Comparative genomics of Brassicaceae crops

The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed.     

Iron-based ferritin nanocore as a contrast agent

Self-assembling protein cages have been exploited as templates for nanoparticle synthesis. The ferritin molecule, a protein cage present in most living systems, stores excess soluble ferrous iron in the form of an insoluble ferric complex within its cavity. Magnetic nanocores formed by loading excess iron within an engineered ferritin from Archaeoglobus fulgidus (AfFtn-AA) were studied as a potential magnetic resonance (MR) imaging contrast agent. The self-assembly characteristics of the AfFtn-AA were investigated using dynamic light scattering technique and size exclusion chromatography. Homogeneous size distribution of the assembled nanoparticles was observed using transmission electron microscopy. The magnetic properties of iron-loaded AfFtn-AA were studied using vibrating sample magnetometry. Images obtained from a 3.0 T whole-body MRI scanner showed significant brightening of T(1) images and signal loss of T(2) images with increased concentrations of iron-loaded AfFtn-AA. The analysis of the MR image intensities showed extremely high R(2) values (5300?mM(-1)?s(-1)) for the iron-loaded AfFtn-AA confirming its potential as a T(2) contrast agent.     

Identification of Rfd1, a novel restorer-of-fertility locus for cytoplasmic male-sterility caused by DCGMS cytoplasm and development of simple PCR markers linked to the Rfd1 locus in radish (Raphanus sativus L.)

Previously, novel cytoplasmic male-sterility (CMS) caused by DCGMS cytoplasm was discovered in radish (Raphanus sativus L.) introduced from Uzbekistan. We performed extensive progeny tests and identified two fertility restorer lines (‘R171’ and ‘R121’) for this new CMS. Two F₁ hybrid populations were self-pollinated and backcrossed to produce F₂ and BC populations. Inheritance patterns of male-sterility in segregating populations varied depending on paternal lines. Segregation of male-sterility in F₂ populations originating from the cross between MS19 and R121 showed that a single locus was involved in fertility restoration. However, populations originating from the cross between MS15 and R171 showed the involvement of more than one restorer-of-fertility genes. The single fertility restorer locus identified in the cross between MS19 and R121 was designated Rfd1 locus. Bulked segregant analysis was performed using RAPD and AFLP, which identified one marker each. Both RAPD and AFLP markers were converted into simple PCR-based co-dominant markers after their isolated flanking sequences were analyzed. Indels 773-bp and 67-bp in length were identified between two Rfd1 allele-linked flanking sequences of the RAPD and AFLP fragments, respectively, then utilized to develop simple PCR markers. In addition, we prove that the newly identified Rfd1 locus is independent of the Rfo locus, another radish fertility restorer for CMS caused by Ogura cytoplasm.     

Insecticidal activities of crude extracts and phospholipids from Chenopodium ficifolium against melon and cotton aphid, Aphis gossypii

Several organic solvent extracts of Chenopodium ficifolium were tested for their insecticidal activity against melon and cotton aphid, Aphis gossypii, on cucumber plants. Both methanol and ethanol extracts, at 5000 μg ml⁻¹, were highly active giving over 80% control. The other crude extracts displayed moderate or weak insecticidal activity giving control in the range of 16–69%. Two phospholipids were isolated as insecticidal active substances from C. ficifolium. Their chemical structures were identified as 1-palmitoyl-2-(3-trans)-hexadecenoyl-sn-glycero-3-phosphoglycerol and 1-palmitoyl-2-linoleoyl-3-glycerophosphocholine by GC–MS, EDS, mass and NMR spectral analyses. Both compounds displayed a dose-dependent mortality of A. gossypii. Furthermore, the liquid formulation that was obtained by partitioning with n-hexane from the methanol extract of C. ficifolium controlled melon and cotton aphid on cucumber plants effectively. These results indicate that extracts of C. ficifolium have potential for development as botanical insecticides for controlling A. gossypii infesting cucumber plants.     

