Recombinant protein production using a Tobacco yellow dwarf virus-based episomal expression vector : control of Rep activity

Over the past decade, plants have been used as expression hosts for the production of pharmaceutically important and commercially valuable proteins. Plants offer many advantages over other expression systems such as lower production costs, rapid scale up of production, similar post-translational modification as animals and the low likelihood of contamination with animal pathogens, microbial toxins or oncogenic sequences. However, improving recombinant protein yield remains one of the greatest challenges to molecular farming. In-Plant Activation (InPAct) is a newly developed technology that offers activatable and high-level expression of heterologous proteins in plants. InPAct vectors contain the geminivirus cis elements essential for rolling circle replication (RCR) and are arranged such that the gene of interest is only expressed in the presence of the cognate viral replication-associated protein (Rep). The expression of Rep in planta may be controlled by a tissue-specific, developmentally regulated or chemically inducible promoter such that heterologous protein accumulation can be spatially and temporally controlled. One of the challenges for the successful exploitation of InPAct technology is the control of Rep expression as even very low levels of this protein can reduce transformation efficiency, cause abnormal phenotypes and premature activation of the InPAct vector in regenerated plants. Tight regulation over transgene expression is also essential if expressing cytotoxic products. Unfortunately, many tissue-specific and inducible promoters are unsuitable for controlling expression of Rep due to low basal activity in the absence of inducer or in tissues other than the target tissue. This PhD aimed to control Rep activity through the production of single chain variable fragments (scFvs) specific to the motif III of Tobacco yellow dwarf virus (TbYDV) Rep. Due to the important role played by the conserved motif III in the RCR, it was postulated that such scFvs can be used to neutralise the activity of the low amount of Rep expressed from a “leaky” inducible promoter, thus preventing activation of the TbYDV-based InPAct vector until intentional induction. Such scFvs could also offer the potential to confer partial or complete resistance to TbYDV, and possibly heterologous viruses as motif III is conserved between geminiviruses. Studies were first undertaken to determine the levels of TbYDV Rep and TbYDV replication-associated protein A (RepA) required for optimal transgene expression from a TbYDV-based InPAct vector. Transient assays in a non-regenerable Nicotiana tabacum (NT-1) cell line were undertaken using a TbYDV-based InPAct vector containing the uidA reporter gene (encoding GUS) in combination with TbYDV Rep and RepA under the control of promoters with high (CaMV 35S) or low (Banana bunchy top virus DNA-R, BT1) activity. The replication enhancer protein of Tomato leaf curl begomovirus (ToLCV), REn, was also used in some co-bombardment experiments to examine whether RepA could be substituted by a replication enhancer from another geminivirus genus. GUS expression was observed both quantitatively and qualitatively by fluorometric and histochemical assays, respectively. GUS expression from the TbYDV-based InPAct vector was found to be greater when Rep was expected to be expressed at low levels (BT1 promoter) rather than high levels (35S promoter). GUS expression was further enhanced when Rep and RepA were co-bombarded with a low ratio of Rep to RepA. Substituting TbYDV RepA with ToLCV REn also enhanced GUS expression but more importantly highest GUS expression was observed when cells were co-transformed with expression vectors directing low levels of Rep and high levels of RepA irrespective of the level of REn. In this case, GUS expression was approximately 74-fold higher than that from a non-replicating vector. The use of different terminators, namely CaMV 35S and Nos terminators, in InPAct vectors was found to influence GUS expression. In the presence of Rep, GUS expression was greater using pInPActGUS-Nos rather than pInPActGUS-35S. The only instance of GUS expression being greater from vectors containing the 35S terminator was when comparing expression from cells transformed with Rep, RepA and REnexpressing vectors and either non-replicating vectors, p35SGS-Nos or p35SGS-35S. This difference was most likely caused by an interaction of viral replication proteins with each other and the terminators. These results indicated that (i) the level of replication associated proteins is critical to high transgene expression, (ii) the choice of terminator within the InPAct vector may affect expression levels and (iii) very low levels of Rep can activate InPAct vectors hence controlling its activity is critical. Prior to generating recombinant scFvs, a recombinant TbYDV Rep was produced in E. coli to act as a control to enable the screening for Rep-specific antibodies. A bacterial expression vector was constructed to express recombinant TbYDV Rep with an Nterminal His-tag (N-His-Rep). Despite investigating several purification techniques including Ni-NTA, anion exchange, hydrophobic interaction and size exclusion chromatography, N-His-Rep could only be partially purified using a Ni-NTA column under native conditions. Although it was not certain that this recombinant N-His-Rep had the same conformation as the native TbYDV Rep and was functional, results from an electromobility shift assay (EMSA) showed that N-His-Rep was able to interact with the TbYDV LIR and was, therefore, possibly functional. Two hybridoma cell lines from mice, immunised with a synthetic peptide containing the TbYDV Rep motif III amino acid sequence, were generated by GenScript (USA). Monoclonal antibodies secreted by the two hybridoma cell lines were first screened against denatured N-His-Rep in Western analysis. After demonstrating their ability to bind N-His-Rep, two scFvs (scFv1 and scFv2) were generated using a PCR-based approach. Whereas the variable heavy chain (VH) from both cell lines could be amplified, only the variable light chain (VL) from cell line 2 was amplified. As a result, scFv1 contained VH and VL from cell line 1, whereas scFv2 contained VH from cell line 2 and VL from cell line 1. Both scFvs were first expressed in E. coli in order to evaluate their affinity to the recombinant TbYDV N-His-Rep. The preliminary results demonstrated that both scFvs were able to bind to the denatured N-His-Rep. However, EMSAs revealed that only scFv2 was able to bind to native N-His-Rep and prevent it from interacting with the TbYDV LIR. Each scFv was cloned into plant expression vectors and co-bombarded into NT-1 cells with the TbYDV-based InPAct GUS expression vector and pBT1-Rep to examine whether the scFvs could prevent Rep from mediating RCR. Although it was expected that the addition of the scFvs would result in decreased GUS expression, GUS expression was found to slightly increase. This increase was even more pronounced when the scFvs were targeted to the cell nucleus by the inclusion of the Simian virus 40 large T antigen (SV40) nuclear localisation signal (NLS). It was postulated that the scFvs were binding to a proportion of Rep, leaving a small amount available to mediate RCR. The outcomes of this project provide evidence that very high levels of recombinant protein can theoretically be expressed using InPAct vectors with judicious selection and control of viral replication proteins. However, the question of whether the scFvs generated in this project have sufficient affinity for TbYDV Rep to prevent its activity in a stably transformed plant remains unknown. It may be that other scFvs with different combinations of VH and VL may have greater affinity for TbYDV Rep. Such scFvs, when expressed at high levels in planta, might also confer resistance to TbYDV and possibly heterologous geminiviruses.

