bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and characterisation of sulfur-oxidising bacteria, including strains of Rhizobium, from calcareous sandy soils and their effects on nutrient uptake and growth of maize (Zea mays L.)
Authors: El-Tarabily Khaled A. , Soaud Abdou A. , Saleh Maher E. , Matsumoto Satoshi
Published: January 2006

Four sulfur-oxidising bacteria were selected among 427 bacterial isolates from calcareous sandy soils in the United Arab Emirates (UAE). These isolates were selected based on their strong ability to oxidise elemental sulfur (S°) in vitro and were identified as Paracoccus versutus CBS 114155, Paracoccus pantotrophus CBS 114154, and 2 strains as Rhizobium spp. NCCB 100053 and NCCB 100054. This is the first published report of a Rhizobium species capable of S° oxidation and also the first record of sulfur-oxidising bacteria from UAE soils. These isolates were tested in a greenhouse in the presence and absence of S° to study their effects on maize growth. Best growth was observed in the treatment with P. versutus application combined with S°, which significantly reduced soil pH, increased soil SO4 level and the uptake of N, S, Fe, Mn, and Zn in maize roots and shoots. The P and Cu uptake in the shoots of maize plants was not significant compared with the treatment that received the application of S° alone. There was no response in plant growth to treatments that included the application of S° combined with P. pantotrophus or Rhizobium strain NCCB 100053 compared with the treatment that received the application of S° alone. There was significant growth inhibition of maize plants in the treatment receiving Rhizobium strain NCCB 100054 with or without the application of S° compared with the treatment that included the application of S° alone. This growth inhibition was associated with a significant decrease in the levels of N, P, S, Fe, Mn, Zn, and Cu in roots and shoots in the absence of S°. Rhizobium strain NCCB 100054 applied with S° significantly decreased the levels of N, S, and Fe in the roots and the levels of N, P, S, Fe, Mn, and Cu in the shoots of maize, with no significant differences in the levels of P and Mn in the roots and in the levels of Zn in the shoots, compared with the treatment with S° alone. These results indicate that the treatment P. versutus combined with S° can be effective as a soil conditioner for horticultural production in calcareous sandy soils.
Cultivar differences in yield distribution patterns in okra [Abelmoschus esculentus (L.) Moench]
Authors: Düzyaman Eftal
Published: January 2006

A total of 15 okra cultivars of Indian, Turkish, West African, and United States origin with diverse plant traits were selected to investigate the distribution patterns of yield throughout the harvest period. The proportion of fruits harvested up to mid-harvest period (FMH) was calculated for each cultivar and taken as a criterion in transforming yield distribution patterns into numerical variables. Cultivars showed a gradation for FMH values ranging from 64.5% to 30.7%. High FMH values were exclusively found in the Indian cultivars, whilst there was no origin-specificity for lower FMH values. Most parts of the plant architecture were associated with FMH. When moving from lower to higher FMH values, the number of lateral branches and consequently the proportion of yield carried by the lateral branches decreased (both at P < 0.001) and flowering initiated earlier (P < 0.001). However, plants showed reduced mean stem diameter (P < 0.05), leaf area (P < 0.001), and fruit weight (P < 0.05). Hence, fewer generative nodes per plant were formed (P < 0.001). However, the proportion of generative nodes translated into fruits was higher (P < 0.001), and consequently a greater number of fruits per plant was harvested (P < 0.01). Coefficient of determination (R 2) analysis revealed that a multiple regression model containing the 3 traits most correlated with FMH [number of days to flowering (r = –0.89), first flowering node (r = –0.84), proportion of generative nodes translated into fruits (r = 0.80)] explained 85% of the variation in FMH. Number of days to flowering alone explained 79% and a complex regression model containing all variables (10 variables) explained 90%. Traits associated with yield distribution patterns may be considered in introducing cultivars to different ecological and production systems, as well as in selection for breeding lines.
Influences on the loin and cellular characteristics of the m. longissimus lumborum of Australian Poll Dorset-sired lambs
Authors: Greenwood P. L. , Davis J. J. , Gaunt G. M. , Ferrier G. R.
Published: January 2006

Offspring of 4 Poll Dorset rams differing in eye muscle depth estimated breeding values (EBVs) were studied to determine sire, sex, and nutritional influences on cellular characteristics in the longissimus lumborum muscle. At 12 weeks of age, 62 lambs were individually fed a concentrate diet with or without protected nutrients ad libitum for 120 days while 39 lambs were grazed on improved pasture. Sire influenced the percentages of type 2A and 2B/2X myofibres, but not myofibre number or size. Progeny of the highest eye muscle depth EBV ram had less type 2A and more 2B/2X myofibres than the lowest ranking sire. At equivalent carcass weight, amount of RNA and protein in the longissimus muscle was influenced by sire, consistent with differences in eye muscle depth EBVs. Sex had little effect on muscle cellular characteristics, whereas lambs fed pasture had less type 1 myofibres than those fed concentrates and had less muscle RNA and a higher ratio of protein to RNA. The findings demonstrate differences in m. longissimus lumborum cellular characteristics in offspring of sires differing in muscle EBVs. The extent to which these differences relate to the Carwell muscle hypertrophy gene remains to be determined.
The accumulation of high molecular weight glutenin subunits (HMW-GS) and their relation to dough rheological quality in Chinese winter wheat
Authors: Deng Zhiying , Tian Jichun , Hu Ruibo
Published: January 2006

