Aquaculture Thesaurus: Descriptors Used in the National Aquaculture Information System

The Aquaculture Thesaurus consists of the descriptors used in entering material into the National Aquaculture Information System {NAIS). Terms have been arranged in a format similar to that used in the Thesaurus of Water Resources Terms published by the U. S. Department of the Interior. The National Aquaculture Information System is a NOAA project which provides computer assisted access to a broad range of information on growing marine, brackish and freshwater organisms. It was developed to answer the need for a centralized source of information in the U.S., and anyone with a need for information on aquaculture can use it

High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice

Table S4. Annotated function of differentially expressed genes identified between parents. (XLSX 1232 kb

Vector Competence and Viral Interactions of Zika Virus

Zika virus (ZIKV) (Flaviviridae: Flavivirus) is a mosquito-borne pathogen that has been linked to life-threatening health complications following its emergence in the Americas. As ZIKV continues its northern expansion, it becomes increasingly important to identify the risk for ZIKV transmission in North America through the determination of competent vector species as well as the potential for flavivirus co-infections. The susceptibility to infection and the potential for ZIKV transmission was investigated in mosquito species local to Southern Ontario, Canada. Wild mosquitoes were exposed to a ZIKV-infected blood meal or sugar meal at a final titer of 105 plaque-forming units. Colony Aedes aegypti (Linnaeus) and Aedes albopictus (Skuse) mosquitoes were also fed a ZIKV-infected bloodmeal alongside the wild mosquitoes. ZIKV transmission was not detected among the blood-fed wild mosquitoes, however, low infection rates of 9.7% and 33.3% were observed in Aedes vexans (Meigan) and Coquillettidia perturbans (Walker), respectively. In the sugar-fed wild mosquitoes, a low infection rate (6.1%) and transmission efficiency (1.2%) was observed for Culex pipiens Linnaeus only. Among the colony mosquitoes, Ae. albopictus displayed a higher transmission efficiency. The results indicate that these mosquitoes are not likely to be competent ZIKV vectors. The infection dynamics of ZIKV were further analyzed following simultaneous and sequential exposure to West Nile virus (WNV) (Flaviviridae: Flavivirus) in mammalian and insect cell lines. Cells were co-infected or superinfected with the viruses at a final multiplicity of infection of 0.01. Viral RNA was subsequently extracted and amplified from the supernatant samples. Viral interference was observed in the mammalian cell line but not in the insect cell line. Additionally, the infection order of the viruses had a significant impact on the estimated viral titer. These results may be applicable in areas where the viruses co-circulate and risk of co-infection exists

Investigating the role of enhancer-mediated gene expression in the human brain and its potential contribution to psychiatric disorders