Characterization of particle number concentrations and PM2.5 in a school : influence of outdoor air pollution on indoor air

Background, Aim and Scope The impact of air pollution on school children’s health is currently one of the key foci of international and national agencies. Of particular concern are ultrafine particles which are emitted in large quantities, contain large concentrations of toxins and are deposited deeply in the respiratory tract. Materials and methods In this study, an intensive sampling campaign of indoor and outdoor airborne particulate matter was carried out in a primary school in February 2006 to investigate indoor and outdoor particle number (PN) and mass concentrations (PM2.5), and particle size distribution, and to evaluate the influence of outdoor air pollution on the indoor air. Results For outdoor PN and PM2.5, early morning and late afternoon peaks were observed on weekdays, which are consistent with traffic rush hours, indicating the predominant effect of vehicular emissions. However, the temporal variations of outdoor PM2.5 and PN concentrations occasionally showed extremely high peaks, mainly due to human activities such as cigarette smoking and the operation of mower near the sampling site. The indoor PM2.5 level was mainly affected by the outdoor PM2.5 (r = 0.68, p<0.01), whereas the indoor PN concentration had some association with outdoor PN values (r = 0.66, p<0.01) even though the indoor PN concentration was occasionally influenced by indoor sources, such as cooking, cleaning and floor polishing activities. Correlation analysis indicated that the outdoor PM2.5 was inversely correlated with the indoor to outdoor PM2.5 ratio (I/O ratio) (r = -0.49, p<0.01), while the indoor PN had a weak correlation with the I/O ratio for PN (r = 0.34, p<0.01). Discussion and Conclusions The results showed that occupancy did not cause any major changes to the modal structure of particle number and size distribution, even though the I/O ratio was different for different size classes. The I/O curves had a maximum value for particles with diameters of 100 – 400 nm under both occupied and unoccupied scenarios, whereas no significant difference in I/O ratio for PM2.5 was observed between occupied and unoccupied conditions. Inspection of the size-resolved I/O ratios in the preschool centre and the classroom suggested that the I/O ratio in the preschool centre was the highest for accumulation mode particles at 600 nm after school hours, whereas the average I/O ratios of both nucleation mode and accumulation mode particles in the classroom were much lower than those of Aitken mode particles. Recommendations and Perspectives The findings obtained in this study are useful for epidemiological studies to estimate the total personal exposure of children, and to develop appropriate control strategies for minimizing the adverse health effects on school children.