Six winter wheat cultivars were categorised into high gluten, medium gluten, and low gluten according to their protein content and gluten index. The object of this study was to determine the accumulation of high molecular weight glutenin subunits (HMW-GS) and their relationship to dough rheological quality. They were grown in 3 replicates on experimental plots at the Shandong Agricultural University research farm in 2001. HMW-GS compositions during grain development were investigated by SDS-PAGE procedures, followed by imaging densitometry to determine quantitative variations. Initial formation time of HMW-GS was different among cultivars. HMW-GS in cultivars with high gluten had formed completely by 10 days after anthesis, but were still only partially formed at this time in cultivars having weak gluten. Accumulation quantities of HMW-GS followed with grain development. Individual HMW-GS accumulated rapidly between 25 days after anthesis and maturity. The kinetic accumulation trend for the individual HMW-GS was similar in the same type of cultivars, but quantities were different. Strong cultivars had more kinetic accumulation quantities of HMW-GS than weak cultivars. HMW-GS kinetic accumulation quantities during grain development were significantly positively correlated with dough rheological characteristics and SDS-sedimentation volume.
In situ
labeling of immune cells with iron oxide particles: An approach to detect organ rejection by cellular MRI
Authors: Wu Yijen L. , Ye Qing , Foley Lesley M. , Hitchens T. Kevin , Sato Kazuya , Williams John B. , Ho Chien
Published: January 2006

In vivo
cell tracking by MRI can provide means to observe biological processes and monitor cell therapy directly. Immune cells, e.g., macrophages, play crucial roles in many pathophysiological processes, including organ rejection, inflammation, autoimmune diseases, cancer, atherosclerotic plaque formation, numerous neurological disorders, etc. The current gold standard for diagnosing and staging rejection after organ transplantation is biopsy, which is not only invasive, but also prone to sampling errors. Here, we report a noninvasive approach using MRI to detect graft rejection after solid organ transplantation. In addition, we present the feasibility of imaging individual macrophages
in vivo
by MRI in a rodent heterotopic working-heart transplantation model using a more sensitive contrast agent, the micrometer-sized paramagnetic iron oxide particle, as a methodology to detect acute cardiac rejection.
Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: Implications for therapy
Authors: Tovar Christian , Rosinski James , Filipovic Zoran , Higgins Brian , Kolinsky Kenneth , Hilton Holly , Zhao Xiaolan , Vu Binh T. , Qing Weiguo , Packman Kathryn , Myklebost Ola , Heimbrook David C. , Vassilev Lyubomir T.
Published: January 2006

The p53 tumor suppressor retains its wild-type conformation and transcriptional activity in half of all human tumors, and its activation may offer a therapeutic benefit. However, p53 function could be compromised by defective signaling in the p53 pathway. Using a small-molecule MDM2 antagonist, nutlin-3, to probe downstream p53 signaling we find that the cell-cycle arrest function of the p53 pathway is preserved in multiple tumor-derived cell lines expressing wild-type p53, but many have a reduced ability to undergo p53-dependent apoptosis. Gene array analysis revealed attenuated expression of multiple apoptosis-related genes. Cancer cells with
mdm2
gene amplification were most sensitive to nutlin-3
in vitro
and
in vivo
, suggesting that MDM2 overexpression may be the only abnormality in the p53 pathway of these cells. Nutlin-3 also showed good efficacy against tumors with normal MDM2 expression, suggesting that many of the patients with wild-type p53 tumors may benefit from antagonists of the p53–MDM2 interaction.
Historical contingency and the purported uniqueness of evolutionary innovations
Authors: Vermeij Geerat J.
Published: January 2006

Many events in the history of life are thought to be singular, that is, without parallels, analogs, or homologs in time and space. These claims imply that history is profoundly contingent in that independent origins of life in the universe will spawn radically different histories. If, however, most innovations arose more than once on Earth, histories would be predictable and replicable at the scale of functional roles and directions of adaptive change. Times of origin of 23 purportedly unique evolutionary innovations are significantly more ancient than the times of first instantiation of 55 innovations that evolved more than once, implying that the early phases of life’s history were less replicable than later phases or that the appearance of singularity results from information loss through time. Indirect support for information loss comes from the distribution of sizes of clades in which the same minor, geologically recent innovation has arisen multiple times. For three repeated molluscan innovations, 28–71% of instantiations are represented by clades of five or fewer species. Such small clades would be undetectable in the early history of life. Purportedly unique innovations either arose from the union and integration of previously independent components or belong to classes of functionally similar innovations. Claims of singularity are therefore not well supported by the available evidence. Details of initial conditions, evolutionary pathways, phenotypes, and timing are contingent, but important ecological, functional, and directional aspects of the history of life are replicable and predictable.
In vivo
disruption of TGF-β signaling by Smad7 leads to premalignant ductal lesions in the pancreas
Authors: Kuang Chenzhong , Xiao Yan , Liu Xubao , Stringfield Teresa M. , Zhang Shaobo , Wang Zhenzhen , Chen Yan
Published: January 2006

