A polymerase chain reaction-based method for isolating clones from a complimentary DNA library in sheep

The sheep (Ovis aries) is favored by many musculoskeletal tissue engineering groups as a large animal model because of its docile temperament and ease of husbandry. The size and weight of sheep are comparable to humans, which allows for the use of implants and fixation devices used in human clinical practice. The construction of a complimentary DNA (cDNA) library can capture the expression of genes in both a tissue- and time-specific manner. cDNA libraries have been a consistent source of gene discovery ever since the technology became commonplace more than three decades ago. Here, we describe the construction of a cDNA library using cells derived from sheep bones based on the pBluescript cDNA kit. Thirty clones were picked at random and sequenced. This led to the identification of a novel gene, C12orf29, which our initial experiments indicate is involved in skeletal biology. We also describe a polymerase chain reaction-based cDNA clone isolation method that allows the isolation of genes of interest from a cDNA library pool. The techniques outlined here can be applied in-house by smaller tissue engineering groups to generate tools for biomolecular research for large preclinical animal studies and highlights the power of standard cDNA library protocols to uncover novel genes.

The ancient gene C12orf29 : an exploration of its role in the chordate body plan

The sheep (Ovis aries) is commonly used as a large animal model in skeletal research. Although the sheep genome has been sequenced there are still only a limited number of annotated mRNA sequences in public databases. A complementary DNA (cDNA) library was constructed to provide a generic resource for further exploration of genes that are actively expressed in bone cells in sheep. It was anticipated that the cDNA library would provide molecular tools for further research into the process of fracture repair and bone homeostasis, and add to the existing body of knowledge. One of the hallmarks of cDNA libraries has been the identification of novel genes and in this library the full open reading frame of the gene C12orf29 was cloned and characterised. This gene codes for a protein of unknown function with a molecular weight of 37 kDa. A literature search showed that no previous studies had been conducted into the biological role of C12orf29, except for some bioinformatics studies that suggested a possible link with cancer. Phylogenetic analyses revealed that C12orf29 had an ancient pedigree with a homologous gene found in some bacterial taxa. This implied that the gene was present in the last common eukaryotic ancestor, thought to have existed more than 2 billion years ago. This notion was further supported by the fact that the gene is found in taxa belonging to the two major eukaryotic branches, bikonts and unikonts. In the bikont supergroup a C12orf29-like gene was found in the single celled protist Naegleria gruberi, whereas in the unikont supergroup, encompassing the metazoa, the gene is universal to all chordate and, therefore, vertebrate species. It appears to have been lost to the majority of cnidaria and protostomes taxa; however, C12orf29-like genes have been found in the cnidarian freshwater hydra and the protostome Pacific oyster. The experimental data indicate that C12orf29 has a structural role in skeletal development and tissue homeostasis, whereas in silico analysis of the human C12orf29 promoter region suggests that its expression is potentially under the control of the NOTCH, WNT and TGF- developmental pathways, as well SOX9 and BAPX1; pathways that are all heavily involved in skeletogenesis. Taken together, this investigation provides strong evidence that C12orf29 has a very important role in the chordate body plan, in early skeletal development, cartilage homeostasis, and also a possible link with spina bifida in humans.

Differential gene expression in breast cancer cell lines and stroma-tumor differences in microdissected breast cancer biopsies revealed by display array analysis

To examine gene-expression patterning in late-stage breast cancer biopsies, we used a microdissection technique to separate tumor from the surrounding breast tissue or stroma. A DD-PCR protocol was then used to amplify expressed products, which were resolved using PAGE and used as probe to hybridize with representative human arrays and cDNA libraries. The probe derived from the tumor–stroma comparison was hybridized with a gene array and an arrayed cDNA library derived from a GCT of bone; 21 known genes or expressed sequence tags were detected, of which 17 showed differential expression. These included factors associated with epithelial to mesenchymal transition (vimentin), the cargo selection protein (TIP47) and the signal transducer and activator of transcription (STAT3). Northern blot analysis was used to confirm those genes also expressed by representative breast cancer cell lines. Notably, 6 genes of unknown function were restricted to tumor while the majority of stroma-associated genes were known. When applied to transformed breast cancer cell lines (MDA-MB-435 and T47D) that are known to have different metastatic potential, DD array analysis revealed a further 20 genes; 17 of these genes showed differential expression. Use of microdissection and the DD-PCR array protocol allowed us to identify factors whose localized expression within the breast may play a role in abnormal breast development or breast carcinogenesis.

