Genetic Characteristic of Indonesian Local Ducks Based on Single Nucleotide Polymorphism (SNP) Analysis in D-loop Region Mitochondria DNA

Abstract. The aim of the study was to know the genetic characteristic and polymorphysm of Indonesian local ducks including Magelang, Tegal, Mojosari, Bali and Alabio duck based on Single Nucleotide Polymorphism (SNP) analysis in D-loop region mtDNA. The long term aim was to set the spesific genetic marker based on SNP D-loop region mtDNA which could differentiate local ducks in Indonesia. In the future, it could be used as selection tool for local duck conservation, and refinement strategy as well as the improvement of genetic quality by utilizing the available native duck germplasm. There were 20 ducks for each duck population and were taken 3 ml of its blood as sample. DNA Isolation Kit high pure PCR template preparation (Geneaid) was uded for Genome DNA isolation.  Amplification with PCR technique used primer DL-AnasPF (L56) as forward and DL-AnasPR (H773) as reverse. Next, PCR product or amplicon were sequenced. Sequence result were analyzed with SNP technique and observed the similarity and difference of its nucleotide sequence between individual and population. The result of the study showed that genome DNA from local duck in Indonesia was successfully isolated. DNA fragment of 718 bp was amplified with primer pair of DL-AnasPF and DL-AnasPR. Nucleotide sequence was 469 nt and analyzed with SNP technique. It was compared with standard nucleotide sequence of Anas platyrhynchos (HM010684.1) in Gen Bank. The result of nucleotide sequence similarity percentage was 99.68±0.56%. Single Nucleotide Polymorphism D-loop region mtDNA Indonesian local duck was 0.32±0.56%.  Some SNP was found in Magelang duck C (Klawu blorok), F (Cemani black),  G (Gambiran), H (Jarakan kalung), I (Jowo plain) and K (Plain white) also Tegal duck 8, 1, 2, 5, 2, 8 and 2 SNP respectively. It could be concluded that polymorphic genetic characteristic similarity were existed in Indonesia local duck populations which was shown by its big standard deviation SNP in D-loop region mtDNA. Magelang duck with different feather color relatively more polymorphic to another local duck in Indonesia. Single Nucleotide Polymorphism which was achieved could be used as genetic marker that differentiate genetic characteristic of Indonesian local ducks.Key words:  genetic characteristic, local duck, Single Nucleotide Polymorphism (SNP), D-loop mtDNAAbstrak.  Penelitian ini bertujuan untuk mengetahui karakteristik genetik dan polimorfisme itik lokal Indonesia yaitu itik Magelang, Tegal, Mojosari, Bali dan Alabio berdasarkan analisis Single Nucleotide Polymorphism (SNP) daerah D-loop mtDNA. Tujuan jangka panjangnya adalah menetapkan marker atau penanda genetik berdasarkan SNP daerah D-loop mtDNA spesifik yang dapat membedakan itik-itik lokal yang ada di Indonesia. Selanjutnya digunakan sebagai  alat bantu seleksi untuk konservasi, pembibitan  dan pengembangbiakan itik lokal.  Populasi masing-masing jenis itik lokal yang digunakan sebanyak 20 ekor untuk diambil 3 ml sampel darahnya. Isolasi DNA genom menggunakan DNA Isolation Kithigh pure PCR template preparation (Geneaid). Amplifikasi dengan teknik PCR menggunakan pasangan primer DL-AnasPF (L56) sebagai forward dan DL-AnasPR (H773) sebagai reverse. Produk PCR atau amplikon yang diperoleh disekuensing. Hasil sekuensing dianalisis dengan teknik SNP dan diamati kesamaan dan perbedaan urutan nukleotida antar individu itik dan antar populasi.  Hasil penelitian menunjukkan bahwa DNA genom dari itik lokal di Indonesia berhasil diisolasi. Amplifikasi dengan teknik PCR berhasil memperoleh fragmen berukuran 718 bp. Urutan nukleotida hasil sekuensing sebesar 469 nt dianalisis dengan teknik SNP dan dibandingkan dengan urutan nukleotida standar dari itik Anas platyrhynchos (HM010684.1) yang ada di Gen Bank, diperoleh persentase kesamaan urutan nukleotid sebesar 99,68±0,56%. Single Nucleotide Polymorphism daerah D-loop mtDNA pada itik lokal di Indonesia sebesar 0,32±0,56%. Sejumlah SNP ditemukan pada itik Magelang C (Klawu blorok), F (Hitam cemani),  G (Gambiran), H (Jarakan kalung), I (Jowo polos) dan K (Putih polos) serta itik Tegal  masing-masing 8, 1, 2, 5, 2, 8 serta 2 SNP. Kesimpulan dari penelitian ini adalah terdapat karakteristik genetik yang polimorfik pada populasi itik lokal di Indonesia, ditunjukkan dengan adanya simpang baku SNP pada daerah D-loop mtDNA yang relatif besar. Itik Magelang dengan warna bulu yang berbeda relatif lebih polimorfik dibandingkan dengan itik lokal lainnya di Indonesia.  Single Nucleotide Polymorphism yang diperoleh dapat digunakan sebagai penanda genetik yang dapat membedakan karakteristik genetik yang dimiliki oleh itik lokal di Indonesia.Kata kunci:  karakteristik genetik, itik lokal, Single NucleotidePolymorphism (SNP),  D-loop mtDNA