TGF-β has been postulated to play an important role in the development of pancreatic cancers. More than 50% of human pancreatic cancers bear mutations of Sma- and Mad-related protein (Smad) 4, a critical protein required for TGF-β signaling. To evaluate the
in vivo
function of TGF-β in the development of pancreatic cancers, we generated a transgenic mouse model with pancreas-specific expression of Smad7, a specific inhibitor of TGF-β signaling. Through the use of elastase I promoter, we directed the tissue specific expression of exogenous Smad7. Consistently, the exogenous Smad7 was detected only in the pancreas in the transgenic mice, and, furthermore, phosphorylation of Smad2 was blocked in the pancreatic tissues. At 6 months of age, most transgenic animals developed premalignant ductal lesions in the pancreas, with characteristics of pancreatic intraepithelial neoplasia (PanIN), a precursor to invasive pancreatic cancers. The premalignant lesions of the pancreas were accompanied by accelerated proliferation of the ductal epithelium and acinar cells, as well as increased fibrosis around the ductal lesions. This study not only demonstrated that
in vivo
inactivation of TGF-β signaling is implicated in the development of early stage of pancreatic cancers, but also provided a promising animal model useful for the investigation and intervention of pancreatic cancers in humans.
Transcriptome of
Salmonella enterica
serovar Typhi within macrophages revealed through the selective capture of transcribed sequences
Authors: Faucher Sébastien P. , Porwollik Steffen , Dozois Charles M. , McClelland Michael , Daigle France
Published: January 2006

The cDNA obtained by selective capture of transcribed sequences is a complex mixture that can be used in conjunction with microarrays to determine global gene expression by a pathogen during infection. We used this method to study genes expressed by
Salmonella enterica
serovar Typhi, the etiological agent of typhoid fever, within human macrophages. Global expression profiles of Typhi grown
in vitro
and within macrophages at different time points were obtained and compared. Known virulence factors, such as the SPI-1- and SPI-2-encoded type III secretion systems, were found to be expressed as predicted during infection by
Salmonella
, which validated our data. Typhi inside macrophages showed increased expression of genes encoding resistance to antimicrobial peptides, used the glyoxylate bypass for fatty acid utilization, and did not induce the SOS response or the oxidative stress response. Genes coding for the flagellar apparatus, chemotaxis, and iron transport systems were down-regulated
in vivo
. Many cDNAs corresponding to genes with unknown functions were up-regulated inside human macrophages and will be important to consider for future studies to elucidate the intracellular lifestyle of this human-specific pathogen. Real-time quantitative PCR was consistent with the microarray results. The combined use of selective capture of transcribed sequences and microarrays is an effective way to determine the bacterial transcriptome
in vivo
and could be used to investigate transcriptional profiles of other bacterial pathogens without the need to recover many nanograms of bacterial mRNA from host and without increasing the multiplicity of infection beyond what is seen in nature.
Transposable elements have contributed to thousands of human proteins
Authors: Britten Roy
Published: January 2006

This is a report of many distant but significant protein sequence relationships between human proteins and transposable elements (TEs). The libraries of human repeated sequences contain the DNA sequences of many TEs. These were translated in all reading frames, ignoring stop codons, and were used as amino acid sequence probes to search with
blastp
for similar sequences in a library of 25,193 human proteins. The probes show regions of significant amino acid sequence similarity to 1,950 different human genes, with an expectation of <10
−3
. In comparison with previous
repeatmasker
(Institute for Systems Biology, Seattle) studies, these probes detect many more TE sequences in more human coding sequences with greater length than previous work using DNA sequences. If the criterion is opened, very many matches are found occurring on 4,653 different genes after correction for the number seen with random amino acid sequence probes. The processes that led to these extensive sets of sequence relationships between TEs and coding sequences of human genes have been a major source of variation and novel genes during evolution. This paper lists the number of sequence similarities seen by amino acid sequence comparison, which is surely an underestimate of the actual number of significant relationships. It appears that many of these are the result of past events of duplication of genes or gene regions, rather than a direct result of TE insertion. This report of observable relationships leaves to the future the functional implications as well as the detection of the events of TE insertion.
Age-dependent cell death and the role of ATP in hydrogen peroxide-induced apoptosis and necrosis
Authors: Miyoshi Noriyuki , Oubrahim Hammou , Chock P. Boon , Stadtman Earl R.
Published: January 2006