The SOS screen in Arabidopsis: a search for functions involved in DNA metabolism

The SOS screen, as originally described by Perkins et al. (1999), was setup with the aim of identifying Arabidopsis functions that might potentially be involved in the DNA metabolism. Such functions, when expressed in bacteria, are prone to disturb replication and thus trigger the SOS response. Consistently, expression of AtRAD51 and AtDMC1 induced the SOS response in bacteria, even affecting E. coli viability. 100 SOS-inducing cDNAs were isolated from a cDNA library constructed from an Arabidopsis cell suspension that was found to highly express meiotic genes. A large proportion of these SOS+ candidates are clearly related to the DNA metabolism, others could be involved in the RNA metabolism, while the remaining cDNAs encode either totally unknown proteins or proteins that were considered as irrelevant. Seven SOS+ candidate genes are induced following gamma irradiation. The in planta function of several of the SOS-inducing clones was investigated using T-DNA insertional mutants or RNA interference. Only one SOS+ candidate, among those examined, exhibited a defined phenotype: silenced plants for DUT1 were sensitive to 5-fluoro-uracil (5FU), as is the case of the leaky dut-1 mutant in E. coli that are affected in dUTPase activity. dUTPase is essential to prevent uracil incorporation in the course of DNA replication.

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.

Rethinking copyrights for the library through Creative Commons licensing

Two recent and related social developments of note for libraries are an upsurge in cultural participation enabled by Web 2.0 media and calls in government policy for enhanced innovation through education. Ironically, these have occurred at the same time that increasingly stringent copyright laws have restricted access to cultural content. Concepts of governmentality are used here to examine these tensions and contradictions. In particular, Foucault’s critique of the author figure and of freedom as part of the will to govern within liberal democratic societies is used to argue for better quality copyright education programs in school libraries and library information science education programs. For purposes of teaching and research, copyrights are defined as agglomerations of legal, economic, and educational discourses that enable and constrain what can and cannot be done with text in homes, schools, and library media centers. The article presents some possibilities for renewal of school libraries around copyright education and Creative Commons licensing.

Re-invent yourself: from London intensive care nursing and the Nigerian oil fields to an an academic library in Brisbane; a career change worth making.

A complete change of career forces a seismic shift in every aspect of your life. From day one, you have to face the loss of long held beliefs, behaviours, the known world of self, and security. We came from professions that themselves are poles apart, and many of the challenges we faced entering the profession were the same: juggling full-time work, part time study, and family commitmemts, taking a pay cut, and loss of social life. But over a short period of time we both transitioned to our new profession successfully. so what make our successful transition possible?

Are library and information professionals ready for evidence based practice?

Evidence based practice (EBP) is recognised as a way of improving the quality of professional practice in many disciplines however its adoption within library and information sciences (LIS) has been gradual. The term was first introduced into the library and information profession‟s vocabulary a decade ago but an impediment to its uptake is the lack of clear understanding regarding how LIS practitioners understand the concept. Partridge, Thorpe, Edwards and Hallam (2007) identified the need to understand how LIS professionals experience or understand evidence based practice and proposed a model of four categories of experience to describe how LIS professionals experience EBP. This paper extends that framework by refining the different conceptions of evidence based practice and identifying relationships which exist between the categories of experience to provide a rich description of the EBP phenomenon. The paper also argues that the phrase “evidence based librarianship” and its variations be abandoned as practitioners do not see a distinction between EBP as applied to librarianship and information practice and industry specific jargon like “evidence based library and information practice”. This research will help current and future LIS practitioners, leaders and educators engage more actively in the establishment of an evidence based culture to improve library and information practice in Australia and internationally.

