Estimating nephron number in the developing kidney using the physical disector/fractionator combination

Over the last decade the development of new molecular biology tools, advanced microscopy, live imaging and systems biology approaches have revolutionized our conception of how embryonic development proceeds. One fundamental aspect of development biology is the concept of morphogenesis: understanding how a group of multipotent cells organize and differentiate into a complex organ. In Kidney Development: Methods and Protocols, expert researchers in the field detail different approaches to tackle kidney development. These approaches include culture and live imaging aspects of kidney development, analyzing the 3-dimensional aspects of branching morphogenesis as well as nephrogenesis, manipulation of the gene/protein expression during kidney development as well as in the adult kidney, and how to assess kidney malformation and disease. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Kidney Development: Methods and Protocols seeks to aid scientists in the further study of the process of morphogenesis which is fundamental important not only for studying developmental biology but also for regenerative medicine.

Investigation into the design and development of the Toad Interactive Multimedia Program (TIMMP) and its use by first year biology undergraduates learning dissection procedures and in situ functional anatomy

Investigates how first year biology undergraduates learn dissection when they have access to such interactive multimedia technology. Related design and developmental factors were evaluated in relation to how they helped students learn the content in the multimedia program. Through the use of interactive technology students can learn at their own pace without the need for actual animal dissection.

Functional imaging to understand biomechanics : a critical tool for the study of biology, pathology and the development of pharmacological solutions

We present four case studies of the literature discussing the effects of physical forces on biological function. While the field of biomechanics has existed for many decades, it may be considered by some a poor cousin to biochemistry and other traditional fields of medical research. In these case studies, including cardiovascular and respiratory systems, we demonstrate that, in fact, many systems historically believed to be controlled by biochemistry are dominated by biomechanics. We discuss both the previous paradigms that have advanced research in these fields and the changing paradigms that will define the progressions of these fields for decades to come. In the case of biomechanical effects of flowing blood on the endothelium, this has been well understood for decades. In the cases of platelet activation and liquid clearance from the lungs during birth, these discoveries are far more recent and perhaps not as universally accepted. While only a few specific examples are examined here, it is clear that not enough attention is paid to the possible mechanical links to biological function. The continued development of these research areas, with the inclusion of physical effects, will hopefully provide new insight into disease development, progression, diagnosis and effective therapies.

Dissecting ADAMTS proteoglycanase biology in development and disease

 This research was focused upon members of the ADAMTS family of 'proteinases', proteins that have enzymatic activity. Their dysregulation can cause developmental defects and disease. This thesis describes the expression and regulation of ADAMTS15, as well as new developmental functions and inhibition of ADAMTS5 in arthritis.

Using bioinformatics techniques for gene identification in drug discovery and development

As more and more evidence has become available, the link between gene and emergent disease has been made including cancer, heart disease and parkinsonism. Analyzing the diseases and designing drugs with respect to the gene and protein level obviously help to find the underlying causes of the diseases, and to improve their rate of cure. The development of modern molecular biology, biochemistry, data collection and analysis techniques provides the scientists with a large amount of gene data. To draw a link between genes and their relation to disease outcomes and drug discovery is a big challenge: How to analyze large datasets and extract useful knowledge? Combining bioinformatics with drug discovery is a promising method to tackle this issue. Most techniques of bioinformatics are used in the first two phases of drug discovery to extract interesting information and find important genes and/or proteins for speeding the process of drug discovery, enhancing the accuracy of analysis and reducing the cost. Gene identification is a very fundamental and important technique among them. In this paper, we have reviewed gene identification algorithms and discussed their usage, relationships and challenges in drug discovery and development.

Focusing in on structural genomics : the University of Queensland structural biology pipeline

The flood of new genomic sequence information together with technological innovations in protein structure determination have led to worldwide structural genomics (SG) initiatives. The goals of SG initiatives are to accelerate the process of protein structure determination, to fill in protein fold space and to provide information about the function of uncharacterized proteins. In the long-term, these outcomes are likely to impact on medical biotechnology and drug discovery, leading to a better understanding of disease as well as the development of new therapeutics. Here we describe the high throughput pipeline established at the University of Queensland in Australia. In this focused pipeline, the targets for structure determination are proteins that are expressed in mouse macrophage cells and that are inferred to have a role in innate immunity. The aim is to characterize the molecular structure and the biochemical and cellular function of these targets by using a parallel processing pipeline. The pipeline is designed to work with tens to hundreds of target gene products and comprises target selection, cloning, expression, purification, crystallization and structure determination. The structures from this pipeline will provide insights into the function of previously uncharacterized macrophage proteins and could lead to the validation of new drug targets for chronic obstructive pulmonary disease and arthritis.