Cell death plays a pivotal role in the body to maintain homeostasis during aging. Studies have shown that damaged cells, which must be removed from the body, accumulate during aging. Decay of the capacity and/or control of cell death during aging is widely considered to be involved in some age-dependent diseases. We investigated the accumulation of protein carbonyls and the role of cell death induced by hydrogen peroxide in human fibroblasts from individuals of various ages (17–80 years). The results showed that levels of oxidatively modified proteins increased with age, not only in whole-cell lysates but also in mitochondrial fractions, and this change correlates with a decline in the intracellular ATP level. Exposure of fibroblasts to hydrogen peroxide led to cell death by apoptosis and necrosis. Younger (<60 years old) cells were more resistant to necrosis induced by hydrogen peroxide than were older cells (>60 years old), which contained lower levels of free ATP than did younger cells. Treatment of cells of all ages with inhibitors of ATP synthesis (oligomycin, 2,4-dinitrophenol, or 2-deoxyglucose) made them more susceptible to cell death but also led to a switch in the death mode from apoptosis to necrosis. Furthermore, hydrogen peroxide treatment led to a greater accumulation of several inflammatory cytokines (IL-6, IL-7, IL-16, and IL-17) and increased necrosis in older cells. These results suggest that age-related decline in the ATP level reduces the capacity to induce apoptosis and promotes necrotic inflammation. This switch may trigger a number of age-dependent disorders.
Development of CD4+T cells expressing a nominally MHC class I-restricted T cell receptor by two different mechanisms
Authors: Ge Qing , Holler Phillip D. , Mahajan Vinay S. , Nuygen Tam , Eisen Herman N. , Chen Jianzhu
Published: January 2006

Differences in T cell receptor (TCR) signaling initiated by interactions among TCRs, coreceptors, and self-peptide–MHC complexes determine the outcome of CD4 versus CD8 lineage of T cell differentiation. The H-2Ldand Kbm3alloreactive 2C TCR is positively selected by MHC class I Kband a yet-to-be identified nonclassical class I molecule to differentiate into CD8+T cells. Here we describe two mechanisms by which CD4+2C T cells can be generated in 2C TCR-transgenic mice. In the RAG−/−background, development of CD4+2C T cells requires the expression of both I-Aband the TAP genes, indicating that both MHC class I and II molecules are required for positive selection of these T cells. Notably, only some of the 2C+RAG−/−mice (≈30%) develop CD4+2C T cells, with frequencies in individual mice varying from 0.5% to as high as ≈50%. In the RAG+background, where endogenous TCRα genes are rearranged and expressed, CD4+2C T cells are generated because these cells express the 2C TCR as well as additional TCRs, consisting of the 2C TCRβ and endogenous TCRα chains. Similarly, T cells expressing the OT-1 TCR, which is nominally MHC class I-restricted, can also develop into CD4+T cells through the same two mechanisms. Thus, expression of two TCRs by a single thymocyte, TCR recognition of multiple MHC molecules, and heterogeneity of TCR, coreceptors, and peptide–MHC interactions in the thymus all contribute to the outcome of CD4 versus CD8 lineage development.
Intermittent administration of human parathyroid fragment (hPTH 1-37) on calcium and phosphorus homeostasis and bone markers in resting horses: a preliminary study
Authors: Vervuert I , Scheidt K Von , Winkelsett S , Forssmann WG , Coenen M
Published: January 2006

Parathyroid hormone (PTH) has been shown to have anabolic and catabolic effects on the skeleton, and in young racing horses the anabolic effects of PTH on bone might be of great importance in reducing the risk of skeletal injury during race training. The aim of this pilot study was to elucidate the effects of intermittent exogenous application of human parathyroid fragment (hPTH 1-37) on calcium homeostasis and bone turnover in resting horses. Five horses were used in this study. Horses were treated subcutaneously with hPTH (hPTH 1-37, 0.5 μg kg−1BW) daily at 600 h over a period of 28 days. A foregoing control trial was conducted under the identical test protocol without hPTH application. Blood samples were taken at defined times for the control and hPTH treatment to analyze ionized Ca (Ca++, AVL), total Ca (AAS), inorganic Pi(flame photometry), intact PTH (RIA), osteocalcin (ELISA) and ICTP (carboxyterminal telopeptide of type-I collagen, RIA). Eight hours after hPTH application, blood ionized Ca++(days 1 and 28) and plasma Pi(days 1–28) increased significantly in comparison to the control. At day 1, 8 h after hPTH application, the decrease in intact plasma PTH was more pronounced after hPTH treatment than in the control, and plasma PTH levels were higher after treatment at day 14 (16 h post-injection,P<0.05), day 18 (16 h post-injection, ns) and day 24 (0 h post-injection). There were no treatment-related differences in total plasma Ca and bone markers. Intermittent PTH administration in healthy horses affected Ca and P homeostasis as well as endogenous PTH secretion, but bone turnover was not affected during the treatment period of 28 days.
Determinants of surface membrane and transverse-tubular excitability in skeletal muscle: implications for high-intensity exercise
Authors: Lindinger Michael I.
Published: January 2006

