bluuebunny/crossref_metadata_2025 huggingface dataset:
Impacts of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area
Authors: Sinigalliano C. D. , Gidley M. L. , Shibata T. , Whitman D. , Dixon T. H. , Laws E. , Hou A. , Bachoon D. , Brand L. , Amaral-Zettler L. , Gast R. J. , Steward G. F. , Nigro O. D. , Fujioka R. , Betancourt W. Q. , Vithanage G. , Mathews J. , Fleming L. E. , Solo-Gabriele H. M.
Published: May 2007

Floodwaters in New Orleans from Hurricanes Katrina and Rita were observed to contain high levels of fecal indicator bacteria and microbial pathogens, generating concern about long-term impacts of these floodwaters on the sediment and water quality of the New Orleans area and Lake Pontchartrain. We show here that fecal indicator microbe concentrations in offshore waters from Lake Pontchartrain returned to prehurricane concentrations within 2 months of the flooding induced by these hurricanes.
Vibrio
and
Legionella
species within the lake were more abundant in samples collected shortly after the floodwaters had receded compared with samples taken within the subsequent 3 months; no evidence of a long-term hurricane-induced algal bloom was observed.
Giardia
and
Cryptosporidium
were detected in canal waters. Elevated levels of fecal indicator bacteria observed in sediment could not be solely attributed to impacts from floodwaters, as both flooded and nonflooded areas exhibited elevated levels of fecal indicator bacteria. Evidence from measurements of
Bifidobacterium
and bacterial diversity analysis suggest that the fecal indicator bacteria observed in the sediment were from human fecal sources. Epidemiologic studies are highly recommended to evaluate the human health effects of the sediments deposited by the floodwaters.
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA
Authors: Bessho Yoshitaka , Shibata Rie , Sekine Shun-ichi , Murayama Kazutaka , Higashijima Kyoko , Hori-Takemoto Chie , Shirouzu Mikako , Kuramitsu Seiki , Yokoyama Shigeyuki
Published: May 2007

tmRNA and small protein B (SmpB) are essential trans-translation system components. In the present study, we determined the crystal structure of SmpB in complex with the entire tRNA domain of the tmRNA from
Thermus thermophilus
. Overall, the ribonucleoprotein complex (tRNP) mimics a long-variable-arm tRNA (class II tRNA) in the canonical L-shaped tertiary structure. The tmRNA terminus corresponds to the acceptor and T arms, or the upper part, of tRNA. On the other hand, the SmpB protein simulates the lower part, the anticodon and D stems, of tRNA. Intriguingly, several amino acid residues collaborate with tmRNA bases to reproduce the canonical tRNA core layers. The linker helix of tmRNA had been considered to correspond to the anticodon stem, but the complex structure unambiguously shows that it corresponds to the tRNA variable arm. The tmRNA linker helix, as well as the long variable arm of class II tRNA, may occupy the gap between the large and small ribosomal subunits. This suggested how the tRNA domain is connected to the mRNA domain entering the mRNA channel. A loop of SmpB in the tRNP is likely to participate in the interaction with alanyl-tRNA synthetase, which may be the mechanism for the promotion of tmRNA alanylation by the SmpB protein. Therefore, the tRNP may simulate a tRNA, both structurally and functionally, with respect to aminoacylation and ribosome entry.
Helical microtubule arrays in a collection of twisting tubulin mutants of
Arabidopsis thaliana
Authors: Ishida Takashi , Kaneko Yayoi , Iwano Megumi , Hashimoto Takashi
Published: May 2007

Anisotropic expansion of plant cells requires organized arrays of cortical microtubules. Mutations in microtubule-associated proteins and a particular mutation in α-tubulins were reported to cause abnormal microtubule arrays and result in helical growth in
Arabidopsis thaliana
. However, the way in which these mutations affect the organization of microtubules remains unknown. We here identified 32
Arabidopsis
twisting mutants that have either missense or amino acid deletion mutations in α- or β-tubulins. Mutations were mapped to the GTPase-activating region in α-tubulin, intra- and interdimer interfaces of tubulin heterodimers, and lateral contact regions among adjacent protofilaments. These dominant-negative tubulin mutants were incorporated into the microtubule polymer and formed shallow helical arrays of distinct handedness along the long axis of the root epidermal cells. A striking correlation exists between the direction in which cortical helical arrays are skewed and the growth direction of elongating roots. The GTPase-activating-region mutant had left-handed helical arrays composed of highly stabilized microtubules, which could be decorated along the entire microtubule lattices with the otherwise tip-localized End Binding 1 protein. A mutation at the intradimer interface, on the other hand, generated highly dynamic microtubules and right-handed helical arrays. Cortical microtubules in wild type and these two tubulin mutants were composed mainly of 13 protofilaments. This comprehensive analysis of tubulin mutations provides insights into the mechanism by which tubulin structures influence microtubule dynamics and organization.
Crystal structure of the Sec4p·Sec2p complex in the nucleotide exchanging intermediate state
Authors: Sato Yusuke , Fukai Shuya , Ishitani Ryuichiro , Nureki Osamu
Published: May 2007