Increased traffic exposure and negative birth outcomes : a prospective cohort in Australia

Background: Pregnant women exposed to traffic pollution have an increased risk of negative birth outcomes. We aimed to investigate the size of this risk using a prospective cohort of 970 mothers and newborns in Logan, Queensland. ----- ----- Methods: We examined two measures of traffic: distance to nearest road and number of roads around the home. To examine the effect of distance we used the number of roads around the home in radii from 50 to 500 metres. We examined three road types: freeways, highways and main roads.----- ----- Results: There were no associations with distance to road. A greater number of freeways and main roads around the home were associated with a shorter gestation time. There were no negative impacts on birth weight, birth length or head circumference after adjusting for gestation. The negative effects on gestation were largely due to main roads within 400 metres of the home. For every 10 extra main roads within 400 metres of the home, gestation time was reduced by 1.1% (95% CI: -1.7, -0.5; p-value = 0.001).----- ----- Conclusions: Our results add weight to the association between exposure to traffic and reduced gestation time. This effect may be due to the chemical toxins in traffic pollutants, or because of disturbed sleep due to traffic noise.

The duplicitous nature of inflammation in wound repair

Skin plays a key role in protecting the body from the onslaught of pathogens and toxins we meet during our lifetime; thus, out of necessity, we have developed a rapid repair mechanism that quickly plugs any holes in this vital organ. Upon injury, a series of highly coordinated overlapping events, that include inflammatory, proliferation and maturation phases, result in the hasty closure of the wound and restoration of skin integrity. Over the past decade it has become clear that a number of immune cells that regulate the inflammatory phase, whilst important for removal of invading pathogens, are not necessary for repair and in fact may be responsible for the subsequent scar formation that seems to have resulted from having such a rapid repair process. The magnitude and length of inflammation in the wound not only appears to dictate the extent of scar formation but also in some cases may even prevent wound closure. In this review we will explore the two sides of inflammation in wound healing and review current and future drug therapies that target inflammation to modulate the healing outcome.

The hypothermic patient

Concepts used in this chapter include: Thermoregulation:- Thermoregulation refers to the body’s sophisticated, multi-system regulation of core body temperature. This hierarchical system extends from highly thermo-sensitive neurons in the preoptic region of the brain proximate to the rostral hypothalamus, down to the brain stem and spinal cord. Coupled with receptors in the skin and spine, both central and peripheral information on body temperature is integrated to inform and activate the homeostatic mechanisms which maintain our core temperature at 37oC.1 Body heat is lost through the skin, via respiration and excretions. The skin is perhaps the most important organ in regulating heat loss. Hyporthermia:- Hypothermia is defined as core body temperature less than 350C and is the result of imbalance between the body’s heat production and heat loss mechanisms. Hypothermia may be accidental, or induced for clinical benefit i.e: neurological protection (therapeutic hypothermia). External environmental conditions are the most common cause of accidental hypothermia, but not the only causes of hypothermia in humans. Other causes include metabolic imbalance; trauma; neurological and infectious disease; and exposure to toxins such as organophosphates. Therapeutic Hypothermia:- In some circumstances, hypothermia can be induced to protect neurological functioning as a result of the associated decrease in cerebral metabolism and energy consumption. Reduction in the extent of degenerative processes associated with periods of ischaemia such as excitotoxic cascade; apoptotic and necrotic cell death; microglial activation; oxidative stress and inflammation associated with ischaemia are averted or minimised.2 Mild hypothermia is the only effective treatment confirmed clinically for improving the neurological outcomes of patient’s comatose following cardiac arrest.3

Bullying in children and adolescents : a modifiable risk factor for mental illness

It is a serious concern to health practitioners and policymakers that, in spite of substantial investment, there has been no meaningful decline in the prevalence of mental illness in Australia (Slade et al., 2009). It is now understood that a complex array of biopsychosocial factors confer varying degrees of risk of mental illness. Genetic predisposition, obstetric complications, environmental toxins, poverty, developmental delay, substance abuse, exposure to loss and trauma, chaotic family environments with accompanying abuse and neglect, chronic physical illness and maladaptive interpersonal interactions all contribute to an increased risk of developing mental disorders (Kieling et al., 2011). Bullying in childhood and adolescence is an identified risk factor for mental disorders, suicide attempts and drug and alcohol problems (Copeland et al., 2013; Moore et al., 2013)...