The fatigue of high-intensity exercise is now believed to reside primarily within the excitation–contraction coupling processes associated with the plasma membrane of skeletal muscle (sarcolemm) and calcium-mediated events leading to myofilament sliding. This paper summarizes recent developments and advances in the identification of factors that contribute to changes in sarcolemmal excitability of mammalian skeletal muscle as a consequence of high-intensity exercise. There is an increasing recognition of the probable role that is played by the transverse tubular system (T-system), a system that comprisesc. 80% of the total sarcolemmal surface capable of ion exchange. Furthermore, the fluid within the T-system has limited access to interstitial fluid bathing myofibres; hence, T-system fluid is probably markedly different from interstitial fluid during high-intensity exercise. Mechanically skinned fibre preparation is providing many new insights into functions of the surface membrane and T-system in fatigue. A scenario is developed whereby accumulation of potassium within the T-system ([K+]o) contributes to reduced membrane excitability, as well as lowering of T-system sodium and chloride, concomitant with loss of intracellular potassium ([K+]i) and accumulation of intracellular sodium ([Na+]) and chloride ([Cl−]). Lowering the [Na+]o/[Na+]iratio and raising myoplasmic [Na+]ihave been shown to decrease membrane excitability and impair action potential propagation. Maintained high [Cl−]omay also have a protective effect in maintaining membrane excitability, and this effect appears to be very pronounced in the presence of raised [K+]o. In contrast to dogma associating high [H+] to fatigue, recent studies have also shown that induced acidosis that results in increased [H+]oand [H+]irestores force production in muscles and skinned fibres fatigued by intermittent tetanic stimulation. This effect may be due to a decrease in surface membrane Cl−permeability that serves to restore membrane excitability. During high-intensity exercise, simultaneous changes in trans-membrane ion concentrations and membrane ion conductances may serve to reduce impairment of membrane excitability that provides for a maintained, though reduced, contractile function.
Assessment of the oxidant–antioxidant blood balance in a field exercise test in Standardbredand eventing horses
Authors: de Moffarts Brieuc , Kirschvink Nathalie , van Erck Emmanuelle , Art Tatiana , Pincemail Joël , Lekeux Pierre
Published: January 2006

The aim of this study was to determine which oxidant–antioxidant blood markers are of interest for a field exercise test (ET) performed on a racetrack. Healthy Standardbred horses (S:n= 12) and healthy eventing horses (E:n=12) were investigated. Exercise was monitored by measuring velocity (V), heart rate (HR), and plasma lactate (LA). Whilst maximal LA did not differ (11.8±0.88 mmol l−1), maximalV(S: 12.3±0.17 m s−1versusE: 11.1±0.24 m s−1,P<0.05) and final HR (S: 222±1versusE: 203±8 beats min−1,P<0.05) were significantly different between groups. Venous blood was collected at rest (R) prior to ET and the following oxidant–antioxidant markers were determined: uric acid (UA), ascorbic acid (AA), α-tocopherol (Vit E), vitamin A (Vit A), superoxide dismutase (SOD), glutathione peroxidase (GPx), glutathione (reduced: GSH and oxidized: GSSG), glutathione redox ratio (GRR), copper (Cu), zinc (Zn) and selenium (Se), oxidized proteins (Protox), lipid peroxides (Pool), antioxidant capacity of water-soluble components (ACW) and antioxidant capacity of lipid-soluble components (ACL). The following markers were further determined 15 min (E15) after the ET: UA, ACW, AA, GSH, Protox, Pool, ACL. Standardbreds had significantly higher concentrations of ACW, GSH, ACL and Protox, whilst Se, Zn and SOD were significantly lower than in eventing horses. Exercise induced a significant increase in ACW and UA. GSH decreased in eventing horses and Pool significantly decreased in both horse groups. This study describes a field ET of high intensity for Standardbred and eventing horses, which could be performed by all animals tested. By sampling blood at rest and at E15, changes of the hydrophilic antioxidant defence were partially assessed, whereas no interpretable changes of the lipophilic antioxidants and of oxidation markers (Protox, Pool) could be detected.
Effect of rider experience on the jumping kinematics of riding horses
Authors: Powers Pippa NR , Kavanagh Anna M
Published: January 2006

The aim of this study was to examine the influence of an experienced rider and a novice rider on the stride kinematics of experienced riding horses. SVHS video recordings (50 Hz) were made of ten experienced riding horses jumping a 1.05 m-high vertical fence. The horses were randomly assigned to jump the fence under two experimental conditions: ridden by an experienced rider and ridden by a novice rider. Three trials for each ridden condition were analysed, and the effects of the rider type on four kinematic variables were examined using a repeated measures ANOVA. No significant differences were found between the riders for velocity and stride length during the approach, or for the take-off and landing distances from the fence. The results suggest that the rider's body position and body movement had no effect on the horse's jumping kinematics as measured in this study, and that each horse jumped the fence in its own manner, regardless of what the rider was doing. This is contrary to the current belief that a horse's jumping technique is strongly influenced by the rider. These findings have relevance for both horses and riders, in that if an experienced horse does not respond to a rider's instructions as expected, then the implications for training of the horse and the rider are considerable.
Effects of different bits and bridles on frequency of induced swallowing in cantering horses
Authors: Manfredi J , Clayton HM , Derksen FJ
Published: January 2006