Vesicular transport during exocytosis is regulated by Rab GTPase (Sec4p in yeast), which is activated by a guanine nucleotide exchange factor (GEF) called Sec2p. Here, we report the crystal structure of the Sec2p GEF domain in a complex with the nucleotide-free Sec4p at 2.7 Å resolution. Upon complex formation, the Sec2p helices approach each other, flipping the side chain of Phe-109 toward Leu-104 and Leu-108 of Sec2p. These three residues provide a hydrophobic platform to attract the side chains of Phe-49, Ile-53, and Ile-55 in the switch I region as well as Phe-57 and Trp-74 in the interswitch region of Sec4p. Consequently, the switch I and II regions are largely deformed, to create a flat hydrophobic interface that snugly fits the surface of the Sec2p coiled coil. These drastic conformational changes disrupt the interactions between switch I and the bound guanine nucleotide, which facilitates the GDP release. Unlike the recently reported 3.3 Å structure of the Sec4p·Sec2p complex, our structure contains a phosphate ion bound to the P-loop, which may represent an intermediate state of the nucleotide exchange reaction.
Rigidity-driven growth and migration of epithelial cells on microstructured anisotropic substrates
Authors: Saez Alexandre , Ghibaudo Marion , Buguin Axel , Silberzan Pascal , Ladoux Benoît
Published: May 2007

The physical properties of the cellular environment are involved in regulating the formation and maintenance of tissues. In particular, substrate rigidity appears to be a key factor dictating cell response on culture surfaces. Here we study the behavior of epithelial cells cultured on microfabricated substrates engineered to exhibit an anisotropic stiffness. The substrate consists of a dense array of micropillars of oval cross-section, so that one direction is made stiffer than the other. We demonstrate how such an anisotropic rigidity can induce directional epithelial growth and guide cell migration along the direction of greatest rigidity. Regions of high tractional stress and large cellular deformations within the sheets of cells are concentrated at the edges, in particular at the two poles of the islands along their long axis, in correlation with the orientation of actin stress fibers and focal adhesions. By inducing scattering activity of epithelial cells, we show that isolated cells also migrate along the direction of greatest stiffness. Taken together, these findings show that the mechanical interactions of cells with their microenvironment can be tuned to engineer particular tissue properties.
Activation-induced cytidine deaminase action is strongly stimulated by mutations of the THO complex
Authors: Gómez-González Belén , Aguilera Andrés
Published: May 2007

Activation-induced cytidine deaminase (AID) is a B cell enzyme essential for Ig somatic hypermutation and class switch recombination. AID acts on ssDNA, and switch regions of Ig genes, a target of AID, form R-loops that contain ssDNA. Nevertheless, how AID action is specifically targeted to particular DNA sequences is not clear. Because mutations altering cotranscriptional messenger ribonucleoprotein (mRNP) formation such as those in THO/TREX in yeast promote R-loops, we investigated whether the cotranscriptional assembly of mRNPs could affect AID targeting. Here we show that AID action is transcription-dependent in yeast and that strong and transcription-dependent hypermutation and hyperrecombination are induced by AID if cells are deprived of THO. In these strains AID-induced mutations occurred preferentially at WRC motifs in the nontranscribed DNA strand. We propose that a suboptimal cotranscriptional mRNP assembly at particular DNA regions could play an important role in Ig diversification and genome dynamics.
A gene from the cellulose synthase-like C family encodes a β-1,4 glucan synthase
Authors: Cocuron Jean-Christophe , Lerouxel Olivier , Drakakaki Georgia , Alonso Ana P. , Liepman Aaron H. , Keegstra Kenneth , Raikhel Natasha , Wilkerson Curtis G.
Published: May 2007

Despite the central role of xyloglucan (XyG) in plant cell wall structure and function, important details of its biosynthesis are not understood. To identify the gene(s) responsible for synthesizing the β-1,4 glucan backbone of XyG, we exploited a property of nasturtium (
Tropaeolum majus
) seed development. During the last stages of nasturtium seed maturation, a large amount of XyG is deposited as a reserve polysaccharide. A cDNA library was produced from mRNA isolated during the deposition of XyG, and partial sequences of 10,000 cDNA clones were determined. A single member of the C subfamily from the large family of
cellulose synthase-like
(
CSL
) genes was found to be overrepresented in the cDNA library. Heterologous expression of this gene in the yeast
Pichia pastoris
resulted in the production of a β-1,4 glucan, confirming that the CSLC protein has glucan synthase activity. The
Arabidopsis CSLC4
gene, which is the gene with the highest sequence similarity to the nasturtium
CSL
gene, is coordinately expressed with other genes involved in XyG biosynthesis. These and other observations provide a compelling case that the
CSLC
gene family encode proteins that synthesize the XyG backbone.
A phylogenetic Gibbs sampler that yields centroid solutions forcis-regulatory site prediction
Authors: Newberg Lee A. , Thompson William A. , Conlan Sean , Smith Thomas M. , McCue Lee Ann , Lawrence Charles E.
Published: May 2007

Motivation: Identification of functionally conserved regulatory elements in sequence data from closely related organisms is becoming feasible, due to the rapid growth of public sequence databases. Closely related organisms are most likely to have common regulatory motifs; however, the recent speciation of such organisms results in the high degree of correlation in their genome sequences, confounding the detection of functional elements. Additionally, alignment algorithms that use optimization techniques are limited to the detection of a single alignment that may not be representative. Comparative-genomics studies must be able to address the phylogenetic correlation in the data and efficiently explore the alignment space, in order to make specific and biologically relevant predictions.

