However, in control females there was some inter–individual variability in the endogenous pattern of plasma E2 levels through the laying cycle which could generate variation in sequence–specific patterns of yolk hormone levels even if these primarily reflect circulating steroid levels.