It has been suggested that the presence of a bit reflexly increases salivation but, at the same time, interferes with the horse's ability to swallow. The objective of this study was to compare swallowing frequency in 12 horses exercising at canter while wearing a head collar, a bitless bridle, a jointed snaffle bit and a Myler correctional-ported barrel bit. Laryngeal movements were recorded videoendoscopically as the horses cantered (8 m s−1) on a high speed treadmill, with the use of side reins to flex the poll. Swallowing was stimulated artificially by infusion of sterile water at a constant rate of 5 ml min−1through a cannula in the endoscope's biopsy port. The results showed large differences in swallowing frequency between horses. Swallowing frequency was lower for the Myler snaffle than for the other conditions (P<0.05). It is concluded that the presence of a bit does not preclude swallowing during exercise at canter with the poll in a flexed position, but certain types of bits may be associated with a reduction in swallowing frequency.
Ventilatory responses of ponies and horses to exercise
Authors: Katz Lisa M , Bayly Warwick M , Hines Melissa T , Sides Raymond H
Published: January 2006

Because athletic horses become hypoxaemic and hypercapnoeic during high-intensity exercise but ponies do not, six Thoroughbred horses and five ponies performed an incremental exercise test at speeds with calculated energy requirements that were 40, 60, 80 and 115% of V˙O2max, with the objective of comparing their blood gas and ventilatory responses to exercise. Expired gas and blood samples were taken and breathing mechanics were assessed before exercise and during the last 15 s at each intensity. Maximal V˙O2and V˙CO2in horses were 153±5 (SEM) and 187±4 ml kg−1min−1, respectively, while corresponding values in ponies were 92±4 and 112±7 ml kg−1min−1. During heavy and supramaximal exercise, horses, but not ponies, became hypoxaemic and hypercapnic. There was no significant difference for V˙Ekg−1between groups during maximal exercise, but PAO2, PaO2and PvO2were lower and PaCO2and [(A−a)O2D] were greater in horses than in ponies. Additionally, the horses' maximal transpulmonary pressure difference was higher and their total pulmonary resistance and ventilatory equivalent lower than in ponies. Flow-volume loops suggested that horses experienced expiratory flow limitation but that ponies did not. These results indicated that horses like Thoroughbreds appear to be expiratory flow-limited and become hypoxaemic and hypercapnic when the demand for gas exchange associated with their high V˙O2maxand V˙CO2maxis greater than can be met by their ventilatory system. Ponies, which are less capable athletes, could better match their ventilatory response with their metabolic capabilities and so were able to maintain PaO2in the pre-exercise range and decrease PaCO2to a tension that was more compatible with acid–base homeostasis.
Effects of exercise on maternal and foetal heart rate in pregnant mares
Authors: Causey RC , Lehnhard RA , Finucane KA , Oliver TM
Published: January 2006

Pregnant mares are often removed from work during gestation. However, little is known about the effects of exercise on the pregnant mare and her foetus. In the present study, maternal and foetal heart rates were monitored by electrocardiography before and after exercise in four equine pregnancies (days 250–285). Exercise consisted of lungeing mares in 20 m circles for 5, 10 and 20 min. Following exercise, significant increases in maternal heart rate were detected (P<0.0001) but not in foetal heart rate (P = 0.4331). All mares gave birth to normal foals uneventfully. While these findings suggest that moderate exercise of the pregnant mare does not appear to be harmful to the equine foetus, data are insufficient to draw conclusions. A larger, more controlled study is necessary.
A field study on warm-up regimes for Thoroughbred and Standardbred racehorses
Authors: Jansson A
Published: January 2006

The exercise performed by Thoroughbred (TB) and Standardbred (SB) racehorses is similar. Nevertheless, warm-up regimes seem to differ between trainers of the two breeds. The aim of this study was to collect some preliminary results on warm-up strategies used by trainers of SB and TB in Sweden and the physiological response to two warm-up regimes of practical relevance. A questionnaire was answered by eight and nine SB and TB trainers, respectively, and showed that the SB trainers tended to perform longer warm-ups than TB trainers. In the exercise study, a long and a short warm-up (LWU and SWU) were designed by two trainers (SB and TB, respectively) and performed prior to an intensive exercise session. The study showed that the recovery period in the LWU trial in SBs was prolonged compared with the SWU trial and associated with increased body temperature (39.6±0.3versus39.1±0.1°C 15 min post-exercise), heart rate, and breathing frequency (66±10versus55±6 beats min−1and 86±11versus56±6 breaths min−115 min post-exercise). In addition, the body weight loss was increased by 129% compared with the SWU. In the TB trial, the post-exercise breathing frequency was higher following SWU compared with LWU (97±7versus71±8 breaths min−115 min post-exercise), indicating increased anaerobic metabolism. Although this study involves few animals, it indicated that the LWU for TBs and the SWU for SBs was most beneficial.
Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen
Authors: Quirke A. M. , Reen F. Jerry , Claesson Marcus J. , Boyd E. Fidelma
Published: January 2006

Genomic islands (GIs) are large chromosomal regions present in a subset of bacterial strains that increase the fitness of the organism under specific conditions. We compared the complete genome sequences of two Vibrio vulnificus strains YJ016 and CMCP6 and identified 14 regions (ranging in size from 14 to 117 kb), which had the characteristics of GIs. Bioinformatic analysis of these 14 GI regions identified the presence of phage-like integrase genes, aberrant GC content and genome signature (dinucleotide frequency) within each GI compared with the core genome indicating that these regions were acquired from an anomalous source. We examined the distribution of the nine GIs from strain YJ016 among 27 V.vulnificus isolates and found that most GIs were absent from the majority of these isolates. The chromosomal insertion sites of three GIs were adjacent to tRNA sites, which contained novel horizontally acquired DNA in all six available sequenced Vibrionaceae genomes.