Results: We describe here a Gibbs sampler that employs a full phylogenetic model and reports an ensemble centroid solution. We describe regulatory motif detection using both simulated and real data, and demonstrate that this approach achieves improved specificity, sensitivity, and positive predictive value over non-phylogenetic algorithms, and over phylogenetic algorithms that report a maximum likelihood solution.

Availability: The software is freely available at http://bayesweb.wadsworth.org/gibbs/gibbs.html

Contact:  William_Thompson_1@brown.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
STOP: searching for transcription factor motifs using gene expression
Authors: Hertzberg Libi , Izraeli Shai , Domany Eytan
Published: May 2007

Motivation: Existing computational methods that identify transcription factor (TF) binding sites on a gene's promoter are plagued by significant inaccuracies. Binding of a TF to a particular sequence is assessed by comparing its similarity score, obtained from the TF's known position weight matrix (PWM), to a threshold. If the similarity score is above the threshold, the sequence is considered a putative binding site. Determining this threshold is a central part of the problem, for which no satisfactory biologically based solution exists.

Results: We present here a method that integrates gene expression data with sequence-based scoring of TF binding sites, for determining a global score threshold for each TF. We validate our method, STOP (Searching TFs Of Promoters), in several ways: (1) we calculate the average expression values of groups of human putative target genes of each TF, and compare them to similar averages derived for random gene groups. The groups of putative targets show significantly higher relative average expression. (2) We find high consistency between the induced lists of putative targets in human and in mouse. (3) The expression patterns associated with human and mouse genes (ordered by PWM scores for each TF) exhibit high similarity between human and mouse, indicating that our method has firm biological basis. (4) Comparison of results obtained by STOP and PRIMA (Elkon et al., 2003) suggests that determining the score threshold using gene expression, as is done in STOP, is more biologically tuned.

Availability: Software package will be available for academic users upon request.

Contact:  eytan.domany@weizmann.ac.il

Supplementary information: Supplementary data are available on Bioinformatics online.
First Report of Powdery Mildew of Eschscholzia californica (California Poppy) caused by Erysiphe cruciferarum in North America
Authors: Glawe Dean A.
Published: May 2007

California poppy is an annual species grown widely in the Pacific Northwest. Once established, populations are self-seeding and require little care. During an ongoing study of Erysiphales, a powdery mildew fungus was collected repeatedly on this species in Seattle, WA. The fungus was determined to be Erysiphe cruciferarum Opiz ex Junell, a species not reported previously on this host in North America. This report documents the occurrence of the disease and provides information on the morphology and identification of the causal agent.

Accepted for publication 8 November 2006. Published 13 December 2006.
First Report of a Serenomyces sp. From Copernicia × burretiana, Latania loddigesii, and Phoenix canariensis in Florida and the United States
Authors: Elliott M. L. , Des Jardin E. A.
Published: May 2007

This is the first report of a Serenomyces sp. on Copernicia × burretiana, L. loddigesii, and P. canariensis in Florida and the United States.

Accepted for publication 6 November 2006. Published 13 December 2006.
First Report of Powdery Mildew Caused by Golovinomyces cichoracearum on Coreopsis leavenworthii
Authors: Seijo Teresa E. , Czarnecki David , Deng Zhanao , Peres Natalia A.
Published: May 2007

Leavenworth's tickseed (Coreopsis leavenworthii) is a native wildflower throughout Florida, and is grown commercially primarily for seed. In 2005, powdery mildew was observed on greenhouse-grown C. leavenworthii. The pathogen was identified as Golovinomyces cichorearum. This is the first report of G. cichoracearum infecting C. leavenworthii and the first report of it infecting any Coreopsis spp. in Florida.

Accepted for publication 25 October 2006. Published 14 December 2006.
Bacterial Diseases of Dry Edible Beans in the Central High Plains
Authors: Harveson Robert M. , Schwartz Howard F.
Published: May 2007

Dry beans may be affected by a number of distinct diseases, including four bacterial diseases often found occurring simultaneously in a complex. Three diseases are commonly encountered — common bacterial blight, halo blight, and bacterial brown spot — with a fourth disease (bacterial wilt) re-emerging in the Central High Plains after an absence of more than 30 years. The information in this guide may be used to identify and distinguish between the various bacterial diseases that may be encountered in dry bean production.

Accepted for publication 14 October 2006. Published 25 January 2007.
Potato Yield Increases Due to Fungicide Treatment in Argentinian Early Blight (Alternaria solani) and Late Blight (Phytophthora infestans) Field Trials During the 1996-2005 Seasons
Authors: Mantecón Jorge D.
Published: May 2007

The effect of fungicides on potato yields in separate early blight and late blight trials during the 1996 to 2005 growing seasons at the INTA Balcarce experimental station was determined. Potato cultivars Pampeana INTA were used for early blight trials while Kennebec ones were used for late blight trials. A randomized complete block design with four replications was used in all trials. The fungicides Folicur 25EC at 0.5 liter/ha and Brestan 60WP at 0.5 kg/ha were tested in early blight trials while Dithane M80WP at 2.5 kg/ha and Ridomil Gold 68WP at 1.25 kg/ha were tested in late blight trials. Early blight infections were rated using a 0 to 50 a rating scale. Late blight severity was rated using a disease index of 0 to 5. Potatoes were graded into two categories, marketable (> 60 g) and undersize tuber “seeds” (< 60 g), and then weighed. Data was subjected to analysis of variance. Early and late blight symptoms were present every season. In early blight trials, the efficacy of the systemic fungicide Folicur 25EC was greater than that of the non-systemic Brestan 60WP. The average yield increase due to fungicide treatment during the ten-year period was 22.4% for marketable and 17.9% for total yield. In late blight trials the efficacies of Dithane M80WP and Ridomil Gold 68WP were similar. The average yield increase due to fungicide treatment during the study was 41.23% for marketable and 33.85% for total yield.