Model Based Estimating System for Civil Concrete Structures

An earlier CRC-CI project on ‘automatic estimating’ (AE) has shown the key benefit of model-based design methodologies in building design and construction to be the provision of timely quantitative cost evaluations. Furthermore, using AE during design improves design options, and results in improved design turn-around times, better design quality and/or lower costs. However, AEs for civil engineering structures do not exist; and research partners in the CRC-CI expressed interest in exploring the development of such a process. This document reports on these investigations. The central objective of the study was to evaluate the benefits and costs of developing an AE for concrete civil engineering works. By studying existing documents and through interviews with design engineers, contractors and estimators, we have established that current civil engineering practices (mainly roads/bridges) do not use model-based planning/design. Drawings are executed in 2D and only completed at the end of lengthy planning/design project management lifecycle stages. We have also determined that estimating plays two important, but different roles. The first is part of project management (which we have called macro level estimating). Estimating in this domain sets project budgets, controls quality delivery and contains costs. The second role is estimating during planning/design (micro level estimating). The difference between the two roles is that the former is performed at the end of various lifecycle stages, whereas the latter is performed at any suitable time during planning/design.

A framework for assessing social policy inclusion proposals

This document outlines a framework that could be used by government agencies in assessing policy interventions aimed at achieving social outcomes from government construction contracts. The framework represents a rational interpretation of the information gathered during the multi-outcomes construction policies project. The multi-outcomes project focused on the costs and benefits of using public construction contracts to promote the achievement of training and employment and public art objectives. The origin of the policy framework in a cost-benefit appraisal of current policy interventions is evidenced by its emphasis on sensitivity to policy commitment and project circumstances (especially project size and scope).The quantitative and qualitative analysis conducted in the multi-outcomes project highlighted, first, that in the absence of strong industry commitment to policy objectives, policy interventions typically result in high levels of avoidance activity, substantial administrative costs and very few benefits. Thus, for policy action on, for example, training or local employment to be successful compliance issues must be adequately addressed. Currently it appears that pre-qualification schemes (similar to the Priority Access Scheme) and schemes that rely on measuring, for example, the training investments of contractors within particular projects do not achieve high levels of compliance and involve significant administrative costs. Thus, an alternative is suggested in the policy framework developed here: a levy on each public construction project – set as a proportion of the total project costs. Although a full evaluation of this policy alternative was beyond the scope of the multi-outcomes construction policies project, it appears to offer the potential to minimize the transaction costs on contractors whilst enabling the creation of a training agency dedicated to improving the supply of skilled construction labour. A recommendation is thus made that this policy alternative be fully researched and evaluated. As noted above, the outcomes of the multi-outcomes research project also highlighted the need for sensitivity to project circumstances in the development and implementation of polices for public construction projects. Ideally a policy framework would have the flexibility to respond to circumstances where contractors share a commitment to the policy objectives and are able to identify measurable social outcomes from the particular government projects they are involved in. This would involve a project-by-project negotiation of goals and performance measures. It is likely to only be practical for large, longer term projects.