Autism spectrum disorder (ASD) and schizophrenia (SCZ) are two neuropsychiatric conditions with variable times of onset and are influenced by both genetic and environmental factors. Genome-wide association studies (GWASs) have led to the identification of numerous genetic loci common to both these disorders, however our understanding remains far from complete, with many clinical cases without a genetic cause. While increasing the statistical power of genome-wide association studies (GWASs) to find additional risk variants could rule-in or rule out rare cases of ASD and SCZ, this presently remains a difficult task. Furthermore, the biological functions for genetic susceptibility loci remains poorly understood, particularly for more-recent discoveries of loci devoid of gene bodies. On the other hand, recent biotechnological developments have made it possible to conduct high-resolution experimental measurements of the three-dimensional architecture of the genome, including enhancer-promoter interactions (EPIs). Such data have been used to connect GWAS risk variants to their potential target genes which, in turn, provide insights into underlying molecular mechanisms and cellular processes. The functions of enhancer-promoter interactions in controlling gene expression programmes is crucial to how implicated genes mediate neurological function and disease. Yet, knowledge on enhancer-promoter interactions remains to be used in conjunction with GWAS data, particularly on such data from specific brain cell types, which may be useful to uncover the biological underpinnings of psychiatric conditions. This thesis examines the role of enhancer-mediated gene expression in the human brain and its potential contribution to psychiatric conditions. In Chapter 2, I report on the identification of significant chromosomal interactions from studies of brain Hi-C data generated from neuronal and glial cells, with the goal to investigate the impact of EPIs genome-wide, as well as to provide a template for an in-depth understanding of how EPIs impact transcriptional regulation. In the Chapter 3, I discuss a novel approach integrating Activity by Contact (ABC) and gene set enrichment analyses of GWAS data in two steps. In the first step, ABC is used to predict enhancer-gene regulatory interactions in a given cell type (e.g., glial cells, neurons). Secondly, Hi-C coupled multi-marker analysis of genomic annotation (H-MAGMA) is used to assign the SNPs located in the regulatory regions identified by ABC to each gene and calculate gene-level association p-values. I applied this novel framework (ABC-HMAGMA) to GWAS data from SCZ and ASD, to identify novel SCZ and ASD trait-associated genes and molecular pathways. In Chapter 4, I have evaluated a potential novel mechanism for the regulation of enhancer activity within cells. I hypothesized that, in addition to its known roles in DNA replication and transcription, Topoisomerase I may regulate enhancer activity in brain cells. To test this hypothesis, I employed RNA-seq and transient transcriptome sequencing (TT-seq) data, a method that enriches for short-lived enhancer derived RNAs. These data showed that Topoisomerase I inhibition leads to significant changes in eRNA expression and offers evidence that such changes are relevant to the homeostatic functions for Top 1 in cellular gene expression regulation

Somatic embryogenesis and cryopreservation of cauliflower (Brassica oleracea var. botrytis)

Abstract Successful efficient whole cauliflower plant regeneration via somatic embryogenesis from root derived callus tissue was achieved. The research confirmed for the first time the capability of mass production of cauliflower somatic embryos through the indirect pathway. The best callus induction and proliferation was on semi solid Murashige and Skoog (MS) medium supplemented with 2, 4-D at 0.15 mg L-1 and Kinetin at 0.1 mg L-1 and 3% sucrose. The response of different explant types (cotyledon, hypocotyls and root) through callus induction and subsequent culture was determined. The best period for subsequent callus culture was 21 days. Continuous immersion in agitated liquid medium technique was subsequently used for primary somatic embryo production. The culture requirements were empirically optimized including: explants source and size of callus tissue, blending duration, plant growth regulator combinations and concentrations as well as carbohydrate type and concentration. The highest mean number of somatic embryos (30.9) per explant was achieved using root derived embryogenic callus tissue on MS medium provided with IAA 0.05 mgL-1 and Kinetin at 0.5 mgL-1 and 2% sucrose. Somatic embryos were developed and matured on this medium and germinated with the highest percentage (60%) on semi-solid MS medium devoid of growth regulators. The culture conditions that led to the formation of secondary somatic embryos were identified. The presence of activated charcoal in the culture medium had an effect on this process but some abnormality of secondary somatic embryos was observed. Artificial seeds were produced by encapsulating the somatic embryos with a sodium alginate gel (2%) and complexing with calcium chloride (100 mM) for 20 min. The ability of these artificial seed for germination was evaluated using various combinations of plant growth regulators that were either incorporated in the artificial matrix or in the germination semi-solid culture medium. It was confirmed that cauliflower root derived embryogenic callus tissue can be cryopreserved following a preculture-dehydration technique. Following cryopreservation, embryogenic cultures can proliferate in agitated liquid medium, and somatic embryos at the globular stage were formed. Also cold storage at 5 °C in the dark was used successfully to store cauliflower callus tissue for three months without diminution of the competence for somatic embryos formation. This ability for cold storage could have a positive effect in reducing costs and efforts that result from subsequent sub-culture. The encapsulation-dehydration technique was assessed for cryopreservation of somatic embryos but failed to lead to survival of any embryos. Somatic embryos that were produced in this study were able to be well acclimated using a reliable weaning procedure that achieved high rates of survival of plantlets and their subsequent growth to normal plants in the field was assessed. Morphological characteristics of somatic plants compared favourably with zygotic plants but although there was phenotypic similarity, some differences in plant height, curd size and time for curd maturity were observed.Iraqi Ministry of Higher Education and Scientific Researc

