Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar ‘Koshihikari’ was performed to extract regions containing large indels (10–51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between ‘Koshihikari’ and other diverse cultivars, we subtracted the indel regions detected in ‘Koshihikari’ from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including ‘Khao Nam Jen’ as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.     

Genetic stability and maintenance of Raphanus sativus lines with an added Brassica rapa chromosome

The genetic stability and maintenance of Raphanus sativus‐Brassica rapa monosomic chromosome addition lines (a‐h‐types MALs, 2n = 19, BC₂), developed by backcrossing the synthesized amphidiploid Raphanobrassica (Raphanus sativus × Brassica rapa, 2n = 38, RRAA) with R. sativus cv. ‘Shogoin’ (2n = 18, RR), was investigated. Transmission of the added alien chromosome through selected smaller seeds (SSS) and the inheritance of morphological traits and random amplified polymorphic DNA (RAPD)‐specific markers together with meiotic chromosome configuration and seed fertility were also investigated for three successive generations (BC₃ to BC₅). The distinctive traits and the RAPD‐specific markers of the eight types of MAL were substantially inherited and stably maintained throughout three generations, although a few variant plants (2n =18) resembling MALs (2n = 19) and hyperploidal plants (2n = 26 and 2n = 37) were generated in the earlier generations of BC₃ and BC₄ in comparison with BC₅. The average transmission rates for three generations ranged from 26% for both the b‐type and the d‐type to 44% for the e‐type through SSS. On the other hand, the transmission rates through randomly selected seeds (RSS) were lower, ranging from 6.5% for the f‐type to 23.5% for the b‐type. In meiosis, more than 90% of PMCs showed the 9II +1I pairing configuration at metaphase I throughout three generations. For seed fertility, when backcrossed with the radish cv. ‘Shogoin’, the values were approximately 180% to 500% with the mode around 300% with the seed harvested from a pod increasing with the advancing generations. Genetic recombination between the radish chromosomes and the added chromosome is probably rare, suggesting that the added chromosome is mostly maintained unaltered in the background of the radish genome.     

Nitrogen uptake in riparian plant communities across a sharp ecological boundary of salmon density

Background

Recent studies of anadromous salmon (Oncorhynchus spp.) on the Pacific Coast of North America indicate an important and previously unrecognized role of salmonid nutrients to terrestrial biota. However, the extent of this uptake by primary producers and consumers and the influences on community structure remain poorly described. We examine here the contribution of salmon nutrients to multiple taxa of riparian vegetation (Blechnum spicant, Menziesii ferruginea, Oplopanax horridus, Rubus spectabilis, Vaccinium alaskaense, V. parvifolium, Tsuga heterophylla) and measure foliar δ¹⁵N, total %N and plant community structure at two geographically separated watersheds in coastal British Columbia. To reduce potentially confounding effects of precipitation, substrate and other abiotic variables, we made comparisons across a sharp ecological boundary of salmon density that resulted from a waterfall barrier to salmon migration.

Results

δ¹⁵N and %N in foliage, and %cover of soil nitrogen indicators differed across the waterfall barrier to salmon at each watershed. δ¹⁵N values were enriched by 1.4‰ to 9.0‰ below the falls depending on species and watershed, providing a relative contribution of marine-derived nitrogen (MDN) to vegetation of 10% to 60%. %N in foliar tissues was slightly higher below the falls, with the majority of variance occurring between vegetation species. Community structure also differed with higher incidence of nitrogen-rich soil indicator species below the waterfalls.

Conclusions

Measures of δ¹⁵N, %N and vegetation cover indicate a consistent difference in the riparian community across a sharp ecological boundary of salmon density. The additional N source that salmon provide to nitrogen-limited habitats appears to have significant impacts on the N budget of riparian vegetation, which may increase primary productivity, and result in community shifts between sites with and without salmon access. This, in turn, may have cascading ecosystem effects in forests adjacent to salmon streams.

     

Bone mineral content of the third metacarpal bone in Quarter Horse foals from birth to one year of age

Dual photon absorptiometry (DPA) is a valid method for bone mineral content (BMC) evaluation, but there are no reports on the use of this technology in in vivo studies in the horse. The aim of the current study was to evaluate the changes of BMC of the third metacarpal bone (MC3) in vivo in foals during their first year of life using DPA. The BMC of the MC3 of 41 Quarter Horse foals was evaluated every 4 weeks during their first year of life by DPA using a bienergetic Gadolinium-153 (¹⁵³Gd) source. To the authors' knowledge, this is the first report of an in vivo study of BMC in foals using DPA by means of a bienergetic ¹⁵³Gd source. The results demonstrated a positive correlation of age, heart girth, and withers height with BMC of the MC3 independent of gender and an exponential behavior of the BMC increment along the first year of life. There was an effect of weaning associated with change in diet and stall confinement on BMC in foals weaned at age 17 weeks, but not in foals weaned at age between 19 and 24 weeks.     

Evaluation of cardiac rhythm in dogs treated with levamisole hydrochloride using 24-hour ambulatory electrocardiography

The objective of this study was to evaluate the electrocardiographic alterations in the cardiac rhythm in dogs treated with levamisole hydrochloride over a period of 24 hours. Thirty-six mixed-breed dogs, both male and female, all clinically healthy, were used in the experiment. The dogs were divided into 6 groups with 6 dogs in each group, according to dosage and route of administration. The Holter test was initiated immediately after the treatment, and was maintained for 24 hours. In the group treated with 10 mg/kg by way of subcutaneous injection, one of them showed ventricular premature complexes, sometimes isolated and other times in pairs, and ventricular tachycardia, concentrated mainly in the first hour after administration of the drug. In the group of 6 animals treated subcutaneously with 25mg/kg, four showed isolated ventricular premature complexes, ventricular bigeminy and trigeminy, mainly during the first 2 hours after administration of the drug. All the animals in the other groups showed sinus arrhythmia followed by sinus arrest. The disturbances in the cardiac rhythm observed in clinically healthy animals treated with levamisole hydrochloride, indicate that it is preferable to avoid subcutaneous administration of levamisole hydrochloride and that the oral administration of the drug should be done with caution.     