Leaf chlorophyll fluorescence discriminates herbicide resistance in Echinochloa species

Timely detection of herbicide resistance at an early stage of crop cultivation is essential to help farmers find alternative solutions to manage herbicide resistance in their fields. In this study, maximum quantum yield of PS II [F_v/F_m = (F_m – F_o)/F_m] was measured at the 4–5 leaf stage to discriminate between herbicide‐resistant and susceptible biotypes of Echinochloa species. The differences in F_v/F_m between herbicide‐resistant and susceptible Echinochloa spp. were consistent with the whole‐plant assay based on I₅₀ (herbicide doses causing a 50% inhibition of F_v/F_m) and GR₅₀ (herbicide doses causing a 50% reduction in plant fresh weight) values and R/S ratios (herbicide resistance index), regardless of the mode of action of the tested herbicides. A PS II inhibitor caused the fastest inhibition of F_v/F_m, compared with ACCase and ALS inhibitors, after herbicide treatment. The required time for discrimination between herbicide‐resistant and susceptible Echinochloa spp. was 64 h after PS II inhibitor treatment, much shorter than those of ACCase and ALS inhibitor‐treated plants, which required 168 and 192 h respectively. The leaf chlorophyll fluorescence assay provided reliable diagnostics of herbicide resistance in Echinochloa spp. with significant time savings and convenient measurement in field conditions compared with the conventional whole‐plant assay.     

Characteristics of ammonia and carbon dioxide releases from layer hen manure

1.?Ammonia (NH₃) is an important gaseous pollutant generated from manure in commercial poultry farms and has been an environmental, ecological, and health concern. Poultry manure also releases carbon dioxide (CO₂), which is a greenhouse gas and is often used as a tracer gas to calculate building ventilation.

2.?A 38-d laboratory study was conducted to evaluate the characteristics of NH₃ and CO₂ releases from layer hen manure using 4 manure reactors (122 cm tall, 38 cm internal diameter), which were initially filled with 66 cm deep manure followed by weekly additions of 5 cm to simulate manure accumulation in commercial layer houses.

3.?The average daily mean (ADM) NH₃ and CO₂ release fluxes for the 4 reactors during the entire study were 161?5 ± 21?1 µg/s.m² (ADM ± 95% confidence interval) and 10?0 ± 0?3 mg/s.m², respectively. The daily mean NH₃ and CO₂ releases in individual reactors varied from 35?2 to 679?1 µg/s.m² and from 6?6 to 20?5 mg/s.m², respectively.

4.?The ADM NH₃ release flux was within the range of those obtained in 4 high-rise layer houses by Liang et al. (2005 Liang, Y, Xin, H, Wheeler, EF, Gates, RS, Li, H, Zajaczkowski, JS, Topper, PA, Casey, KD, Behrends, BR, Burnham, DJ and Zajaczkowski, FJ. 2005. Ammonia emissions from US laying hen houses in Iowa and Pennsylvania. Transactions of the ASAE, 48: 1927–1941. [Crossref] [Google Scholar], Transactions of the ASAE, 48). However, the CO₂ release flux in this study was about 10 to 13 times as high as the data reported by Liang et al. (2005 Liang, Y, Xin, H, Wheeler, EF, Gates, RS, Li, H, Zajaczkowski, JS, Topper, PA, Casey, KD, Behrends, BR, Burnham, DJ and Zajaczkowski, FJ. 2005. Ammonia emissions from US laying hen houses in Iowa and Pennsylvania. Transactions of the ASAE, 48: 1927–1941. [Crossref] [Google Scholar]). Fresh manure had greater NH₃ release potential than the manure in the reactors under continuous ventilation. Manure with higher contents of moisture, total nitrogen, and ammonium in the 4th weekly addition induced 11 times higher NH₃ and 75% higher CO₂ releases immediately after manure addition compared with pre-addition releases.     