Suppressors of cytokine signaling : functions in normal biology and roles in disease

Suppressor of cytokine signaling (SaCS) proteins have been identified as key negative regulators of cytokine and growth factor signaling. Therefore, given the diverse roles played by cytokines and growth factors in development and disease, it is not surprising that the sacs proteins themselves possess equally diverse and important functions, such as the control of hematopoiesis, immune function, growth and placental development. Significantly, more recent studies are increaSingly highlighting the crucial roles played by SOCS proteins in disease, particularly their tumor suppressor and anti-infammatory functions. Collectively, this research has served to confirm the importance of this class of proteins and suggests that therapeutic strategies for modulating SOCS proteins might be relevant for a range of diseases.

Studies of the biology of four species of Dicranoloma

Populations of Dicranoloma billardierei (Brid) Par., D. dicarpum (Nees.) Par., D. menziesii (Tayl.) Par. and D. platycaulon (C. Muell) Dix, from two pockets of cool temperate rainforest within the Yarra Ranges National Park (Cement Creek and Myrtle Loop), were sampled for a period of two years to establish their reproductive biology. The population dynamics within quadrats of D. billardierei, D. menziesii and D. platycaulon at Cement Creek also was investigated over a two year period, through the seasonal recording of shoot loss and/or gain, The four species of Dicranoloma were dioicous and sexually dimorphic, with dwarf males epiphytic on the female plants. Antheridia were initiated before archegonia and required ca, 6 months to reach maturity, compared with 1 to 2 months for archegonia. More archegonia than antheridia occurred per inflorescence and were more variable Fertilization occurred during winter in D. billardierei and summer/ autumn in D. menziesii and D. platycaulon. The duration of the sporophyte cycle of D. menziesii was 12 months, shorter than that of D. billardierei and D. platycaulon which lasted for a period of 18 months to 2 years. In the latter two species an overlap of sporophyte generations occurred. This was particularly pronounced in D. billardierei as sporophytes remained in the swollen venter maturation stage for a period of 6 months. The duration of the sporophyte cycle could not be ascertained as few fruiting stems of D. dicarpum were found. All four species of Dicranoloma regenerated from fragments cultured in the laboratory, and only two of the species showed evidence of production of asexual propagules in the field. Dicranoloma dicarpum was found to produce gemmae, an observation which had not been recorded before, and most of the leaves on stems of D. platycaulon had detached subulas. Shoot loss was minimal in all four species, and when it did occur, (eg D. billardierei) it was attributed to disturbance by animals. Within quadrats there was an increase in shoot density which resulted from the development of innovation(s) and/or side branches rather than from the recruitment of new plants from spores or the regeneration of asexual propagules. The four species of Dicranoloma investigated were robust, perennial mosses and formed an important component of the bryophytes found within the study area. Dicranoloma menziesii was the predominant species establishing on a variety of substrata, particularly as an epiphyte on Nothofagus cunninghamii The other species were more selective in their choice of substratum. Dicranoloma platycaulon was found exclusively on the trunks of myrtle beech and D. billardierei on fallen logs and exposed roots. Dicranoloma dicarpum which was not common, grew as an epiphyte on myrtle beech and on rocks.

Control of ovarian development in the yabby (Cherax destructor)