The role of meta-topolins on the physiology of micropropagated 'Williams' bananas (Musa spp. AAA)

Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.Banana production ranks fifth behind cereals as a food crop and has potential, along with other major crops, to feed the world's increasing population. Globally, continuous efforts and techniques including the use of plant tissue culture (PTC) have been devised for increasing the production of several Musa species. The choice of cytokinin (CK) is one of the most critical factors in developing a successful PTC protocol. Since the discovery of topolins as naturally occurring aromatic CKs, they have emerged as genuine alternatives to the long serving CKs (benzyladenine = BA, zeatin = Z and kinetin = KIN) in PTC. Globally, the past 15 years has witnessed a surge in the use of topolins and their derivatives in research laboratories. Topolins have demonstrated great potential during culture initiation and protocol optimization as well as for counteracting various in vitro induced physiological disorders in some species. In terms of general physiology (growth, phytochemical and photosynthetic pigment contents as well as genetic fidelity), the topolins were compared with BA using 'Williams' bananas with minimal residual exogenous CK carry-over effects. The five topolins tested were meta-Topolin (mT); meta-Topolin riboside (mTR); meta-Methoxy topolin (MemT); meta-Methoxy topolin riboside (MemTR) and meta-Methoxy topolin 9-tetrahydropyran-2-yl (MemTTHP). Based on evidence of potential CK- and auxin-like activity of smoke-water (SW) and karrikinolide (KAR1) at low concentrations, a similar comparative study involving both compounds and mT was performed. For a further understanding of banana physiology in vitro, the effect of supplementing either mT- or BA-requiring cultures with roscovitine (a cyclin-dependent kinase and N-glucosylation inhibitor) and INCYDE (an inhibitor of CK degradation) on the endogenous CK profiles was investigated. In addition, greenhouse experiments geared towards improving the acclimatization competence of tissue-cultured banana plantlets via application of different concentrations of SW and vermicompost leachate was conducted. Sterile shoot-tip explants were cultured on modified Murashige and Skoog (MS) media supplemented with 10, 20 or 30 μM of the tested CKs for 42 days while rooting experiments involved the use of classic auxins as well as SW and KAR1. Apart from 10 μM BA and 30 μM MemTTHP treatments, the number of shoots produced with all the CK treatments were significantly higher than the control. Treatment with 30 μM mT resulted in the highest number of shoots (7.3±1.0) which is an indication of the requirement of exogenous CK for increased shoot proliferation in 'Williams' bananas The use of 10 μM MemTTHP had the least root inhibitory effect during the shoot proliferation phase. As an indication of the toxicity of applied CK, MemT- and MemTR-regenerants were the most deformed while mTR-regenerated plantlets demonstrated the best quality across all the CKs tested. In mT- and BA-derived shoots, SW and KAR1 significantly increased the number and length of roots compared to the control. During the rooting phase, topolin treatments produced more off-shoots than BA-treated ones which inevitably improved the overall number of regenerated shoots. Total phenolic levels were highest in 10 μM mT- and 30 μM MemTTHP-treated plantlets detected in the aerial and underground parts, respectively. It is interesting that in the underground parts, 10 μM mT resulted in the production of the highest amount of proanthocyanidins which was approximately five-fold higher than in the control plants. On the other hand, 10 μM MemTTHP-treated plantlets had significantly higher total flavonoids within the aerial parts. In view of the stimulation of secondary metabolites in the majority of the CK-treated plantlets, the current results indicate the role of the type and concentration of applied CK as potential elicitors in PTC. Generally, the maximum photosynthetic pigment content was attained between 40-50 days. The control plantlets had the highest pigment content (1150 μg/g FW) while 10 μM MemTTHP had the best pigment stimulatory effect among the tested CKs. Nevertheless, in vitro propagation of banana devoid of CKs is not a practical option due to low shoot proliferation rates. Scanning electron microscopy (SEM) of the foliar surface showed that the stomatal density was highest in 10 μM MemTTHP-treated and lowest in 10 μM MemTR-treated plantlets. Prolonging the culture duration as well as increasing CK concentrations reduced the pigment content. However, the