Carcass conformation and cut composition of Creole goat from Guadeloupe

Carcass data base of 164 Creole male goats was used in order to provide factual data on the carcass conformation. Standardised procedures of carcass measuring and cutting were followed. The European official grid of light lamb is implemented for meat goat in the French West Indies and included five levels. Weights of carcass, cuts and tissues, quality scores and linear measurements were analysed. Feeding system, age at slaughter and weight were taken into account for statistical analysis. There were significant differences among carcass conformation classes (CC) for many traits except for the fat score, leg length and compactness ratio (carcass width on length): 2.2, 34.5 cm and 0.30 on average, respectively. The values of chilled carcass weight and yield and the carcass linear measurements steadily increased until conformation class 4 or 5: 6.7 to 11.2 kg, 49% to 55% and 52.4 to 58.0 cm carcass length. For the weights of carcass cuts, significant differences appeared between two groups: classes 1 and 2 vs. classes 3, 4 and 5. Regardless of the carcass weight, the distribution of prime cuts remained similar. The indices calculated on a weight basis (kg/cm), either for the carcass or the leg, increased significantly (P < 0.01): with 54% and 63% difference between the two extreme classes, respectively. The muscle, bone and fat proportions in the shoulder did not vary between CC with 0.72, 0.22 and 0.06, respectively. Corresponding traits in leg were 0.74, 0.23 and 0.03; the last two were different (P < 0.05) from class 1 to class 5. The muscle/bone ratios calculated either in shoulder or in leg ranged from 3.1 to 3.6 (P > 0.05).     

Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms

How scaffold proteins control information flow in signaling pathways is poorly understood: Do they simply tether components, or do they precisely orient and activate them? We found that the yeast mitogen-activated protein (MAP) kinase scaffold Ste5 is tolerant to major stereochemical perturbations; heterologous protein interactions could functionally replace native kinase recruitment interactions, indicating that simple tethering is largely sufficient for scaffold-mediated signaling. Moreover, by engineering a scaffold that tethers a unique kinase set, we could create a synthetic MAP kinase pathway with non-natural input-output properties. These findings demonstrate that scaffolds are highly flexible organizing factors that can facilitate pathway evolution and engineering.     

Tear film breakup times in young healthy cats before and after anesthesia

The objectives of this study were: (i) to determine tear film breakup times (BUTs) in young healthy cats; (ii) to determine tear film BUTs in feline eyes within 8-20 h following general anesthesia; (iii) to determine if tear film BUTs vary significantly preoperatively when compared with values obtained 8-20 h postoperatively; (iv) to determine if Schirmer tear test (STT) values correlate with tear film BUTs in young healthy cats; and (v) to determine if the isolation of particular etiologic agents from conjunctival swabs of healthy cats affects tear film BUTs. We studied eighteen healthy Domestic Short-haired (n=14) and Domestic Long-haired (n=4) cats, with normal ocular examinations, ranging in age from 0.5 to 3 years. Complete ophthalmic examinations, including tear film BUTs, were performed on all cats. Conjunctival swabs from each eye of all cats and blood samples from all cats were collected and submitted for polymerase chain reaction screening for feline herpes virus, Chlamydophila felis, Mycoplasma spp., and calicivirus. In 10 of 18 cats, STT values and tear film BUTs were measured before general anesthesia was administered and again within 8-20 h following the end of anesthesia. Mean preanesthesia tear film BUTs for all 18 cats were 17.4+/-4.6 s OD and 16.0+/-4.5 s OS. Mean postanesthesia tear film BUT results were 12.5+/-4.3 and 13.1+/-4.0 s OD and OS, respectively. Postanesthesia tear film BUTs were significantly more rapid than those measured before anesthesia (OD only). There was also a positive correlation, both before and after anesthesia, between STT values in both eyes (OU) and tear film BUTs OU. The isolation or lack of isolation of conjunctival microorganisms using PCR did not significantly affect tear film BUTs. Mean tear film BUT in young healthy domestic cats is 16.7+/-4.5 s. Tear BUT is positively correlated with STT values. Although mean tear film BUTs OD at 8-20 h following anesthesia were more rapid than preanesthesia values, this difference did not appear clinically relevant.