The peer-to-patent initiative : revitalizing patent examination with peer review

Every day we hear someone complain that this or that patent should not have been granted. People complain that the patent system is now a threat to existing business and innovation be- cause the patent office grants with alarming regularity patents for inventions that are neither novel nor non-obvious. People argue that the patent office cannot keep up with the job of examining the backlog of hundreds of thousands of patents and that, even if it could, the large volumes of prior art literature that need to be considered each time a patent application is received make the decision as to whether a patent should be granted or not a treacherous one.

BLAST Atlas : a function based multiple genome browser

BLAST Atlas is a visual analysis system for comparative genomics that supports genome-wide gene characterisation, functional assignment and function-based browsing of one or more chromosomes. Inspired by applications such as the WorldWide Telescope, Bing Maps 3D and Google Earth, BLAST Atlas uses novel three-dimensional gene and function views that provide a highly interactive and intuitive way for scientists to navigate, query and compare gene annotations. The system can be used for gene identification and functional assignment or as a function-based multiple genome comparison tool which complements existing position based comparison and alignment viewers.

Peer-to-Patent Australia: First Anniversary Report, December 2010

Peer-to-Patent Australia will initially run as a 12 month pilot project designed to test whether an open community of reviewers can effectively locate prior art that might not otherwise be located by the patent office during a typical examination. Patent applications will be made available for peer review for a period of 6 months and there will follow a 6 month period of joint qualitative and quantitative assessment of the pilot project by IP Australia and QUT. The objective of Peer-to-Patent Australia is to improve the patent examination process and the quality of issued patents by utilising the knowledge and skills of experts in the broader community. It is a way of linking the scientific and technical expertise of anyone with an Internet connection with the expertise of a patent examiner. That community participation consists of members of the public reviewing patent applications and contributing relevant prior art references and comments within a web-based forum. The aim is to bring to light prior art, particularly non-patent prior art, that might otherwise not be identified by patent examiners. The better the prior art resources a patent examiner has at his or her disposal, the more likely a patent application will be assessed properly in terms of novelty and inventive step. The role of Peer-to-Patent Australia in this regard is to act as both a facilitator of discussion and a collector of prior art submissions. Peer-to-Patent Australia collects relevant prior art references on behalf of the reviewing community and forwards that prior art to IP Australia. Section 27 of the Patents Act 1990 (Cth) allows for the Commissioner of Patents to receive submissions of prior art by third parties relevant to the novelty and inventiveness of a particular patent application.

Complete Nucleotide Sequence of Rice Tungro Spherical Virus Genome of a Highly Virulent Strain Vt6

The complete nucleotide sequence of rice tungro spherical virus (RTSV) strain Vt6, originally from Mindanao, the Philippines, with higher virulence to resistant rice cultivars, was determined and compared with the published sequence for the Philippine-type strain A (RTSV-A-Shen). It was reported that RTSV-A was not able to infect a rice resistant cultivar TKM 6 (10). RTSV-Vt6 and RTSV-A-Shen share 90% and 95% homology at nucleotide and amino-acid levels, respectively. The N-terminal leader sequence of RTSV-Vt6 contained a 39-amino acids-region (positions 65 to 103) which was totally different from that of RTSV-A-Shen; the difference resulted from frame shifting by nucleotide insertions and deletions. To confirm the amino-acid sequence differences of the leader polypeptide, the same region was cloned and sequenced using a newly obtained variant of RTSV-type 6, which had been collected in the field of IRRI, and seven field isolates from Mindanao, the Philippines. Since all the sequences of the target region are identical to that of the Vt6 leader polypeptide, the sequence difference in the leader region seems not to correlate with the virulence of Vt6.

ATM mediated phosphorylation of CHD4 contributes to genome maintenance

Background: In order to maintain cellular viability and genetic integrity cells must respond quickly following the induction of cytotoxic double strand DNA breaks (DSB). This response requires a number of processes including stabilisation of the DSB, signalling of the break and repair. It is becoming increasingly apparent that one key step in this process is chromatin remodelling. Results: Here we describe the chromodomain helicase DNA-binding protein (CHD4) as a target of ATM kinase. We show that ionising radiation (IR)-induced phosphorylation of CHD4 affects its intranuclear organization resulting in increased chromatin binding/retention. We also show assembly of phosphorylated CHD4 foci at sites of DNA damage, which might be required to fulfil its function in the regulation of DNA repair. Consistent with this, cells overexpressing a phospho-mutant version of CHD4 that cannot be phosphorylated by ATM fail to show enhanced chromatin retention after DSBs and display high rates of spontaneous damage. Conclusion: These results provide insight into how CHD4 phosphorylation might be required to remodel chromatin around DNA breaks allowing efficient DNA repair to occur.

Multiple human single-stranded DNA binding proteins function in genome maintenance : structural, biochemical and functional analysis

DNA exists predominantly in a duplex form that is preserved via specific base pairing. This base pairing affords a considerable degree of protection against chemical or physical damage and preserves coding potential. However, there are many situations, e.g. during DNA damage and programmed cellular processes such as DNA replication and transcription, in which the DNA duplex is separated into two singlestranded DNA (ssDNA) strands. This ssDNA is vulnerable to attack by nucleases, binding by inappropriate proteins and chemical attack. It is very important to control the generation of ssDNA and protect it when it forms, and for this reason all cellular organisms and many viruses encode a ssDNA binding protein (SSB). All known SSBs use an oligosaccharide/oligonucleotide binding (OB)-fold domain for DNA binding. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating strand-exchange proteins and helicases, and mediation of protein–protein interactions. Recently two additional human SSBs have been identified that are more closely related to bacterial and archaeal SSBs. Prior to this it was believed that replication protein A, RPA, was the only human equivalent of bacterial SSB. RPA is thought to be required for most aspects of DNA metabolism including DNA replication, recombination and repair. This review will discuss in further detail the biological pathways in which human SSBs function.