Contact:  f.boyd@ucc.ie

Supplementary information: Supplementary data are available at Bioinformatics online.
Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale
Authors: Li Haiquan , Li Jinyan , Wong Limsoon
Published: January 2006

Motivation: Protein–protein interaction, mediated by protein interaction sites, is intrinsic to many functional processes in the cell. In this paper, we propose a novel method to discover patterns in protein interaction sites. We observed from protein interaction networks that there exist a kind of significant substructures called interacting protein group pairs, which exhibit an all-versus-all interaction between the two protein-sets in such a pair. The full-interaction between the pair indicates a common interaction mechanism shared by the proteins in the pair, which can be referred as an interaction type. Motif pairs at the interaction sites of the protein group pairs can be used to represent such interaction type, with each motif derived from the sequences of a protein group by standard motif discovery algorithms. The systematic discovery of all pairs of interacting protein groups from large protein interaction networks is a computationally challenging problem. By a careful and sophisticated problem transformation, the problem is solved using efficient algorithms for mining frequent patterns, a problem extensively studied in data mining.

Results: We found 5349 pairs of interacting protein groups from a yeast interaction dataset. The expected value of sequence identity within the groups is only 7.48%, indicating non-homology within these protein groups. We derived 5343 motif pairs from these group pairs, represented in the form of blocks. Comparing our motifs with domains in the BLOCKS and PRINTS databases, we found that our blocks could be mapped to an average of 3.08 correlated blocks in these two databases. The mapped blocks occur 4221 out of total 6794 domains (protein groups) in these two databases. Comparing our motif pairs with iPfam consisting of 3045 interacting domain pairs derived from PDB, we found 47 matches occurring in 105 distinct PDB complexes. Comparing with another putative domain interaction database InterDom, we found 203 matches.

Availability:  

Contact:  jinyan@i2r.a-star.edu.sg

Supplementary information:   and Bioinformatics online.
A novel domain suggests a ciliary function for ASPM, a brain size determining gene
Authors: Ponting Chris P.
Published: January 2006

The N-terminal domain of abnormal spindle-like microcephaly-associated protein (ASPM) is identified as a member of a novel family of ASH (ASPM, SPD-2, Hydin) domains. These domains are present in proteins associated with cilia, flagella, the centrosome and the Golgi complex, and in Hydin and OCRL whose deficiencies are associated with hydrocephalus and Lowe oculocerebrorenal syndrome, respectively. Genes encoding ASH domains thus represent good candidates for primary ciliary dyskinesias. ASPM has been proposed to function in neurogenesis and to be a major determinant of cerebral cortical size in humans. Support for this hypothesis stems from associations between mutations in ASPM and primary microcephaly, and from the rapid evolution of ASPM during recent hominid evolution. The identification of the ASH domain family instead indicates possible roles for ASPM in sperm flagellar or in ependymal cells' cilia. ASPM's rapid evolution may thus reflect selective pressures on ciliary function, rather than pressures on mitosis during neurogenesis.

Contact:  chris.ponting@anat.ox.ac.uk
Thermodynamics of RNA–RNA binding
Authors: Mückstein Ulrike , Tafer Hakim , Hackermüller Jörg , Bernhart Stephan H. , Stadler Peter F. , Hofacker Ivo L.
Published: January 2006

Background: Reliable prediction of RNA–RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA–mRNA binding and antisense interactions. The thermodynamics of such RNA–RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to ‘open’ the binding site and (2) the energy gained from hybridization.

Methods: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired.

Results: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable with a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target.

Availability:  RNAup will be distributed as part of the Vienna RNA Package,

Contact:  ivo@tbi.univie.ac.at
Enhancing instance-based classification with local density: a new algorithm for classifying unbalanced biomedical data
Authors: Plant Claudia , Böhm Christian , Tilg Bernhard , Baumgartner Christian
Published: January 2006

Motivation: Classification is an important data mining task in biomedicine. In particular, classification on biomedical data often claims the separation of pathological and healthy samples with highest discriminatory performance for diagnostic issues. Even more important than the overall accuracy is the balance of a classifier, particularly if datasets of unbalanced class size are examined.

Results: We present a novel instance-based classification technique which takes both information of different local density of data objects and local cluster structures into account. Our method, which adopts the basic ideas of density-based outlier detection, determines the local point density in the neighborhood of an object to be classified and of all clusters in the corresponding region. A data object is assigned to that class where it fits best into the local cluster structure. The experimental evaluation on biomedical data demonstrates that our approach outperforms most popular classification methods.

