Genomic approach to organ-specific growth control

Growth is a fundamental aspect of life cycle of all organisms. Body size varies highly in most animal groups, such as mammals. Moreover, growth of a multicellular organism is not uniform enlargement of size, but different body parts and organs grow to their characteristic sizes at different times. Currently very little is known about the molecular mechanisms governing this organ-specific growth. The genome sequencing projects have provided complete genomic DNA sequences of several species over the past decade. The amount of genomic sequence information, including sequence variants within species, is constantly increasing. Based on the universal genetic code, we can make sense of this sequence information as far as it codes proteins. However, less is known about the molecular mechanisms that control expression of genes, and about the variations in gene expression that underlie many pathological states in humans. This is caused in part by lack of information about the second genetic code that consists of the binding specificities of transcription factors and the combinatorial code by which transcription factor binding sites are assembled to form tissue-specific and/or ligand-regulated enhancer elements. This thesis presents a high-throughput assay for identification of transcription factor binding specificities, which were then used to measure the DNA binding profiles of transcription factors involved in growth control. We developed ‘enhancer element locator’, a computational tool, which can be used to predict functional enhancer elements. A genome-wide prediction of human and mouse enhancer elements generated a large database of enhancer elements. This database can be used to identify target genes of signaling pathways, and to predict activated transcription factors based on changes in gene expression. Predictions validated in transgenic mouse embryos revealed the presence of multiple tissue-specific enhancers in mouse c- and N-Myc genes, which has implications to organ specific growth control and tumor type specificity of oncogenes. Furthermore, we were able to locate a variation in a single nucleotide, which carries a susceptibility to colorectal cancer, to an enhancer element and propose a mechanism by which this SNP might be involved in generation of colorectal cancer.

Extended Conversation Pieces

'Extended Conversation Pieces' brings together conversations about art, and conversation as art. The exhibition features collaborative works by six Brisbane-based artists, Catherine or Kate (Catherine Sagin and Kate Woodcroft), Scott Ferguson (Erika Scott and Brooke Ferguson) and Courtney Coombs and Caitlin Franzmann. These artists engage with ideas of contemporary feminism through processes of dialogue and exchange; exploring subjectivity, humour and intimacy in performance and installation works. 'Extended Conversation Pieces' showcases the distinctive approach to contemporary practice at Boxcopy, an artist run initiative focused on supporting and commissioning new experimental works by Australian artists, and engaging with collaborative processes and practices. This project was commissioned by the Melbourne Art Foundation and presented at the MAF Project Rooms, Melbourne Art Fair, Melbourne in 2014.

Conversation Pieces

This curated exhibition presented works by Australian artists Agatha Gothe-Snape, Alex Martinis Roe and Hannah Raisin and collaborative works by Catherine or Kate (Catherine Sagin and Kate Woodcroft), Scott Ferguson (Erika Scott and Brooke Ferguson) and Courtney Coombs and Caitlin Franzmann. These artists engage with ideas of contemporary feminism through processes of dialogue and exchange, exploring subjectivity, humour and intimacy in performance and installation artworks. These works are generated by physical, verbal or textual dialogues between collaborators, participants or the artist and audience; and spark a conversation about contemporary feminist art practice in Australia today.

Bone Health in Children and Adolescents with Juvenile Idiopathic Arthritis and Solid Organ Transplant

Osteoporosis is a skeletal disorder characterized by compromised bone strength that predisposes to increased fracture risk. Childhood and adolescence are critical periods for bone mass gain. Peak bone mass is mostly acquired by the age of 18 years and is an important determinant of adult bone health and lifetime risk for fractures. Medications, especially glucocorticoids (GCs), chronic inflammation, decreased physical activity, hormonal deficiencies, delayed puberty, and poor nutrition may predispose children and adolescents with a chronic disease to impaired bone health. In this work, we studied overall bone health, the incidence and prevalence of fractures in children and adolescents who were treated for juvenile idiopathic arthritis (JIA) or had undergone solid organ transplantation. The first study cohort included 62 patients diagnosed with JIA and treated with GCs. The epidemiology of fractures after transplantation was investigated in 196 patients and a more detailed analysis of bone health determinants was performed on 40 liver (LTx) and 106 renal (RTx) transplantation patients. Bone mineral density (BMD) and vertebral morphology were assessed by dual-energy x-ray absorptiometry. Standard radiographs were obtained to detect vertebral fractures and to determine bone age; BMD values were adjusted for skeletal maturity. Our study showed that median BMD values were subnormal in all patient cohorts. The values were highest in patients with JIA and lowest in patients with LTx. Age at transplantation influenced BMD values in LTx but not RTx patients; BMD values were higher in patients who had LTx before the age of two years. BMD was lowest during the immediate posttransplantation years and increased subnormally during puberty. Delayed skeletal maturation was common in all patient groups. The prevalence of vertebral fractures ranged from 10% to 19% in the cohorts. Most of the fractures were asymptomatic and diagnosed only at screening. Vertebral fractures were most common in LTx patients. Vitamin D deficiency was common in all patient groups, and only 3% of patients with JIA and 25% of transplantation patients were considered to have adequate serum vitamin D levels. The total cumulative weight-adjusted dose of GC was not associated with BMD values in JIA or LTx patients. The combination of female gender and age over 15 years, parathyroid hormone concentration over 100 ng/L, and cumulative weight-adjusted methylprednisolone dose over 150 mg/kg during the three preceding years were found to be important predictors for low lumbar spine BMD in RTx patients. Based on the high prevalence of osteoporosis in the study cohorts more efforts should be put to prevention and early diagnosis of osteoporosis in these pediatric patients.