Electronic tendering: an industry perspective

The construction industry is categorised as being an information-intensive industry and described as one of the most important industries in any developed country, facing a period of rapid and unparalleled change (Industry Science Resources 1999) (Love P.E.D., Tucker S.N. et al. 1996). Project communications are becoming increasingly complex, with a growing need and fundamental drive to collaborate electronically at project level and beyond (Olesen K. and Myers M.D. 1999; Thorpe T. and Mead S. 2001; CITE 2003). Yet, the industry is also identified as having a considerable lack of knowledge and awareness about innovative information and communication technology (ICT) and web-based communication processes, systems and solutions which may prove beneficial in the procurement, delivery and life cycle of projects (NSW Government 1998; Kajewski S. and Weippert A. 2000). The Internet has debatably revolutionised the way in which information is stored, exchanged and viewed, opening new avenues for business, which only a decade ago were deemed almost inconceivable (DCITA 1998; IIB 2002). In an attempt to put these ‘new avenues of business’ into perspective, this report provides an overall ‘snapshot’ of current public and private construction industry sector opportunities and practices in the implementation and application of web-based ICT tools, systems and processes (e-Uptake). Research found that even with a reserved uptake, the construction industry and its participating organisations are making concerted efforts (fortunately with positive results) in taking up innovative forms of doing business via the internet, including e-Tendering (making it possible to manage the entire tender letting process electronically and online) (Anumba C.J. and Ruikar K. 2002; ITCBP 2003). Furthermore, Government (often a key client within the construction industry),and with its increased tendency to transact its business electronically, undoubtedly has an effect on how various private industry consultants, contractors, suppliers, etc. do business (Murray M. 2003) – by offering a wide range of (current and anticipated) e-facilities / services, including e-Tendering (Ecommerce 2002). Overall, doing business electronically is found to have a profound impact on the way today’s construction businesses operate - streamlining existing processes, with the growth in innovative tools, such as e-Tender, offering the construction industry new responsibilities and opportunities for all parties involved (ITCBP 2003). It is therefore important that these opportunities should be accessible to as many construction industry businesses as possible (The Construction Confederation 2001). Historically, there is a considerable exchange of information between various parties during a tendering process, where accuracy and efficiency of documentation is critical. Traditionally this process is either paper-based (involving large volumes of supporting tender documentation), or via a number of stand-alone, non-compatible computer systems, usually costly to both the client and contractor. As such, having a standard electronic exchange format that allows all parties involved in an electronic tender process to access one system only via the Internet, saves both time and money, eliminates transcription errors and increases speed of bid analysis (The Construction Confederation 2001). Supporting this research project’s aims and objectives, researchers set to determine today’s construction industry ‘current state-of-play’ in relation to e-Tendering opportunities. The report also provides brief introductions to several Australian and International e-Tender systems identified during this investigation. e-Tendering, in its simplest form, is described as the electronic publishing, communicating, accessing, receiving and submitting of all tender related information and documentation via the internet, thereby replacing the traditional paper-based tender processes, and achieving a more efficient and effective business process for all parties involved (NT Governement 2000; NT Government 2000; NSW Department of Commerce 2003; NSW Government 2003). Although most of the e-Tender websites investigated at the time, maintain their tendering processes and capabilities are ‘electronic’, research shows these ‘eTendering’ systems vary from being reasonably advanced to more ‘basic’ electronic tender notification and archiving services for various industry sectors. Research also indicates an e-Tender system should have a number of basic features and capabilities, including: • All tender documentation to be distributed via a secure web-based tender system – thereby avoiding the need for collating paperwork and couriers. • The client/purchaser should be able to upload a notice and/or invitation to tender onto the system. • Notification is sent out electronically (usually via email) for suppliers to download the information and return their responses electronically (online). • During the tender period, updates and queries are exchanged through the same e-Tender system. • The client/purchaser should only be able to access the tenders after the deadline has passed. • All tender related information is held in a central database, which should be easily searchable and fully audited, with all activities recorded. • It is essential that tender documents are not read or submitted by unauthorised parties. • Users of the e-Tender system are to be properly identified and registered via controlled access. In simple terms, security has to be as good as if not better than a manual tender process. Data is to be encrypted and users authenticated by means such as digital signatures, electronic certificates or smartcards. • All parties must be assured that no 'undetected' alterations can be made to any tender. • The tenderer should be able to amend the bid right up to the deadline – whilst the client/purchaser cannot obtain access until the submission deadline has passed. • The e-Tender system may also include features such as a database of service providers with spreadsheet-based pricing schedules, which can make it easier for a potential tenderer to electronically prepare and analyse a tender. Research indicates the efficiency of an e-Tender process is well supported internationally, with a significant number, yet similar, e-Tender benefits identified during this investigation. Both construction industry and Government participants generally agree that the implementation of an automated e-Tendering process or system enhances the overall quality, timeliness and cost-effectiveness of a tender process, and provides a more streamlined method of receiving, managing, and submitting tender documents than the traditional paper-based process. On the other hand, whilst there are undoubtedly many more barriers challenging the successful implementation and adoption of an e-Tendering system or process, researchers have also identified a range of challenges and perceptions that seem to hinder the uptake of this innovative approach to tendering electronically. A central concern seems to be that of security - when industry organisations have to use the Internet for electronic information transfer. As a result, when it comes to e-Tendering, industry participants insist these innovative tendering systems are developed to ensure the utmost security and integrity. Finally, if Australian organisations continue to explore the competitive ‘dynamics’ of the construction industry, without realising the current and future, trends and benefits of adopting innovative processes, such as e-Tendering, it will limit their globalising opportunities to expand into overseas markets and allow the continuation of international firms successfully entering local markets. As such, researchers believe increased knowledge, awareness and successful implementation of innovative systems and processes raises great expectations regarding their contribution towards ‘stimulating’ the globalisation of electronic procurement activities, and improving overall business and project performances throughout the construction industry sectors and overall marketplace (NSW Government 2002; Harty C. 2003; Murray M. 2003; Pietroforte R. 2003). Achieving the successful integration of an innovative e-Tender solution with an existing / traditional process can be a complex, and if not done correctly, could lead to failure (Bourn J. 2002).