Accepted for publication 23 October 2006. Published 2 February 2007.
First Report of Fusarium circinatum, Causal Agent of Pitch Canker Disease, from the Roots of Mature Aleppo Pines in California
Authors: Garbelotto M. , Schweigkofler W. , Shaw D.
Published: May 2007

A rapid decline of Aleppo pines was observed in the parking lot of the Legoland amusement park in San Diego Co., CA. Although Aleppo pine is a known host for Fusarium circinatum, this is the first report describing resin-soaked sapwood lesions in the roots of mature trees. Previous reports on root infections regarded seedlings. The infestation in this location may have begun with infected roots in planted saplings. The persistent infestation at Legoland represents a significant source of inoculum for this pathogen exotic to California.

Accepted for publication 7 June 2006. Published 19 February 2007.
Potential for Soybean Cyst Nematode Reproduction on Winter Weeds and Cover Crops in Tennessee
Authors: Donald P. A. , Hayes Robert , Walker Eric
Published: May 2007

The soybean cyst nematode (SCN), Heterodera glycines, is a major yield limiting pest of soybean (Glycine max). Current SCN management strategies include resistant soybean varieties and rotation with non-host crops. Increased adoption of the early soybean production system (ESPS) combined with a greater incidence of winter weeds from no-tillage practices may increase the population density of SCN during the noncrop period since several winter weeds and cover crops are hosts for SCN. A field experiment with a split-strip design was conducted over three years to evaluate whether SCN reproduced on weeds and cover crops during the noncrop period. Winter weeds and crimson clover roots were examined for females and cysts with eggs. The soil was sampled to determine if an increase in SCN egg population density occurred. We found no indication of SCN reproduction on winter weeds during the noncrop period or on the cover crop crimson clover.

Accepted for publication 2 November 2006. Published 26 February 2007.
Desiccation at Ambient Temperature Effectively Preserves Plant Tissues Infected with Phytophthoras
Authors: Ockels Frances S. , DiLeo Matthew V. , Bonello Pierluigi
Published: May 2007

Conventionally, plant samples collected in the course of field surveys for Phytophthora spp. (e.g., in the context of the US Forest Service-sponsored national P. ramorum survey of forest environments) are either processed immediately or stored at low temperatures and processed as soon as possible for detection by molecular methods. In order to extend the useful life of the sample, a method involving tissue desiccation was explored for effectively storing Phytophthora-infected plant leaves. In one experiment, rhododendron leaves inoculated with an unknown Phytophthora sp. and desiccated for seven days yielded DNA of sufficient quality for species identification via sequencing of the ITS region. In a second experiment, P. ramorum was successfully detected by PCR in inoculated leaves of California bay laurel, California buckeye, bigleaf maple, rhododendron, and viburnum that were desiccated and stored at room temperature for four months. Therefore, desiccation might be a viable, reliable, and less expensive alternative to storing foliar samples at low temperature.

Accepted for publication 11 November 2006. Published 2 March 2007.
Phytophthora citricola Causes a Stem Canker in Black Walnut (Juglans nigra)
Authors: Beckerman Janna , Ruhl Gail
Published: May 2007

Black walnut (Juglans nigra) is considered a premier species in the lumber industry. To our knowledge, this is the first report of Phytophthora citricola causing a stem canker on black walnut in North America.

Accepted for publication 22 December 2006. Published 20 April 2007.
First Report of Melampsora euphorbiae on Poinsettia (Euphorbia pulcherrima) in Norway
Authors: Gjærum H. B. , Talgø V. , Toppe B. , Herrero M. L. , Stensvand A.
Published: May 2007

Melampsora euphorbiae (Schub.) Cast. is reported from all continents but Antarctica. The rust fungus is living on a great number of Euphorbia species. In Norway it is found on five Euphorbia species (wild growing or cultivated outdoors), including the common weed sun spurge. To our knowledge M. euphorbiae on poinsettia has previously been reported only three times, namely in India, Tanzania, and Mauritius.

Accepted for publication 16 December 2006. Published 23 April 2007.
Estimated Economic Losses Associated with the Destruction of Plants Due to Phytophthora ramorum Quarantine Efforts in Washington State
Authors: Dart Norman L. , Chastagner Gary A.
Published: May 2007

The number and retail value of plants destroyed in Washington State nurseries due to Phytophthora ramorum quarantine efforts was estimated using Emergency Action Notification forms (EANs) issued by the United States Department of Agriculture Animal and Plant Health Inspection Service between 2004 and 2005. Data collected from EANs indicate that during this period 17,266 containerized nursery plants were destroyed at 32 nurseries, worth an estimated $423,043. The mean loss per nursery was estimated at $11,188 in 2004, $11,798 in 2005, and at $13,220 per nursery over the 2-year period.