Endocrine, haematological and metabolic responses to sevoflurane anaesthesia in lambs

Objective To compare the magnitude and duration of the peri‐operative haematological, endocrine and metabolic effects of surgery performed under sevoflurane anaesthesia. Study Design Prospective randomized study. Animals Ten, 55‐day‐old lambs of both sexes, mean weight 20.8 ± 0.3 kg (range 18.5–23.6 kg). Methods Animals were randomly allocated to two equal groups. All were anaesthetized with sevoflurane for 3 hours. Surgery (end‐to‐end anastomosis of the right carotid artery and right jugular vein) was performed in animals of Group 1 only. The electrocardiogram, pulse oximetry, cardiac output and noninvasive arterial blood pressure (NIBP) were monitored. Venous blood samples (5 mL) were taken 30 minutes before induction of anaesthesia (T = 0) and 1 (T1), 24 (T2), 48 hours (T3) and 7 days (T4) after anaesthesia in order to measure plasma cortisol, ACTH, insulin, cyclic adenosine monophosphate (cAMP), glucose, protein concentrations and haematological variables. Results Sevoflurane decreased NIBP (minimum mean value: 64 ± 3 mm Hg) in both groups. Plasma cortisol and ACTH concentration increased in Group 1 (maximum mean values: cortisol: 136.2 nmol L^?1, ACTH: 54.5 pmol L^?1) and Group 2 (maximum mean values: cortisol: 128.7 nmol L^?1, ACTH: 44.0 pmol L^?1). Cyclic AMP increased only in Group 1 (9.3 nmol) 1 hour after anaesthesia. Neutrophilia, lymphopaenia and a decreased PCV were observed in both groups 1 hour after anaesthesia. Plasma protein and glucose concentrations did not change. Conclusions Increased ACTH and cortisol concentrations recorded 1 hour after anaesthesia suggest that sevoflurane induces a stress response in lambs. Clinical relevance The study did not identify the mechanism by which sevoflurane induces a stress response although hypotension is implicated.     

Comparison of femoral and auricular arterial blood pressure monitoring in pigs

Objective To compare arterial blood pressure measurements obtained from the femoral and auricular arteries in anaesthetized pigs. Study design Prospective experimental study. Animals Fifteen female Large White pigs were used weighing 21.3 ± 2.3 kg. Methods The pigs were anaesthetized with tiletamine/zolazepam and xylazine administered intramuscularly, and anaesthesia maintained with isoflurane delivered in oxygen/nitrogen. Arterial oxygen partial pressures were maintained between 11.3 and 13.3 kPa and PaCO₂ between 4.6 and 6.0 kPa. Monitoring included electrocardiogram, capnography and invasive blood pressure. The auricular and femoral arteries were catheterized for continuous systolic (SAP), diastolic (DAP) and mean arterial pressure (MAP) measurements. Measurements were recorded every 15 minutes. Statistical analysis involved a Bland–Altman plot analysis. Results The mean difference ± confidence intervals between the femoral and the auricular arterial diastolic, systolic and mean blood pressure measurements during hypotension were 2 ± 7, 2 ± 5 and 2 ± 5 mmHg respectively. In conditions of normotension mean difference ± confidence intervals, of femoral and auricular arterial blood pressure measurements of diastolic, systolic and mean blood pressure were 4 ± 5, 3 ± 7 and 4 ± 4 mmHg respectively. In conditions of increased arterial blood pressure, mean difference ± confidence intervals, of femoral and auricular arterial blood pressure measurements of diastolic, systolic and mean blood pressure were 4 ± 5, 3 ± 8 and 4 ± 4 mmHg respectively. Conclusion Auricular artery catheterization is easier and quicker to perform. Pressure measurements from the auricular artery compared well with the femoral artery. Clinical relevance We found that auricular arterial blood pressures were similar to femoral arterial values under the conditions of this experiment. We did not test extremes of blood pressure or significant alterations in body temperature.     

MAGNETIC RESONANCE IMAGING OF THE NORMAL EQUINE BRAIN

The purpose of this investigation was to define the magnetic resonance (MR) imaging appearance of the brain and associated structures of the equine head. MR images were acquired in oblique dorsal (T2-weighted), sagittal (T1-weighted), and transverse planes (T2-weighted), using a magnet of 1.5 Tesla and a human body coil. Relevant anatomic structures were identified and labeled at each level. The resulting images provided excellent anatomic detail of the cranioencephalic structures. Annotated MR images from this study are intended as a reference for clinical imaging studies of the equine head, specially in the diagnosis of brain diseases in the horse.     

Identification of Disulfide Proteins in the Salt Soluble Fraction of Rice (Oryza sativa) Seed

Evidence has been accumulating to suggest that disulfide bonding is one of the key causes of allergenicity. Recently we developed the “disulfide proteome”, a technique for the comprehensive analysis of disulfide bonding of proteins. We applied this new technique to the rice seed's salt‐soluble fraction, which has long been known to be allergenic. Most proteins in the fraction, including α‐amylase/trypsin inhibsitor, α‐ globulin, and glutelin fragments, have formed intramolecular disulfide bonds. Also, unknown proteins, including one sharing similarities with known allergens, had disulfide bonds, from which we can infer possible allergenicity. This is a preliminary study to screen allergens from the basis of disulfide bonding.