BRITE report 2004

This document reports on an innovation survey of the Australian construction industry undertaken by the BRITE Project of the CRC for Construction Innovation in 2004. The survey sample was drawn from 3,500 businesses in the road/bridge and commercial building sectors in NSW, Vic and Qld, covering main contractors, trade contractors, consultants, suppliers and clients. One-third of this population was sampled and a response rate of 30% was achieved. The survey investigates innovation determinants in the industry, comprising various aspects of business strategy and business environment.

Brite innovation survey : executive summary

This report summarises the fi ndings of an innovation survey of the Australian construction industry undertaken by the BRITE Project of the CRC for Construction Innovation in 2004. The BRITE Innovation Survey can be viewed in full at www.brite.crcci.info.The objective of the BRITE project is to improve the incidence and quality of innovation in the Australian construction industry. Many stakeholders in the industry are sceptical about the potential for innovation and its likely benefi ts. Many also lack the linkages and capabilities required for successful innovation. The BRITE Project is redressing this situation through demonstration and benchmarking activities. The term ‘innovation’ is defi ned as a new or signifi cantly improved technology or advanced business practice. Innovation may be technological or organisational, and it may be new to the world, or just new to the industry or business concerned. The defi nition includes the adoption of existing advancements developed outside a particular business. The survey sample was drawn from 3,500 businesses in the road/bridge and commercial building sectors in New South Wales, Victoria and Queensland, covering main contractors, trade contractors, consultants, suppliers and clients. Onethird of this population was sampled and a response rate of almost 30% was achieved. The survey collected information about respondents’ perceptions of innovation determinants in the industry, comprising various aspects of business strategy and business environment.

Review of international procurement procedures

Contractor selection is a crucial element in construction procurement (Drew & Skitmore 1993, p. 363). Contractors are selected through the tender process, which varies according to country, state and contracting organisation and is subject to individual differences. This paper reviews a range of international tender processes, highlighting the ethical features that govern these guidelines. The paper is part of a project to develop ethical guidelines for procurement for major contracting authorities. By reviewing tender guidelines we are able to gain an indication of the type of ethical standards reserved for procurement. The need for good business ethics in the tender process stems from the belief that ‘good ethical practice’ is critical in meeting organisational goals (Vee & Skitmore 2003, p. 125). Hence, an ethical tender process will select ethical contractors who are viewed as beneficial to the contracting authority.

Ethical behaviour in the construction procurement process

In construction, inter-organisational relationships are of the highest importance. Ethical practice and behaviour is a means for improving inter-organisational relationships by providing a clear understanding of the rights and obligations of all parties, improving productivity, affecting long-term business dealings, and influencing quality, time and costs. Therefore, the ability to build sustainable relationships grounded in ethical practice is important to the construction industry. Establishing ethical standards at the beginning of the procurement process provides an ethical platform for the project life cycle and the relationship between procurers and contractors. Therefore it is important to determine what the ethical issues are in the Australian construction industry from members of the industry themselves; including clients. This “bottom up” approach is not a particularly new concept. Ever since the Gyles Royal Commission in 1992 there has been a considerable effort by government agencies to develop policies to improve the ethical behaviour of the industry.

Being the best

Being the Best investigates the ways in which highly innovative contractors sustain their market leadership. The businesses consulted are quoted extensively, as a means of sharing their insights. This report is intended as a resource for contractors that want to improve their innovation outcomes and business performance.

Brite Innovation Gallery 2007

In 2006, the BrITE project of the CrC for Construction Innovation researched the learning behaviours of twenty of australia’s most innovative contractors.