Missing pieces in the puzzle of plant microRNAs

Plant microRNAs (miRNAs) are important regulatory switches. Recent advances have revealed many regulatory layers between the two essential processes, miRNA biogenesis and function. However, how these multilayered regulatory processes ultimately control miRNA gene regulation and connects miRNAs and plant responses with the surrounding environment is still largely unknown. In this opinion article, we propose that the miRNA pathway is highly dynamic and plastic. The apparent flexibility of the miRNA pathway in plants appears to be controlled by a number recently identified proteins and poorly characterized signaling cascades. We further propose that altered miRNA accumulation can be a direct consequence of the rewiring of interactions between proteins that function in the miRNA pathway, an avenue that remains largely unexplored.

Sensory-organ-like response determines the magnetism of zigzag-edged honeycomb nanoribbons

We present an analytical effective theory for the magnetic phase diagram for zigzag-edge terminated honeycomb nanoribbons described by a Hubbard model with an interaction parameter U. We show that the edge magnetic moment varies as ln U and uncover its dependence on the width W of the ribbon. The physics of this owes its origin to the sensory-organ-like response of the nanoribbons, demonstrating that considerations beyond the usual Stoner-Landau theory are necessary to understand the magnetism of these systems. A first-order magnetic transition from an antiparallel orientation of the moments on opposite edges to a parallel orientation occurs upon doping with holes or electrons. The critical doping for this transition is shown to depend inversely on the width of the ribbon. Using variational Monte Carlo calculations, we show that magnetism is robust to fluctuations. Additionally, we show that the magnetic phase diagram is generic to zigzag-edge terminated nanostructures such as nanodots. Furthermore, we perform first-principles modeling to show how such magnetic transitions can be realized in substituted graphene nanoribbons. DOI: 10.1103/PhysRevB.87.085412

Development of an ex vivo organ culture model using human gastro-intestinal tissue and Campylobacter jejuni.

Campylobacter jejuni is an important food-borne pathogen. However, relatively little is understood regarding its pathogenesis, and research is hampered by the lack of a suitable model. Recently, a number of groups have developed assays to study the pathogenic mechanisms of C. jejuni using cell culture models. Here, we report the development of an ex vivo organ culture model, allowing for the maintenance of intestinal mucosal tissue, to permit more complex host-bacterium interactions to be studied. Ex vivo organ culture highlights the propensity for C. jejuni to adhere to mucosal tissue via the flagellum, either as discrete colonies or as multicellular units.

Length-weight relationship and organ indices of pond raised and wild population of C. gariepinus (Burchell 1822) pisces-Claridae

Samples of C. gariepinus collected from the wild and cultured populations in Plateau and Niger States of Nigeria were analyzed for length-weight relationship and organ indices (Gonadosomatic index (GSI), hepatosomatic index (HSI), renalsomatic index (RSI) and somatic fat deposit index (PDI). High correlation and linear relationship between body length and body weight was observed in all sample population (P<0.05). A significant difference was observed between the GSI of males and females of both wild and cultured population and also between females of the wild and cultured population,(P < 0.05).There was no significant difference in HSI, CSI RSI and PDI of all the sample populations (P < 0.05).The importance of length-weight relationship and organ indices in fish production are discussed

An epizootic of infectious hepatopancreatic and lymphoid organ necrosis disease in cultured Penaeus monodon: a case study

Shrimp disease of viral origin have caused large production losses worldwide. This paper presents a case study of shrimp (Penaeus monodon; Penaeus indicus) epizootic disease, covering an area of 1,050 ha in Andhra Pradesh, India. The disease struck shrimp farms in the area in July 1994. Samples from 26 shrimp farms were studied in the laboratory, and the pattern of the disease and of mortality recorded. The disease was classified as infectious hepatopancreatic and lymphoid organ necrosis disease (IHLN).