Accepted for publication 26 January 2007. Published 8 May 2007.
Lip Incompetence and Psychosocial Effects: A Pilot Study
Authors: de Oliveira Domingos Savio Ferreira , Atherino Ciriaco Cristóvão Tavares , Cervasio Marina Ribeiro , de Melo Cruz Gerarda , Cervasio Olivia Ribeiro , Bruggeman Heleen , Cornelis Liesbeth , Haspeslagh Lieve , Van Borsel John
Published: May 2007

Objective: The purpose of the study was to determine whether children are more negatively perceived because of a lip incompetence.

Study Design: A sample survey study.

Methods: Two sets of colored pictures (1 set with the mouth open and 1 set with the mouth closed) were taken of four children with lip incompetence and mouth breathing and four children with normal lip closure and breathing patterns. These pictures were presented to a group of judges in Belgium and Brazil. Judges were presented either pictures of the closed mouth sets or pictures of the open mouth sets and were asked to rate on a 10‐point scale the chance that the child was shy, had few friends, belonged to a lower socioeconomic class, had problems with reading, writing, or arithmetic, had ever manifested thumb‐sucking, and had difficulties breathing through the nose. In each child, scores obtained for the open mouth set were compared with those obtained for the closed mouth set.

Results: There was no consistent pattern of higher scores being assigned to the pictures of the open mouth set, neither in the Belgian survey nor in the Brazilian survey.

Conclusion: Contrary with past and present claims, results suggest that children with a lip incompetence are not necessarily perceived negatively.
Body size evolution simultaneously creates and collapses species boundaries in a clade of scincid lizards
Authors: Richmond Jonathan Q , Jockusch Elizabeth L
Published: May 2007

Speciation is generally viewed as an irreversible process, although habitat alterations can erase reproductive barriers if divergence between ecologically differentiated species is recent. Reversed speciation might also occur if geographical contact is established between species that have evolved the same reproductive isolating barrier in parallel. Here, we demonstrate a loss of intrinsic reproductive isolation in a clade of scincid lizards as a result of parallel body size evolution, which has allowed for gene flow where large-bodied lineages are in secondary contact. An mtDNA phylogeny confirms the monophyly of thePlestiodon skiltonianusspecies complex, but rejects that of two size-differentiated ecomorphs. Mate compatibility experiments show that the high degree of body size divergence imposes a strong reproductive barrier between the two morphs; however, the strength of the barrier is greatly diminished between parallel-evolved forms. Since two large-bodied lineages are in geographical contact in the Sierra Nevada Mountains of California, we were also able to test for postzygotic isolation under natural conditions. Analyses of amplified fragment length polymorphisms show that extensive gene exchange is occurring across the contact zone, resulting in an overall pattern consistent with isolation by distance. These results provide evidence of reversed speciation between clades that diverged from a common ancestor more than 12 Myr ago.
Economic principles motivating social attention in humans
Authors: Hayden Benjamin Y , Parikh Purak C , Deaner Robert O , Platt Michael L
Published: May 2007

We know little about the processes by which we evaluate the opportunity to look at another person. We propose that behavioural economics provides a powerful approach to understanding this basic aspect of social attention. We hypothesized that the decision process culminating in attention to another person follows the same economic principles that govern choices about rewards such as food, drinks and money. Specifically, such rewards are discounted as a function of time, are tradable for other rewards, and reinforce work. Behavioural and neurobiological evidence suggests that looking at other people can also be described as rewarding, but to what extent these economic principles apply to social orienting remains unknown. Here, we show that the opportunity to view pictures of the opposite sex is discounted by delay to viewing, substitutes for money and reinforces work. The reward value of photos of the opposite sex varied with physical attractiveness and was greater in men, suggesting differential utility of acquiring visual information about the opposite sex in men and women. Together, these results demonstrate that choosing whom to look at follows a general set of economic principles, implicating shared neural mechanisms in both social and non-social decision making.
Sex‐specific differences in compensation for poor neonatal nutrition in the zebra finchTaeniopygia guttata
Authors: E. Arnold Kathryn , D. Blount Jonathan , B. Metcalfe Neil , J. Orr Kate , Adam Aileen , Houston David , Monaghan Pat
Published: May 2007

Individuals can compensate for poor early nutrition by accelerating their growth rates once diet improves, but if malnutrition occurs at a key stage of development only certain body structures may compensate fully. This degrees of compensation is predicted to differ between the sexes and also between species with different life history strategies. In this paper we determine how males and females in a short‐lived bird species, with only slight size dimorphism, differ in their abilities to compensate for a poor start in life. Here, zebra finchTaeniopygia guttatachicks from 93 broods were reared on either a standard quality (SQ), or low quality (LQ) diet for the first 15 d of life, followed by a standard diet for the rest of their lives. Thus, the period of nutritional manipulation was relatively short compared with previous studies. Nestlings on a LQ diet showed slower body mass and tarsus growth rates than those on SQ diet but this was reversed after the diet of the LQ birds was improved. LQ birds of both sexes were able to fully compensate in terms of body mass and beak colour, but not tarsus length. Body size and beak colour are sexually selected traits in male zebra finches. By adulthood LQ females had significantly shorter wings than other birds, apparently directing resources into sex‐specific structures instead of feather and skeletal growth. Thus, our experiment showed that the sexes differed in how they phenotypically compensated for a poor start in life. Males in particular invested sparse resources into structures associated with mate acquisition, as proposed by life history theory for a species that ‘lives fast and dies young.’ We predict that this relatively short period of malnutrition during early development will have long term, sex‐specific, fitness consequences for these birds.
Timing of copulations and the pattern of paternity in relation to laying order in tree swallows Tachycineta bicolor
Authors: A. Barber Colleen , J. Robertson Raleigh
Published: May 2007