drastic breakdown in chlorophyll pigments beyond 50 days was slightly inhibited by the presence of mT, mTR, MemTTHP and BA compared to the control. Current findings indicate the potential anti-senescence activity of the topolins such as mT, mTR and MemTTHP under in vitro conditions. This study articulates that the right choice and concentration of CKs applied during in vitro propagation may alleviate photomixotrophic-induced physiological stress that usually accompanies the transfer of plantlets to ex vitro conditions. Findings indicate that the effect of subculturing contributed significantly to the higher rate of variation in 'Williams' bananas in vitro. The presence of CK in the culture media apparently aggravated the stress on the explants as indicated in the relatively higher percentage polymorphic bands compared to the controls. Among the tested CKs, the use of mTR and MemTTHP caused the least detrimental effect on the regenerants while mT-treated plantlets had the most polymorphic bands. Hence, it is recommended that subculturing cycles from the initial explant establishment should be limited to a maximum of five. The use of SW and KAR1 improved the level of photosynthetic pigment and phenolic compounds in the micropropagated bananas. However, they had a negative effect on shoot proliferation; hence their inclusion is more desired when used at the rooting phase of micropropagation. Perhaps, these compounds could be used in conjunction with auxin to increase the number of roots prior to the acclimatization stage. The enhanced photosynthetic pigment level resulting from addition of SW and KAR1 would also play a vital role during acclimatization of the micropropagated plants. The present finding serves as an alternative approach, available to researchers for improving the quantity of secondary metabolites in micropropagated plants. The highest regeneration rate (93%) was observed in BA + roscovitine treatment while mT + INCYDE-treated plantlets produced most shoots. Treatment with BA + roscovitine had the highest shoot length and biomass. Although not significant, there was more proanthocyanidins in BA + roscovitine treatments compared to the treatment with BA alone. On the contrary, total phenolics were significantly higher in mT + roscovitine treatment than in the mT-treated regenerants. The presence of roscovitine and/or INCYDE had no significant effect on the photosynthetic pigments of the banana plantlets. Forty-seven aromatic and isoprenoid CKs categorized into nine CK-types were detected at varying concentrations. The presence of mT + roscovitine and/or INCYDE increased the levels of O-glucosides, while 9-glucosides remained the major derivative in the presence of BA. Generally, the underground parts had higher CK levels than the aerial parts; however the presence of INCYDE increased the level of CK quantified in the aerial parts of both CK treated plantlets. Apparently, the presence of INCYDE serves to enhance transportation of the CK towards the aerial regions. From a practical perspective, the use of roscovitine and INCYDE in PTC could be crucial in the alleviation of commonly observed in vitro-induced physiological abnormalities. Soil drenching with SW significantly increased the root length (1:1000 and 1:500 dilutions) as well as fresh and dry weight (1:1000; 1:500 and 1:250 dilutions) when compared to foliar application. Vermicompost leachate (1:10 and 1:5 dilutions) significantly enhanced the shoot length, root length, leaf area and dry weights. Vermicompost leachate (1:20; 1:10 and 1:5 dilutions) also significantly increased the number of off-shoots. The positive effect on rooting is beneficial for acclimatization and establishment of tissue-cultured banana plantlets in nurseries and subsequent transfer to the field. However, field trials will be necessary to substantiate the effects demonstrated by these compounds. In an attempt to contribute to improving banana micropropagation, the current findings provide additional evidence on the increasing advantage of topolins over BA. Nevertheless, some detrimental physiological effects observed with some of the topolins (for example, MemT and MemTR) are clear indication that they should not be taken as a panacea in PTC. Besides optimizing efficient PTC protocols through stringent choice of CKs, other associated physiological and metabolic events taking place in culture during the optimization process need more in-depth investigation. In addition to contributing towards the better understanding of the mode of action of these CKs, such an approach will help solve associated physiological and developmental problems in vitro