Hairy Canola (Brasssica napus) re-visited: Down-regulating TTG1 in an AtGL3-enhanced hairy leaf background improves growth, leaf trichome coverage, and metabolite gene expression diversity

Primer sequences used in the construction and analysis of B. napus transgenic lines. Table S1B. Blast of batch leaf Q-PCR primers to the B. rapa, B. oleracea, and B. napus genomes for five trichome regulatory genes and two control genes in B. napus. Table S1C. “Detectable” B. napus homologues of five trichome regulatory genes in first true leaves (from RNA sequencing). Table S1D. BlastP for five Arabidopsis trichome regulatory genes against the Brassica napus genome in NCBI. Table S2A. Differentially expressed leaf trichome ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy line K-5-8 relative to semi-glabrous cv. Westar. Table S2B. Leaf trichome genes with no significant expression differences (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy line K-5-8 relative to semi-glabrous cv. Westar. Table S3. Differentially expressed leaf flavonoid ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S4. Differentially expressed leaf phenylpropanoid and lignin ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S5. Differentially expressed leaf phenolic ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S6. Differentially expressed leaf shikimate ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S7. Differentially expressed leaf isoprenoid and terpene ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S8. Differentially expressed leaf glucosinolate-related and miscellaneous sulphur-related ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S9. Differentially expressed leaf alkaloid-related and miscellaneous N-metabolizing ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S10. Differentially expressed leaf cell wall structural carbohydrate ESTs ((p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S11. Differentially expressed leaf mucilage ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S12. Differentially expressed leaf wax ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S13. Differentially expressed leaf hormone ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S14. Differentially expressed leaf secondary metabolism ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S15. Differentially expressed leaf redox-related ESTs (p < 0.05)) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S16. Differentially expressed leaf protein modification ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S17. Differentially expressed leaf protein degradation ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. Table S18. Differentially expressed leaf transcription factor ESTs (p < 0.05) in hairy AtGL3+ B. napus or ultra-hairy K-5-8 relative to semi-glabrous cv. Westar. (XLSX 400 kb

Hairy Canola (Brasssica napus) re-visited: Down-regulating TTG1 in an AtGL3-enhanced hairy leaf background improves growth, leaf trichome coverage, and metabolite gene expression diversity

Background Through evolution, some plants have developed natural resistance to insects by having hairs (trichomes) on leaves and other tissues. The hairy trait has been neglected in Brassica breeding programs, which mainly focus on disease resistance, yield, and overall crop productivity. In Arabidopsis, a network of three classes of proteins consisting of TTG1 (a WD40 repeat protein), GL3 (a bHLH factor) and GL1 (a MYB transcription factor), activates trichome initiation and patterning. Introduction of a trichome regulatory gene AtGL3 from Arabidopsis into semi-glabrous Brassica napus resulted in hairy canola plants which showed tolerance to flea beetles and diamondback moths; however plant growth was negatively affected. In addition, the role of BnTTG1 transcription in the new germplasm was not understood. Results Here, we show that two ultra-hairy lines (K-5-8 and K-6-3) with BnTTG1 knock-down in the hairy AtGL3+ B. napus background showed stable enhancement of trichome coverage, density, and length and restored wild type growth similar to growth of the semi-glabrous Westar plant. In contrast, over-expression of BnTTG1 in the hairy AtGL3+ B. napus background gave consistently glabrous plants of very low fertility and poor stability, with only one glabrous plant (O-3-7) surviving to the T3 generation. Q-PCR trichome gene expression data in leaf samples combining several leaf stages for these lines suggested that BnGL2 controlled B. napus trichome length and out-growth and that strong BnTTG1 transcription together with strong GL3 expression inhibited this process. Weak expression of BnTRY in both glabrous and trichome-bearing leaves of B. napus in the latter Q-PCR experiment suggested that TRY may have functions other than as an inhibitor of trichome initiation in the Brassicas. A role for BnTTG1 in the lateral inhibition of trichome formation in neighbouring cells was also proposed for B. napus. RNA sequencing of first leaves identified a much larger array of genes with altered expression patterns in the K-5-8 line compared to the hairy AtGL3+ B. napus background (relative to the Westar control plant). These genes particularly included transcription factors, protein degradation and modification genes, but also included pathways that coded for anthocyanins, flavonols, terpenes, glucosinolates, alkaloids, shikimates, cell wall biosynthesis, and hormones. A 2nd Q-PCR experiment was conducted on redox, cell wall carbohydrate, lignin, and trichome genes using young first leaves, including T4 O-3-7-5 plants that had partially reverted to yield two linked growth and trichome phenotypes. Most of the trichome genes tested showed to be consistant with leaf trichome phenotypes and with RNA sequencing data in three of the lines. Two redox genes showed highest overall expression in K-5-8 leaves and lowest in O-3-7-5 leaves, while one redox gene and three cell wall genes were consistently higher in the two less robust lines compared with the two robust lines. Conclusion The data support the strong impact of BnTTG1 knockdown (in the presence of strong AtGL3 expression) at restoring growth, enhancing trichome coverage and length, and enhancing expression and diversity of growth, metabolic, and anti-oxidant genes important for stress tolerance and plant health in B. napus. Our data also suggests that the combination of strong (up-regulated) BnTTG1 expression in concert with strong AtGL3 expression is unstable and lethal to the plant

Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map

Increased map density and transferability of markers are essential for the genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F2 population (VRS-F2) that was derived by selfing a single F1 from a Vitis riparia x ‘Seyval blanc’ cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera ‘PN40024’ genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq transferable markers were identified that can be used in pairs (one pistillate and one hermaphroditic) to predict pistillate and hermaphrodite flower type with ≥99.7% accuracy. Total and individual anthocyanin diglucoside QTL mapped to chromosome 9 near a 5-O-GLUCOSYLTRANSFERASE candidate gene. Malic acid QTL were observed on chromosome 1 and 6 with two MALATE DEHYRDROGENASE CYTOPLASMIC 1 and ALUMINUM-ACTIVATED MALATE TRANSPORTER 2-LIKE (ALMT) candidate genes, respectively. Modeling malic acid identified a potential QTL on chromosome 8 with peak position in proximity of another ALMT. A first-ever reported QTL for the grassy smelling volatile (E)-2-hexenal was found on chromosome 2 with a PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE candidate gene near peak markers

Analysing stillbirth data using dynamic self organizing maps

Even with the presence of modern obstetric care, stillbirth rate seems to stay stagnant or has even risen slightly in countries such as England and has become a significant public health concern [1]. In the light of current medical research, maternal risk factors such as diabetes and hypertensive disease were identified as possible risk factors and are taken into consideration in antenatal care. However, medical practitioners and researchers suspect possible relationships between trends in maternal demographics, antenatal care and pregnancy information of current stillbirth in consideration [2]. Although medical data and knowledge is available appropriate computing techniques to analyze the data may lead to identification of high risk groups. In this paper we use an unsupervised clustering technique called Growing Self organizing Map (GSOM) to analyse the stillbirth data and present patterns which can be important to medical researchers

Estimating signal strengths prior to field trials in wireless local loop networks

One issue in giving WIRELESS LOCAL LOOP connections in a rural area is the difficulty of conducting field trials due to poor road conditions and the hilly terrain in Sri Lanka. Extremely poor condition of access roads reduces the efficiency of giving new wireless subscriber connections. Even though at the installation of a base station, the coverage area is defined (around 20 Km radius from base station) due to the hilly and mountainous terrain in Sri Lanka signal strength varies drastically for about 100 m change of distance. There are number of Radio network planning tools or Wireless calculators in the industry with real time corrections like body losses, penetration losses and thermal noise density. But when we apply those in Sri Lankan context, we do not get the correct coverage diagrams. Therefore we propose two new path loss exponents which is suitable for countries like Sri Lanka where the population spread in hills and mountains

Antenatal diagnosis of midgut volvulus with successful immediate post-natal management

Fetal volvulus of the midgut occurs when the bowel twists around the axis of the superior mesenteric artery. It is usually diagnosed postnatally but with improving ultrasonography, there have been increasing number of cases reporting antenatal diagnosis that had allowed planning of obstetric intervention and prompt surgery in the postnatal period. We present a case of dichorionic diamniotic twin pregnancy wherein Twin A had multiple anomalies, which included an Ivemark heterotaxy syndrome with a double outlet right ventricle. This twin developed dilated bowel loops at 33 weeks of gestation. The pregnancy continued to have regular antenatal surveillance and was managed by a multidisciplinary team. At 36 weeks of gestation, these bowel loops were found to have absence of peristalsis compared to previous ultrasounds. An emergency caesarean section was performed, which was uncomplicated and Twin A weighing 2760g was born with Apgars of 61 and 85. The diagnosis of volvulus in Twin A was confirmed during its emergency laparotomy along with a Type IV jejunal atresia and was successfully treated surgically with resection and administration of tissue plasminogen activator (TPA). This is the first description of a case treated with TPA after fetal diagnosis. Keywords: Volvulus, Antenatal diagnosis, Tissue plasminogen activator, Congenital anomalie

Prenatal diagnosis and implications of microphthalmia and anophthalmia with a review of current ultrasound guidelines: two case reports

Abstract Background Microphthalmia and anophthalmia are rare congenital fetal abnormalities. The combined incidence is estimated at 1 in 10,000 births. These two conditions arise from complex and incompletely understood genetic and/or environmental causes. Prenatal diagnosis is neither frequent nor easy and relies on precise, high-quality ultrasonography. Current antenatal ultrasound protocols for imaging of the fetal eye are inconsistent and inadequate to screen for the spectrum of ocular malformations, and there are no clear guidelines on detection of these rare abnormalities. Our study of two cases highlights the importance of early detection, and we review current practice and suggest a definitive fetal imaging protocol. Case presentation We present two antenatal cases, one each of microphthalmia and anophthalmia, both diagnosed at the morphology scan at our tertiary fetal medicine unit. In both cases, the parents (a 36-year-old woman of Mauritanian ethnicity and a non-consanguineous partner of Nepalese descent, and a 31-year-old Caucasian woman and non-consanguineous Caucasian partner) elected to terminate their pregnancies and made unremarkable recoveries. Subsequent fetal autopsy confirmed the ultrasound scan findings. Conclusions We recommend that antenatal ultrasound guidelines are updated to specify use of a curvilinear transducer (2–9 MHz) to image both orbits in the axial and coronal planes, aided by use of a transvaginal probe when the transabdominal approach is inadequate to generate these images. When applicable, three-dimensional reverse-face imaging should be obtained to aid the diagnosis. The presence, absence, or non-visualization of lenses and hyaloid arteries should be documented in reports and these cases referred for a tertiary-level ultrasound scan and fetal medicine review. Imaging of the orbits should occur from 12 weeks’ gestation. Magnetic resonance imaging and amniocentesis with chromosome microarray testing may provide additional genetic and structural information that may affect the overall morbidity associated with a diagnosis of microphthalmia or anophthalmia