The impact of the environment on health in Mongolia : a systematic review

Mongolia has significant exposure to environmental risk factors because of poor environmental management and behaviors, and children are increasingly vulnerable to these threats. This study aimed to assess levels of exposure and summarize the evidence for associations between exposures to environmental risk factors and adverse health outcomes in Mongolia, with a particular focus on children. A systematic review was conducted using the PubMed, EMBASE, Web of Science, Global Health Library, CINAHL, CABI, Scopus, and mongolmed.mn electronic databases up to April 2014 . A total of 59 studies meeting the predetermined criteria were included. Results indicate that the Mongolian population has significant exposure to outdoor and indoor air pollution, metals, environmental tobacco smoke, and other chemical toxins, and these risk factors have been linked to respiratory and cardiovascular diseases among adults and respiratory diseases and neurodevelopmental disorders among children. Well-designed epidemiological investigations in vulnerable populations especially in pregnant women and children are recommended.

Environmental contributions to autism: Explaining the rise in incidence of autistic spectrum disorders

The incidence of autism spectrum disorders, a heterogenous group of neurodevelopmental disorders is increasing. In response, there has been a concerted effort by researchers to identify environmental risk factors that explain the epidemiological changes seen with autism. Advanced parental age, maternal migrant status, maternal gestational stress, pregnancy and birth complications, maternal obesity and gestational diabetes, maternal vitamin D deficiency, use of antidepressants during gestation and exposure to organochlorine pesticides during pregnancy are all associated with an increased risk of autism. Folic acid use prior to pregnancy may reduce the risk of autism. Exposure to antenatal ultrasonography, maternal gestational cigarette and alcohol use do not appear to influence the risk of autism in offspring. There is little evidence that exposure to environmental toxins such as thimerosal, polybrominated diphenyl ethers and di-(2-ethylhexyl) phthalate in early childhood increases the risk of autism. Apart from birth complications, the current evidence suggests that the majority of environmental factors increasing the risk of autism occur in the antenatal period. Consistent with the rise in incidence in autism, some of these environmental factors are now more common in developed nations. Further research is required to determine how these environmental exposures translate to an increased risk of autism. Understanding how these exposures alter neurodevelopment in autistic children may inform both the aetiopathogenesis and the strategies for prevention of autism.

Mid-Holocene Aboriginal occupation of offshore islands in northern Australia? A reassessment of Wurdukanhan, Mornington Island, southern Gulf of Carpentaria, Australia

Claims for mid-Holocene Aboriginal occupation at the shell matrix site of Wurdukanhan, Mornington Island, Gulf of Carpentaria, Australia, are reassessed through an analysis of the excavated assemblage coupled with new surveys and an extensive dating program. Memmott et al. (2006, pp. 38, 39) reported basal ages of c.5000–5500 years from Wurdukanhan as 'the oldest date yet obtained for any archaeological site on the coast of the southern Gulf of Carpentaria' and used these dates to argue for 'a relatively lengthy occupation since at least the mid-Holocene'. If substantiated, with the exception of western Torres Strait, these claims make Mornington Island the only offshore island used across northern Australia in the mid-Holocene where it is conventionally thought that Aboriginal people only (re)colonised islands after sea-level maximum was achieved after the mid-Holocene. Our analysis of Wurdukanhan demonstrates high shellfish taxa diversity, high rates of natural shell predation and high densities of foraminifera throughout the deposit demonstrating a natural origin for the assemblage. Results are considered in the context of other dated shell matrix sites in the area and a geomorphological model for landscape development of the Sandalwood River catchment.

Genetic evidence for natural hybridization between Red Snow Crab (Chionoecetes japonicus) and Snow Crab (Chionoecetes opilio) in Korea

Both red snow crab (Chionoecetes japonicus Rathbun, 1932) and snow crab (Chionoecetes opilio Fabricius, 1788) are commercially important species in Korea. The geographical ranges of the two species overlap in the East Sea, where both species are fished commercially. Morphological identification of the two species and putative hybrids can be difficult because of their overlapping morphological characteristics. The presence of putative hybrids can affect the total allowable catch (TAC) of C. japonicus and C. opilio, and causes problems managing C. japonicus and C. opilio wild resources. To date, however, no natural hybridization has been reported between C. japonicus and C. opilio, despite their overlapping distributions along the coast of the East Sea. In this study, the internal transcribed spacer (ITS) region of major ribosomal RNA genes from the nuclear genome and the cytochrome oxidase I (CO I) gene from the mitochondrial genome were sequenced to determine whether natural hybridization occurs between the two species. Our results revealed that all putative hybrids identified using morphological traits had two distinct types of ITS sequences corresponding to those of both parental species. Mitochondrial CO I gene sequencing showed that all putative hybrids had sequences identical to C. japonicus. A genotyping assay based on single nucleotide polymorphisms in the ITS1 region and the CO I gene produced the most efficient and accurate identification of all hybrid individuals. Molecular data clearly demonstrate that natural hybridization does occur between C. japonicus and C. opilio, but only with C. japonicus as the maternal parent.