Access to medicine and the dangers of patent linkage : lessons from Bayer Corp v. Union of India

In February 2010, the Delhi High Court delivered its decision in Bayer Corp v Union of India in which Bayer had appealed against an August 2009 decision of the same court. Both decisions prevented Bayer from introducing the concept of patent linkage into India’s drug regulatory regime. Bayer appealed to the Indian Supreme Court, the highest court in India, which agreed on 2 March 2010 to hear the appeal. Given that India is regarded as a global pharmaceutical manufacturer of generic medications, how its judiciary and government perceive their international obligations has a significant impact on the global access to medicines regime. In rejecting the application of patent linkage, the case provides an opportunity for India to further acknowledge its international human rights obligations.

Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum

Nuclear Factor Y (NF-Y) is a trimeric complex that binds to the CCAAT box, a ubiquitous eukaryotic promoter element. The three subunits NF-YA, NF-YB and NF-YC are represented by single genes in yeast and mammals. However, in model plant species (Arabidopsis and rice) multiple genes encode each subunit providing the impetus for the investigation of the NF-Y transcription factor family in wheat. A total of 37 NF-Y and Dr1 genes (10 NF-YA, 11 NF-YB, 14 NF-YC and 2 Dr1) in Triticum aestivum were identified in the global DNA databases by computational analysis in this study. Each of the wheat NF-Y subunit families could be further divided into 4-5 clades based on their conserved core region sequences. Several conserved motifs outside of the NF-Y core regions were also identified by comparison of NF-Y members from wheat, rice and Arabidopsis. Quantitative RT-PCR analysis revealed that some of the wheat NF-Y genes were expressed ubiquitously, while others were expressed in an organ-specific manner. In particular, each TaNF-Y subunit family had members that were expressed predominantly in the endosperm. The expression of nine NF-Y and two Dr1 genes in wheat leaves appeared to be responsive to drought stress. Three of these genes were up-regulated under drought conditions, indicating that these members of the NF-Y and Dr1 families are potentially involved in plant drought adaptation. The combined expression and phylogenetic analyses revealed that members within the same phylogenetic clade generally shared a similar expression profile. Organ-specific expression and differential response to drought indicate a plant-specific biological role for various members of this transcription factor family.

Physicality in the Information Age : a normative perspective on the patent eligibility of non-physical methods

There has been much conjecture of late as to whether the patentable subject matter standard contains a physicality requirement. The issue came to a head when the Federal Circuit introduced the machine-or-transformation test in In re Bilski and declared it to be the sole test for determining subject matter eligibility. Many commentators criticized the test, arguing that it is inconsistent with Supreme Court precedent and the need for the patent system to respond appropriately to all new and useful innovation in whatever form it arises. Those criticisms were vindicated when, on appeal, the Supreme Court in Bilski v. Kappos dispensed with any suggestion that the patentable subject matter test involves a physicality requirement. In this article, the issue is addressed from a normative perspective: it asks whether the patentable subject matter test should contain a physicality requirement. The conclusion reached is that it should not, because such a limitation is not an appropriate means of encouraging much of the valuable innovation we are likely to witness during the Information Age. It is contended that it is not only traditionally-recognized mechanical, chemical and industrial manufacturing processes that are patent eligible, but that patent eligibility extends to include non-machine implemented and non-physical methods that do not have any connection with a physical device and do not cause a physical transformation of matter. Concerns raised that there is a trend of overreaching commoditization or propertization, where the boundaries of patent law have been expanded too far, are unfounded since the strictures of novelty, nonobviousness and sufficiency of description will exclude undeserving subject matter from patentability. The argument made is that introducing a physicality requirement will have unintended adverse effects in various fields of technology, particularly those emerging technologies that are likely to have a profound social effect in the future.

Standardisation and patent ambush : potential liability under Australian competition law

This article examines the problem of patent ambush in standard setting, where patent owners are sometimes able to capture industry standards in order to secure monopoly power and windfall profits. Because standardisation generally introduces high switching costs, patent ambush can impose significant costs on downstream manufacturers and consumers and drastically reduce the efficiency gains of standardisation.This article considers how Australian competition law is likely to apply to patent ambush both in the development of a standard (through misrepresenting the existence of an essential patent) and after a standard is implemented (through refusing to license an essential patented technology either at all or on reasonable and non-discriminatory (RAND) terms). This article suggests that non-disclosure of patent interests is unlikely to restrained by Part IV of the Trade Practices Act (TPA), and refusals to license are only likely to be restrained if the refusal involves leveraging or exclusive dealing. By contrast, Standard Setting Organisations (SSOs) which seek to limit this behaviour through private ordering may face considerable scrutiny under the new cartel provisions of the TPA. This article concludes that SSOs may be best advised to implement administrative measures to prevent patent hold-up, such as reviewing which patents are essential for the implementation of a standard, asking patent holders to make their licence conditions public to promote transparency, and establishing forums where patent licensees can complain about licence terms that they consider to be unreasonable or discriminatory. Additionally, the ACCC may play a role in authorising SSO policies that could otherwise breach the new cartel provisions, but which have the practical effect of promoting competition in the standards setting environment.