Achieving better stewardship of major infrastructure assets through configuration of governance arrangements utilising Stewardship Theory

Major infrastructure assets are often governed by a mix of public and private organizations, each fulfilling a specific and separate role i.e. policy, ownership, operation or maintenance. This mix of entities is a legacy of Public Choice Theory influenced NPM reforms of the late 20th century. The privatization of the public sector has resulted in agency theory based ‘self-interest’ relationships and governance arrangements for major infrastructure assets which emphasize economic efficiency but which do not do not advance non-economic public values and the collective Public Interest. The community is now requiring that governments fulfill their stewardship role of also satisfying non-economic public values such as sustainability and intergenerational responsibility. In the 21st century governance arrangements which minimize individual self-interest alone and look to also pursue the interests of other stakeholders have emerged. Relational contracts, Public-Private Partnerships (PPP’s) and hybrid mixes of organizations from the state, market and network modes (Keast et al 2006) provide options for governance which better meet the interests of contractors, government and the community there is emerging a body of research which extends the consideration of the immediate governance configuration to the metagovernance environment constituted by hierarchy, regulation, industry standards, trust, culture and values. Stewardship theory has reemerged as a valuable aid in the understanding of the features of governance configurations which establish relationships between principal and agent which maximize the agent acting in the interests of the principal, even to the detriment of the agent. This body of literature suggests that an improved stewardship outcome from infrastructure governance configurations can be achieved by the application of the emerging options as to the immediate governance configuration, and the surrounding metagovernance environment. Stewardship theory provides a framework for the design of the relationships within that total governance environment, focusing on the achievement of a better, complete stewardship outcome. This paper explores the directions future research might take in seeking to improve the understanding of the design of the governance of major, critical infrastructure assets.

Procurement selection in the public sector : a tale of two states.

The decision as to which procurement system to adopt is a complex and challenging task for clients of construction projects. Despite a plethora of tools and techniques available for selecting a procurement method, clients are still uncertain about what method to adopt for a given construction project to achieve success. This paper examines ‘how and why’ procurement methods are selected by public sector clients in Queensland (QLD) and Western Australia (WA). Findings from workshops with senior managers in procurement selection revealed that traditional lump sum methods (TLS) are preferred even though alternative forms could be better suited for a given project. Participants of the workshops agreed that alternative procurement forms should be considered for projects but an embedded culture of uncertainty avoidance meant the selection of TLS methods. It was perceived that only a limited number of contractors operating in the marketplace have the resources and experience to deliver projects using the non-traditional methods.

Uptake of an OHS code of practice by Australian construction firms

The Australian construction industry is moving towards the implementation of a voluntary code of practice (VCP) for occupational health and safety (OHS). The evidence suggests that highly-visible clients and project management firms, in addition to their subcontractors, will embrace such a code, while smaller firms not operating in high-profile contracting regimes may prove reticent. This paper incorporates qualitative data from a research project commissioned by Engineers Australia and supported by the Australian Contractors’ Association, Property Council of Australia, Royal Australian Institute of Architects, Association of Consulting Engineers Australia, Australian Procurement and Construction Council, Master Builders Australia and the Australian CRC for Construction Innovation. The paper aims to understand the factors that facilitate or prevent the uptake of the proposed VCP by smaller firms, together with pathways to adoption.

Uptake of an OHS code of practice by construction firms : barriers and enablers in an Australian industry

The Australian construction industry, reflecting a global trend, is moving towards the implementation of a voluntary code of practice (hereafter VCP) for occupational health and safety. The evidence suggests that highlyvisible clients and project management firms, in addition to their subcontractors, look set to embrace such a code. However, smaller firms not operating in high-profile contracting regimes may prove reticent to adopt a VCP. This paper incorporates qualitative data from a high-profile research project commissioned by Engineers Australia and supported by the Australian Contractors’ Association, Property Council of Australia, Royal Australian Institute of Architects, Association of Consulting Engineers Australia, Australian Procurement and Construction Council, Master Builders Australia and the Australian CRC for Construction Innovation. The paper aims to understand the factors that facilitate or prevent the uptake of the VCP by smaller firms, together with pathways to the adoption of a VCP by industry.

Extending knowledge management across the supply chains in the construction industry : knowledge sharing in construction supply chains

Supply chain management and knowledge management have emerged as two distinct business philosophies in the last decade. Both are making rapid inroads into the construction industry. The premise of this paper is that knowledge management would make it possible for all the trading partners in a supply chain to reap benefits. Current research in knowledge management in the construction industry is generally targeting those big organisations that are main contractors. This has restricted the scope of knowledge management, and limits the benefits to a few, rather than the whole industry. If the construction industry as a whole is to prosper and improve its productivity, strategies for knowledge management strategy at the industry level must be established. This paper argues the case for extending the scope of knowledge management across the full extent of the supply chain, and attempts to identify the benefits that may arise out of sharing knowledge across the supply chain.