Availability: The algorithm LCF is available for testing under

Contact:  christian.baumgartner@umit.at
Costs and benefits of symbiont infection in aphids: variation among symbionts and across temperatures
Authors: Russell Jacob A , Moran Nancy A
Published: February 2006

Symbiosis is prevalent throughout the tree of life and has had a significant impact on the ecology and evolution of many bacteria and eukaryotes. The benevolence of symbiotic interactions often varies with the environment, and such variation is expected to play an important role in shaping the prevalence and distributions of symbiosis throughout nature. In this study, we examine how the fitness of aphids is influenced by infection with one of three maternally transmitted bacteria, ‘CandidatusSerratia symbiotica’, ‘CandidatusHamiltonella defensa’ and ‘CandidatusRegiella insecticola’, addressing how symbiont benevolence varies with temperature. We find that the effects of these ‘secondary’ symbionts onAcyrthosiphon pisumdepend on when and whether aphids are exposed to a brief period of heat shock. We also demonstrate that symbionts—even closely related isolates—vary in their effects on hosts. Our results indicate similar effects ofS. symbioticaandH. defensain conferring tolerance to high temperatures and a liability ofR. insecticolaunder these same conditions. These findings reveal a role for heritable symbionts in the adaptation of aphids to their abiotic environments and add to an expanding body of knowledge on the adaptive significance of symbiosis.
Evolution of anti-predator traits in response to a flexible targeting strategy by predators
Authors: Jackson Andrew L , Beauchamp Guy , Broom Mark , Ruxton Graeme D
Published: January 2006

Anti-predator benefits increase with vigilance rate and group size in many species of animal, while simultaneously resource intake rates usually decrease. This implies that there is an optimal group size and vigilance rate that will maximize individual fitness. While this basic theory of vigilance has been modelled and tested extensively, it has often been assumed that the predator represents a ‘fixed-risk’ such that groups of prey are essentially independent entities that exert little or no effect on one another either directly or indirectly. We argue that this is an over-simplification, and propose that the behaviour of one group of prey will likely affect the fitness of another local group of prey if the predator preferentially attacks the most vulnerable group—rather than attack both with constant rates. Using a numerical simulation model, we make the first examination of this game and allow the prey to dynamically evolve both optimal group size distributions between two habitats and vigilance rates in response to a predator with a preference for whichever group is the more vulnerable. We show that the density of prey in the population and the sensitivity of a predator to differences in prey vulnerability are likely to drive the dynamics of such a game. This novel approach to vigilance theory opens the door to several challenging lines of future research, both experimental and theoretical.
Fitness landscapes support the dominance theory of post-zygotic isolation in the musselsMytilus edulisandM. galloprovincialis
Authors: Bierne Nicolas , Bonhomme François , Boudry Pierre , Szulkin Marta , David Patrice
Published: January 2006

We studied the genetic basis of post-zygotic isolation in the marine musselsMytilus edulisandMytilus galloprovincialis. Evidence was obtained for a high number of recessive Dobzhansky–Muller substitutions in the genome of these two mussel taxa. We analysed the segregation of unlinked diagnostic markers in the progeny of two backcrosses and an F2cross, 36 h and 200 days after fertilization. Directional selection favouringM. galloprovincialisgenotypes was observed in both kinds of cross. In the F2, epistatic interactions between each pair of chromosome fragments mapped by the markers were identified in addition. Our results imply that homozygous–homozygous interactions are required for breakdown of coadaptation, in accordance with the dominance theory of post-zygotic isolation. Endogenous post-zygotic selection distributed over many loci throughout the genome provides the missing factor explaining the astonishing persistence and strength of barriers to neutral introgression in such a dispersive taxon asMytilus.
Introduction
Authors: Hooker S.M , Jaroszynski D.A , Burnett K
Published: January 2006

An overview is provided of the papers presented at the Discussion Meeting on ‘Laser-driven particle accelerators: new sources of energetic particles and radiation’ which was held at the Royal Society on 6 and 7 June 2005. A discussion of the future prospects of the field, held during the last session of the meeting, is summarized and the conclusions of this presented.
Laser guiding for GeV laser–plasma accelerators
Authors: Leemans Wim , Esarey Eric , Geddes Cameron , Schroeder Carl , Tóth Csaba
Published: January 2006

Guiding of relativistically intense laser beams in preformed plasma channels is discussed for development of GeV-class laser accelerators. Experiments using a channel guided laser wakefield accelerator at Lawrence Berkeley National Laboratory (LBNL) have demonstrated that near mono-energetic 100 MeV-class electron beams can be produced with a 10 TW laser system. Analysis, aided by particle-in-cell simulations, as well as experiments with various plasma lengths and densities, indicate that tailoring the length of the accelerator, together with loading of the accelerating structure with beam, is the key to production of mono-energetic electron beams. Increasing the energy towards a GeV and beyond will require reducing the plasma density and design criteria are discussed for an optimized accelerator module. The current progress and future directions are summarized through comparison with conventional accelerators, highlighting the unique short-term prospects for intense radiation sources based on laser-driven plasma accelerators.