A study under controlled conditions of ovarian development and rematuration in the yabby (Cherax destructot) was undertaken. The purpose of the study was to improve fundamental understanding of the reproductive biology of the species and provide a basis for application to hatchery management in culture. A review was made of the current status of yabby culture in Australia and the present understanding of reproductive biology of decapod Crustacea. The review emphasised factors controlling several aspects of ovarian development, in particular the processes of vitellogenesis. The subsequent study was designed within the context of current hatchery practice and was based on existing knowledge of decapod reproduction, The sexual differentiation of the yabby after hatching was investigated by serial histological sections, and experiments were carried out to investigate the possibility of sex reversal of males. Most of this Investigation was concerned with removing the influence of the androgenic gland in directing male development, with the intent of observing the development of the elementary gonadal tissue into ovary. It was found that in contrast to other crustacean species, the sex of the yabby becomes fixed before the development of external secondary sexual characteristics, and before the androgenic gland can be discerned. Ovarian tissue developed in females at less than 8 weeks after hatching. A preliminary examination was undertaken for feminising parasites in gonadal tissue of a hermaphrodite yabby. Investigation of the ovary after spawning demonstrated that whilst the female was held under constant conditions of temperature and photoperiod, little rematuration occurred. Except for generation of previtellogenic oocytes during the first two days, the gonaciosomatic index remained low for up to 5 months after spawning. If the temperature of the female was reduced to 10°C and maintained constant, the previtellogenic oocytes were partially resorbed over a three week period. Rematuration then commenced, albeit at a low rate because of the reduced temperature, A method for standardising gonadosomatic indices was developed which took into account differences in hepatopancreatic nutrient reserves of individuals and loss of one or more appendages. This part of the study also considered constraints to rematuration and developed a method of accounting for differences in the ability of females to remature after spawning. Experiments were carried out to investigate the effect of crowding and temperature manipulation on initiating ovarian rematuration and to determine the rate of rematuration at 22°C once initiated. The duration of low temperature had no effect on rematuration; an overnight cooling was sufficient to initiate the process, Rematuration to the end of stage 2 vltellogenesis was substantially complete within 10 days. Crowding of females suppressed rematuration, but less than ideal water quality was not found to have any effect. The presence of a male initiated rematuration at a similar rate, but also led to stage 3 vitetlogenesis and spawning. A study was made of the pheromonal influence of the male through water borne factors without success. Rematuration could not be induced in ovigerous females. The literature review indicated that ovarian rematuration was under the control of an ovary stimulating hormone produced by the thoracic nerve ganglia. Attempts were therefore made to stimulate ovarian rematuration by incorporating the thoracic nerve into the diet of females. Attempts were also made to induce the release of ovary stimulating hormone from the thoracic nerve with 5-hydroxytryptamine, and also with octopamine. No effects were found, but a significant difference between the neurophysiology of the yabby and northern hemisphere crayfish was observed, and the implications of this finding are discussed. The study did not produce any conclusive evidence of an ovary stimulating hormone for the yabby. A model of ovarian rematuration which collects the findings of the experimental investigations was developed, and was used to suggest a hatchery broodstock management protocol. This model differs from existing models in that rematuration triggers and nutritional status are considered.

The fishery, biology and management of three inland water-bodies, Vietnam

This study was carried out from 1997 to 2004 and its findings have significantly enhanced our understanding on fishery, biology, and management of three inland water bodies in Vietnam. The study also provides insights into development of management guidelines and recommendations for future fisheries development in the research area.

Exploring online communities of practice for biology teachers in Botswana

This study, which sought to determine the potential of an online community of practice among biology teachers in Botswana, has identified teacher level, school level and systemic influences as shaping the process and outcome of an online intervention into a teacher professional development programme run by the University of Botswana.

Biology and management of Murray cod reproduction within controlled environments

The emerging Murray cod aquaculture industry is currently restricted by a lack of consistent and year-round production of fingerlings. Biological information and reproductive technologies developed during this research have facilitated the development of indoor, environmentally-controlled breeding practices for this species, thereby enabling Murray cod juveniles to be produced on-demand.

Embedding academic skills development in course delivery

Innovative approaches need to be adopted to meet the challenge of ensuring that graduates at the end of their course of study are not only strong in their discipline, but also have the required generic skills to give them a good standing within their selected professions. This paper reports on a study that examined how well academic skills are embedded into the undergraduate Environmental Science curriculum at Deakin University in Australia. It reports on students’ self evaluation of their essay writing skills, and a case study that involves a discipline specialist working with an academic skills advisor to enhance student generic skills. It discusses the patchy nature of current implementation of programs for generic skill education.

Development of microfluidic-based analytical methodology for studying the effects of chemotherapy agents on cancer tissue

Whilst a multitude of techniques have been employed to study the biology of tumour tissue and its response to chemotherapeutic reagents, most current methodologies do not capture the sophistication of the in vivo environment. Microfluidics however offers the ability to maintain and interrogate primary tissue samples in an environment with biomimetic flow characteristics. In this study head and neck squamous cell carcinoma (HNSCC) tumour biopsies have been used to investigate the performance of a microfluidic device for generating clinically-useful information. The response of fresh and cryogenically-frozen primary HNSCC or metastatic lymph node samples to chemotherapy drugs (cisplatin, 5-flurouracil or docetaxel), alone and in combination, were monitored for both proliferation (water-soluble tetrazolium salt metabolism) and cell death biomarker release (lactate dehydrogenase, LDH) “off-chip”. The frozen tissue showed no significant difference in terms of either proliferation or LDH release in comparison with the matched fresh samples. Administration of all drugs caused cell death, in a dose-response manner, with the combination showing the greatest amount of cytotoxicity particularly at days 8 and 9; correlating well with published clinical data. The system described here offers an innovative method for studying the tumour microenvironment in vitro and, through incorporation of relevant analytical modules, provides the basis of a pre-clinical device that can be used to define personalised treatment regimens.