It is well established that extra‐pair young are present to varying degrees in nests of most avian species. However, the timing of extra‐pair copulations during a female's fertile cycle is not well known, nor is how these copulations translate into the distribution of extra‐pair young within the laying sequence. We determined the rates of successful within‐pair copulations where at least one cloacal contact was achieved, and the number of extra‐pair copulations/attempts in 17 pairs of tree swallows Tachycineta bicolor during the mornings encompassing the female's fertile period. We also examined nestling paternity with respect to laying order in eighteen mixed‐paternity tree swallow broods. The rate of successful within‐pair copulations peaked three days prior to a female laying her first egg, and decreased steadily throughout the laying period. We therefore predicted that extra‐pair young would be more likely to hatch out of later‐laid than earlier‐laid eggs within a female's brood. We found no evidence of an increased frequency of extra‐pair young with laying order. Instead, extra‐pair young appear to be randomly distributed within the laying sequence of tree swallows.
Serum M‐spike and transplant outcome in patients with multiple myeloma
Authors: Dingli David , Pacheco Jorge M. , Dispenzieri Angela , Hayman Suzanne R. , Kumar Shaji K. , Lacy Martha Q. , Gastineau Dennis A. , Gertz Morie A.
Published: May 2007

High dose therapy with autologous stem cell transplantation (HDT‐ASCT) has prolonged survival in patients with multiple myeloma. Patients who achieve a complete response (CR) benefit the most from this form of therapy. Thus, achieving a CR is an important goal of therapy and it will be beneficial if the probability of achieving CR can be determined for any patient before transplant. Here we report that pretransplant monoclonal protein level (M‐spike) was found to be an important predictor. Thus, we used knowledge of the rate of M‐protein production by myeloma cells together with the clearance of the protein to estimate the pretransplant disease burden. We show that the pretransplant disease burden, based on the M‐spike, is the only predictor for achieving CR. A simple function that describes this probability is presented. We also provide an estimate of the rate of tumor regrowth in patients who obtain a CR and in patients who only get a partial response with HDT‐ASCT. The significant expansion of myeloma cells after HDT‐ASCT is clearly evident. Clinical trials must be designed that take into account these kinetic aspects of the disease. (Cancer Sci 2007; 98: 1035–1040)
Partitioning the diversity of riverine fish: the roles of habitat types and non‐native species
Authors: ERőS TIBOR
Published: May 2007

1. Quantifying how biological diversity is distributed in the landscape is one of the central themes of conservation ecology. For this purpose, landscape classifications are being intensively used in conservation planning and biodiversity management, although there is still little information about their efficacy.

2. I used data from 158 running water sites in Hungary to examine the contribution of six a priori established habitat types to regional level diversity of fish assemblages. Three community measures [species richness, diversity (Shannon, Simpson indices), assemblage composition] were examined at two assemblage levels (entire assemblage, the native assemblage). The relative role of non‐native species was quantified to examine their contribution to patterns in diversity in this strongly human influenced landscape.

3. Additive diversity partitioning revealed the primary importance of beta diversity (i.e. among‐site factors) to patterns in species richness. Landscape‐scale patterns in species richness were best explained by between‐habitat type (beta2: 41.2%), followed by within‐habitat type (beta1: 37.7%) and finally within‐site (alpha: 21.1%) diversity. Diversity indices showed patterns different from species richness, indicating the importance of relative abundance distributions on the results. Exclusion of non‐natives from the analysis gave similar results to the entire‐assemblage level analysis.

4. Canonical analysis of principal coordinates, complemented with indicator species analysis justified the separation of fish assemblages among the habitat types, although classification error was high. Multivariate dispersion, a measure of compositional beta diversity, showed significant differences among the habitat types. Contrary to species diversity (i.e. richness, diversity indices), patterns in compositional diversity were strongly influenced by the exclusion of non‐natives from the analyses.