Molecular and functional characterizations of a Kunitz-type serine protease inhibitor FcKuSPI of the shrimp Fenneropenaeus chinensis

Serine proteinase inhibitors play important and diverse roles in biological processes such as coagulation, defense mechanisms, and immune responses. Here, we identified and characterized a Kunitz-type proteinase inhibitor, designated FcKuSPI, of the BPTI/Kunitz family of serine proteinase inhibitors from the hemocyte cDNA library of the shrimp Fenneropenaeus chinensis. The deduced amino acid sequence of FcKuSPI comprises 80 residues with a putative signal peptide of 15 amino acids. The predicted molecular weight of the mature peptide is 7.66 kDa and its predicted isoelectric point is 8.84. FcKuSPI includes a Kunitz domain containing six conserved cysteine residues that are predicted to form three disulfide bonds. FcKuSPI shares 44e53% homology with BPTI/Kunitz family members from other species. FcKuSPI mRNAwas expressed highly in the hemocytes and moderately in muscle in healthy shrimp. Recombinant FcKuSPI protein demonstrated anti-protease activity against trypsin and anticoagulant activity against citrated human plasma in a dose-dependent manner in in vitro assays.

Comparative proteomics of uropathogenic Escherichia coli during growth in human urine identify UCA-like (UCL) fimbriae as an adherence factor involved in biofilm formation and binding to uroepithelial cells

Uropathogenic Escherichia coli (UPEC) are the primary cause of urinary tract infection (UTI) in humans. For the successful colonisation of the human urinary tract, UPEC employ a diverse collection of secreted or surface-exposed virulence factors including toxins, iron acquisition systems and adhesins. In this study, a comparative proteomic approach was utilised to define the UPEC pan and core surface proteome following growth in pooled human urine. Identified proteins were investigated for subcellular origin, prevalence and homology to characterised virulence factors. Fourteen core surface proteins were identified, as well as eleven iron uptake receptor proteins and four distinct fimbrial types, including type 1, P, F1C/S and a previously uncharacterised fimbrial type, designated UCA-like (UCL) fimbriae in this study. These pathogenicity island (PAI)-associated fimbriae are related to UCA fimbriae of Proteus mirabilis, associated with UPEC and exclusively found in members of the E. coli B2 and D phylogroup. We further demonstrated that UCL fimbriae promote significant biofilm formation on abiotic surfaces and mediate specific attachment to exfoliated human uroepithelial cells. Combined, this study has defined the surface proteomic profiles and core surface proteome of UPEC during growth in human urine and identified a new type of fimbriae that may contribute to UTI.

Age-related changes in hepatic function: An update on implications for drug therapy

The accumulation of deficits with increasing age results in a decline in the functional capacity of multiple organs and systems. These changes can have a significant influence on the pharmacokinetics and pharmacodynamics of prescribed drugs. Although alterations in body composition and worsening renal clearance are important considerations, for most drugs the liver has the greatest effect on metabolism. Age-related change in hepatic function thereby causes much of the variability in older people’s responses to medication. In this review, we propose that a decline in the ability of the liver to inactivate toxins may contribute to a proinflammatory state in which frailty can develop. Since inflammation also downregulates drug metabolism, medication prescribed to frail older people in accordance with disease-specific guidelines may undergo reduced systemic clearance, leading to adverse drug reactions, further functional decline and increasing polypharmacy, exacerbating rather than ameliorating frailty status. We also describe how increasing chronological age and frailty status impact liver size, blood flow and protein binding and enzymes of drug metabolism. This is used to contextualise our discussion of appropriate prescribing practices. For example, while the general axiom of ‘start low, go slow’ should underpin the initiation of medication (titrating to a defined therapeutic goal), it is important to consider whether drug clearance is flow or capacity-limited. By summarising the effect of age-related changes in hepatic function on medications commonly used in older people, we aim to provide a guide that will have high clinical utility for practising geriatricians.