A constructivist approach to media literacy education: The role of the library

An informed citizenry is essential to the effective functioning of democracy. In most modern liberal democracies, citizens have traditionally looked to the media as the primary source of information about socio-political matters. In our increasingly mediated world, it is critical that audiences be able to effectively and accurately use the media to meet their information needs. Media literacy, the ability to access, understand, evaluate and create media content is therefore a vital skill for a healthy democracy. The past three decades have seen the rapid expansion of the information environment, particularly through Internet technologies. It is obvious that media usage patterns have changed dramatically as a result. Blogs and websites are now popular sources of news and information, and are for some sections of the population likely to be the first, and possibly only, information source accessed when information is required. What are the implications for media literacy in such a diverse and changing information environment? The Alexandria Manifesto stresses the link between libraries, a well informed citizenry and effective governance, so how do these changes impact on libraries? This paper considers the role libraries can play in developing media literate communities, and explores the ways in which traditional media literacy training may be expanded to better equip citizens for new media technologies. Drawing on original empirical research, this paper highlights a key shortcoming of existing media literacy approaches: that of overlooking the importance of needs identification as an initial step in media selection. Self-awareness of one’s actual information need is not automatic, as can be witnessed daily at reference desks in libraries the world over. Citizens very often do not know what it is that they need when it comes to information. Without this knowledge, selecting the most appropriate information source from the vast range available becomes an uncertain, possibly even random, enterprise. Incorporating reference interview-type training into media literacy education, whereby the individual will develop the skills to interrogate themselves regarding their underlying information needs, will enhance media literacy approaches. This increased focus on the needs of the individual will also push media literacy education into a more constructivist methodology. The paper also stresses the importance of media literacy training for adults. Media literacy education received in school or even university cannot be expected to retain its relevance over time in our rapidly evolving information environment. Further, constructivist teaching approaches highlight the importance of context to the learning process, thus it may be more effective to offer media literacy education relating to news media use to adults, whilst school-based approaches focus on types of media more relevant to young people, such as entertainment media. Librarians are ideally placed to offer such community-based media literacy education for adults. They already understand, through their training and practice of the reference interview, how to identify underlying information needs. Further, libraries are placed within community contexts, where the everyday practice of media literacy occurs. The Alexandria Manifesto stresses the link between libraries, a well informed citizenry and effective governance. It is clear that libraries have a role to play in fostering media literacy within their communities.

Library technician course recognition : meeting the challenge of a distributed national education program

This paper looks at the challenges presented for the Australian Library and Information Association by its role as the professional association responsible for ensuring the quality of Australian library technician graduates. There is a particular focus on the issue of course recognition, where the Association's role is complicated by the need to work alongside the national quality assurance processes that have been established by the relevant technical education authorities. The paper describes the history of course recognition in Australia; examines the relationship between course recognition and other quality measures; and describes the process the Association has undertaken recently to ensure appropriate professional scrutiny in a changing environment of accountability.

"I'm thinking 'bout moving in"... An examination of the issues impacting on the recruitment of secondary school graduates to the library and information profession

In recent years concern has been expressed internationally about the future of the library and information services (LIS) profession: recruitment and retention, changing skill sets and declining numbers of people choosing librarianship as a career are all factors contributing to an uncertain future. One area yet explored in any depth is the topic of why LIS studies are not perceived, let alone promoted, as a good first professional qualification for high school graduates. This paper considers the professional literature that examines the uptake of librarianship as a first qualification by school leavers and discusses, in the context of the Australian library sector, the role of professional associations, library schools, National and State Libraries, as well as individual libraries and librarians. Examples of best practice are presented to highlight the opportunities for inspiring and motivating students through well structured and stimulating work experience programs. The topic is relevant to all librarians who are interested in the future of the LIS profession. It is argued that the focus of the present conference on ‘moving up’ and ‘moving on’ can only have real significance when the profession has a more complete understanding of the barriers to and the opportunities for ‘moving in’.

Aligning policy with practice: an evaluation of vocational education and training in the library and information services sector

Vocational education and training for the library and information services (LIS) sector in Australia offers students the career pathway to become library technicians. Library technicians play a valuable role in drawing on sound practical knowledge and skills to support the delivery of library and information services that meet client needs. Over the past forty years, the Australian Library and Information Association (ALIA) has monitored the quality of library technician courses. Since 2005, ALIA has run national professional development days for library technician educators with the goal of establishing an alternative model for course recognition focusing on the process of peer review to benchmark good practice and stimulate continuous improvement in library technician education. This initial developmental work has culminated in 2009 with site visits to all library technician courses in Australia. The paper presents a whole-of-industry case study to critically review the work undertaken to date.

University library virtual reference services : best practices and continuous improvement

The inclusion or not of chat services within Virtual Reference (VR) is an important topic for university libraries. Increasingly, email supported by a Frequently Asked Questions (FAQ) database is suggested in the scholarly literature as the preferred, cost-effective means for providing university VR services. This paper examines these issues and identifies some best practices for university library VR services relating to chat and email service, collaborative service provision, services staffing, and staff training. Further studies are required to more completely identify best practices for the complete range of VR services.

neXus2. An investigation into the library and information services workforce in Australia: The institutional perspective. Final report prepared for the Australian Library and Information Association and National and State Libraries Australia

The neXus2 research project has sought to investigate the library and information services (LIS) workforce in Australia, from the institutional or employer perspective. The study builds on the neXus1 study, which collected data from individuals in the LIS workforce in order to present a snapshot of the profession in 2006, highlighting the demographics, educational background and career details of library and information professionals in Australia. To counterbalance this individual perspective, library institutions were invited to participate in a survey to contribute further data as employers. This final report on the neXus2 project compares the findings from the different library sectors, ie academic libraries, TAFE libraries, the National and State libraries, public libraries, special libraries and school libraries.