5. This study is the first to quantify how running water habitat types contribute to fish diversity at the landscape scale and how non‐native species influence this pattern. These results on riverine fish assemblages support the hypothesis that environmental variability (i.e. the diversity of habitat types) is an indication of biodiversity and can be used in large‐scale conservation designs. The study emphasises the joint application of additive diversity partitioning and multivariate statistics when exploring the contribution of landscape components to the overall biodiversity of the landscape mosaic.
Annual carbon fixation in terrestrial populations of Nostoc commune (Cyanobacteria) from an Antarctic dry valley is driven by temperature regime
Authors: NOVIS PHIL M. , WHITEHEAD DAVID , GREGORICH ED G. , HUNT JOHN E. , SPARROW ASHLEY D. , HOPKINS DAVID W. , ELBERLING BO , GREENFIELD LAURIE G.
Published: May 2007

Nostoc commune Vaucher (a cyanobacterium) is a very conspicuous terrestrial primary producer in Victoria Land, continental Antarctica. Because polar ecosystems are considered to be especially sensitive to environmental changes, understanding the environmental constraints on net carbon (C) fixation by N. commune is necessary to determine the effects of environmental changes on the ecological functioning of ice‐free areas of the continent. A model describing net C fixation in terrestrial populations of N. commune in an Antarctic dry valley was constructed using field and laboratory measurements in which N. commune colonies were exposed to different combinations of incident irradiance (400–700 nm), temperature, and degree of desiccation. For desiccated N. commune mats with water content ≤ 30% saturation, net C fixation was highly variable between replicates and could not be modelled. However, for colonies at > 30% saturation, rates of net C fixation and dark respiration depended strongly on irradiance and temperature. Net C fixation reached a maximum rate of 21.6 μg C m− 2 s− 1 at irradiance of approximately 250 μmol m− 2 s− 1 and the optimum temperature of 20.5 °C. Agreement between predicted short‐term net C fixation and field and laboratory measurements allowed estimation of total seasonal fixation, using previously published environmental data. Annual net C fixation was estimated in the range 14.5–21.0 g C fixed m− 2Nostoc mat, depending on year/season. Estimates for different seasons correlated with thermal time (accumulated hours above 0 °C during the year) rather than irradiance, in contrast to communities in local lacustrine environments, where irradiance is the main driver of primary productivity. In the terrestrial habitat, N. commune appears to compromise between an ability to capitalize on short periods of higher temperature and efficient utilization of lower irradiance at low temperature. The relationship between thermal time and net annual C fixation by N. commune is strongly linear.
Orthopaedic limb salvage with a mega prosthesis in a patient with haemophilia A and inhibitors – a case report
Authors: STUMPF U. C. , EBERHARDT C. , KURTH A. A.
Published: May 2007

Summary.  Inhibitors against FVIII or FIX in patients with haemophilia are a common and serious complication. Until recently, elective surgery was associated with major bleeding despite the availability of a sufficient substitution therapy. We report about the major orthopaedic reconstruction of the right limb in a patient with severe haemophilia A and inhibitors. This reconstruction was the after effect of a traumatic periprosthetic fracture of the right femur after total knee replacement 6 months ago. This fracture could be stabilized by internal fixation. Two months later, a non‐traumatic femur fracture occurred. Therefore, we removed the distal part of the femur and the joint replacement, and implanted a custom made tumour prosthesis (Type MUTARS ©, Münster). These three successive operations, which included emergency and elective surgery, were performed within 8 months. This is, to the best of our knowledge, the first patient with inhibitors undergoing such a complicated reconstruction of a limb. We conclude that successful elective orthopaedic surgery could be accomplished safely in this patient with high responding inhibitors using recombinant FVIIa. After a follow‐up of 9 months, no major complications were seen.
Should prophylaxis be used in adolescent and adult patients with severe haemophilia? An European survey of practice and outcome data
Authors: RICHARDS M. , ALTISENT C. , BATOROVA A. , CHAMBOST H. , DOLAN G. , DE MOERLOOSE P. , FRAGA M. , HERMANS C. , KARAFOULIDOU A. , KLAMROTH R. , LASSILA R. , ROTHSCHILD C. ,   ON BEHALF OF THE EUROPEAN HAEMOPHILIA THERAPY STANDARDISATION BOARD
Published: May 2007

Summary.  A survey of 21 haemophilia doctors, throughout Europe, who care for a total of approximately 5000 patients with bleeding disorders addressing practice and opinions regarding prophylaxis in patients aged 16–24 years and adults aged over 50 years, is presented. The outcome of adolescent patients who reduced or stopped prophylaxis was recorded. Eighteen of 19 respondents would consider modification of established prophylaxis in the adolescent age group, principal considerations being avoidance of risks of further concentrate exposure, predicted poor compliance and treatment costs. The preferred age for modification was 16–20 years, but there was very little consensus on the particular prophylactic regime recommended. Approximately, half of a cohort of 218 patients with severe haemophilia successfully reduced or stopped prophylaxis when they reached adolescence. Only 26 of 92 (28%) of the patient cohort who stopped prophylaxis, required reintroduction of a prophylactic regime and 12 of 59 (20%) of those who reduced the intensity of prophylaxis had to reintroduce a more intensive regime. A majority of respondents would consider starting prophylaxis in those over 50 years. There was no consensus as to indications for this practice or the nature of the prophylaxis protocol. We conclude that there is an absence of consensus on the management of patients with severe haemophilia, as they pass through adolescence and young adulthood, and reach the age of 50. Aggregate outcome data suggest a significant proportion of patients in the 18–22 years age range may be able to reduce or stop prophylaxis. A substantial number of older patients are on prophylaxis.
Lipopolysaccharide enhances in vivo interleukin‐2 production and proliferation by naive antigen‐specific CD4 T cells via a Toll‐like receptor 4‐dependent mechanism
Authors: Costalonga Massimo , Zell Traci
Published: May 2007

Microbial adjuvants are essential for the development of T‐cell‐dependent antibody production, recall T‐cell proliferation and interferon‐γ production following immunization with protein antigens. Using an adoptive transfer approach, we showed that the adjuvant lipopolysaccharide enhanced the frequency of cells producing interleukin‐2, enhanced clonal expansion by antigen‐specific CD4 T cells and increased CD86 and interleukin‐1α production by antigen‐presenting cells. All of these effects were dependent on Toll‐like receptor‐4 (TLR4) expression by cells other than the antigen‐specific CD4 T cells. The ability of lipopolysaccharides to increase the number of antigen‐specific CD4 T cells that survive after immunization probably explains the previous finding that antigen‐specific proliferation by T cells from normal mice depends on previous exposure to antigen and adjuvant.
Expression of 5‐lipoxygenase (5‐LOX) in T lymphocytes
Authors: Cook‐Moreau Jeanne M. , El‐Makhour Hojeij Yola , Barrière Guislaine , Rabinovitch‐Chable Hélène C. , Faucher Karine S. , Sturtz Franck G. , Rigaud Michel A.
Published: May 2007

5‐lipoxygenase (5‐LOX) is the key enzyme responsible for the synthesis of the biologically active leukotrienes. Its presence has been reported in cells of the myeloid lineage and B lymphocytes but has not been formally defined in T lymphocytes. In this study, we provide evidence for 5‐LOX expression on both transcriptional and translational levels in highly purified peripheral blood T cells as well as in human T lymphoblastoid cell lines (MOLT4 and Jurkat). Messenger RNA (mRNA) of 5‐LOX was amplified by conventional reverse transcription–polymerase chain reaction (RT‐PCR; MOLT4 and Jurkat cells) and by in situ RT‐PCR (T lymphocytes). 5‐LOX protein expression was confirmed by Western blot and immunofluorescence studies. 5‐LOX was present primarily in the cytoplasm with some nuclear localization and was translocated to the nuclear periphery after culture in a mitosis‐supporting medium. Fluorescence‐activated cell sorter analysis of different T‐lymphocyte populations, including CD4, CD8, CD45RO, CD45RA, T helper type 2, and T‐cell receptor‐αβ and ‐γδ expressing cells, did not identify a differential distribution of the enzyme. Purified peripheral blood T lymphocytes were incapable of synthesizing leukotrienes in the absence of exogenous arachidonic acid. Jurkat cells produced leukotriene C4 and a small amount of leukotriene B4 in response to CD3–CD28 cross‐linking. This synthesis was abolished by two inhibitors of leukotriene synthesis, MK‐886 and AA‐861. The presence of 5‐LOX in T lymphocytes but the absence of endogenous lipoxygenase metabolite production compared to Jurkat cells may constitute a fundamental difference between resting peripheral lymphocytes and leukaemic cells.
Structure of the sulfakinin cDNA and gene expression from the Mediterranean field cricket Gryllus bimaculatus
Authors: Meyering‐Vos M. , Müller A.
Published: May 2007

The sulfakinins are multifunctional insect neuropeptides displaying sequence similarities with the gastrin/ cholecystokinin (CCK) peptide family. In vertebrates, the peptides gastrin and CCK are involved in the regulation of digestion and food‐intake. In this study sulfakinin cDNA was cloned and sequenced from the Mediterranean field cricket Gryllus bimaculatus. The cDNA encodes two peptides flanked by endoproteolytic processing sites, designated GrybiSKI (QSDDYGHMRFG) and GrybiSKII (EPFDDYGHMRFG). The peptides include the characteristic amino acid Tyr, which is potentially sulphated, and a Gly, as a recognition site for amidation yeilding the common C‐terminal amino acid sequence of the sulfakinin peptide family. RT‐PCR studies indicate an expression of the gene restricted to the brain, with a constant level of expression throughout the last larval stage, but showing an age‐dependent decrease of expression in adult females.
Erectile dysfunction is associated with low bioactive testosterone levels and visceral adiposity in men with type 2 diabetes
Authors: Kapoor D. , Clarke S. , Channer K. S. , Jones T. H.
Published: May 2007

Low testosterone levels in men are associated with type 2 diabetes mellitus. Erectile dysfunction (ED) is a frequent complication of type 2 diabetes. The aim of our cross‐sectional study was to investigate the relationship between ED and total, bioavailable and free testosterone levels in 198 men with type 2 diabetes. In addition, we examined the associations of various cardiovascular risk factors involved in the development of ED in type 2 diabetic men. We found that bioavailable and free testosterone levels were significantly lower in men with ED (p = 0.006 and 0.027 respectively) than those without ED. Sex hormone‐binding globulin levels were also reduced, but there was no significant difference in total testosterone (TT) levels between men with and without ED. The severity of ED as assessed by International Index of Erectile Function scores was significantly associated with TT (r = 0.32; p < 0.001), bioavailable testosterone (r = 0.32; p < 0.001) and calculated free testosterone (r = 0.35; p < 0.001) levels. ED was more frequently observed in men with hypertension and a higher waist circumference (p = 0.03). There was also a higher prevalence of ED among smokers (p = 0.06), but there were no significant associations between ED and alcohol consumption or with BMI > 30. This study has shown that ED is associated with low bioavailable and free testosterone levels, age, visceral adiposity and hypertension in type 2 diabetic men.