Cloning and characterization of a novel human gene related to vascular endothelial growth factor

This paper describes the cloning and characterization of a new member of the vascular endothelial growth factor (VEGF) gene family, which we have designated VRF for VEGF-related-factor. Sequencing of cDNAs from a human fetal brain library and RT-PCR products from normal and tumor tissue cDNA pools indicate two alternatively spliced messages with open reading frames of 621 and 564 bp, respectively. The predicted proteins differ at their carboxyl ends resulting from a shift in the open reading frame. Both isoforms show strong homology to VEGF at their amino termini, but only the shorter isoform maintains homology to VEGF at its carboxyl terminus and conserves all 16 cysteine residues of VEGF165. Similarity comparisons of this isoform revealed overall protein identity of 48% and conservative substitution of 69% with VEGF189. VRF is predicted to contain a signal peptide, suggesting that it may be a secreted factor. The VRF gene maps to the D11S750 locus at chromosome band 11q13, and the protein coding region, spanning approximately 5 kb, is comprised of 8 exons that range in size from 36 to 431 bp. Exons 6 and 7 are contiguous and the two isoforms of VRF arise through alternate splicing of exon 6. VRF appears to be ubiquitously expressed as two transcripts of 2.0 and 5.5 kb; the level of expression is similar among normal and malignant tissues.

Compilation of somatic mutations of the CDKN2 gene in human cancers : non-random distribution of base substitutions

The CDKN2 gene, encoding the cyclin-dependent kinase inhibitor p16, is a tumour suppressor gene that maps to chromosome band 9p21-p22. The most common mechanism of inactivation of this gene in human cancers is through homozygous deletion; however, in a smaller proportion of tumours and tumour cell lines intragenic mutations occur. In this study we have compiled a database of over 120 published point mutations in the CDKN2 gene from a wide variety of tumour types. A further 50 deletions, insertions, and splice mutations in CDKN2 have also been compiled. Furthermore, we have standardised the numbering of all mutations according to the full-length 156 amino acid form of p16. From this study we are able to define several hot spots, some of which occur at conserved residues within the ankyrin domains of p16. While many of the hotspots are shared by a number of cancers, the relative importance of each position varies, possibly reflecting the role of different carcinogens in the development of certain tumours. As reported previously, the mutational spectrum of CDKN2 in melanomas differs from that of internal malignancies and supports the involvement of UV in melanoma tumorigenesis. Notably, 52% of all substitutions in melanoma-derived samples occurred at just six nucleotide positions. Nonsense mutations comprise a comparatively high proportion of mutations present in the CDKN2 gene, and possible explanations for this are discussed.

The CDKN2A (p16) gene and human cancer

CDKN2A, the gene encoding the cell-cycle inhibitor p16CDKN2A, was first identified in 1994. Since then, somatic mutations have been observed in many cancers and germline alterations have been found in kindreds with familial atypical multiple mole/melanoma (FAMMM), also known as atypical mole syndrome. In this review we tabulate the known mutations in this gene and discuss specific aspects, particularly with respect to germline mutations and cancer predisposition.

Haplotype analysis of two recurrent CDKN2A mutations in 10 melanoma families : evidence for common founders and independent mutations

Germ-line mutations in CDKN2A have been shown to predispose to cutaneous malignant melanoma. We have identified 2 new melanoma kindreds which carry a duplication of a 24bp repeat present in the 5' region of CDKN2A previously identified in melanoma families from Australia and the United States. This mutation has now been reported in 5 melanoma families from 3 continents: Europe, North America, and Australasia. The M53I mutation in exon 2 of CDKN2A has also been documented in 5 melanoma families from Australia and North America. The aim of this study was to determine whether the occurrence of the mutations in these families from geographically diverse populations represented mutation hotspots within CDKN2A or were due to common ancestors. Haplotypes of 11 microsatellite markers flanking CDKN2A were constructed in 5 families carrying the M53I mutation and 5 families carrying the 24bp duplication. There were some differences in the segregating haplotypes due primarily to recombinations and mutations within the short tandem-repeat markers; however, the data provide evidence to indicate that there were at least 3 independent 24bp duplication events and possibly only 1 original M53I mutation. This is the first study to date which indicates common founders in melanoma families from different continents.

Look before you leap : a confidence-based method for selecting species criticality while avoiding negative populations in τ-leaping

The stochastic simulation algorithm was introduced by Gillespie and in a different form by Kurtz. There have been many attempts at accelerating the algorithm without deviating from the behavior of the simulated system. The crux of the explicit τ-leaping procedure is the use of Poisson random variables to approximate the number of occurrences of each type of reaction event during a carefully selected time period, τ. This method is acceptable providing the leap condition, that no propensity function changes “significantly” during any time-step, is met. Using this method there is a possibility that species numbers can, artificially, become negative. Several recent papers have demonstrated methods that avoid this situation. One such method classifies, as critical, those reactions in danger of sending species populations negative. At most, one of these critical reactions is allowed to occur in the next time-step. We argue that the criticality of a reactant species and its dependent reaction channels should be related to the probability of the species number becoming negative. This way only reactions that, if fired, produce a high probability of driving a reactant population negative are labeled critical. The number of firings of more reaction channels can be approximated using Poisson random variables thus speeding up the simulation while maintaining the accuracy. In implementing this revised method of criticality selection we make use of the probability distribution from which the random variable describing the change in species number is drawn. We give several numerical examples to demonstrate the effectiveness of our new method.

Food(ing): between human-computer and human-food-experience

This workshop is a continuation and extension to the successful past workshops exploring the intersection of food, technology, place, and people, namely 2009 OZCHI workshop, Hungry 24/7? HCI Design for Sustainable Food Culture and Sustainable Interaction with Food, Technology, and the City [1] and 2010 CHI panel Making Food, Producing Sustainability [3]. The workshop aims to bring together experts from diverse backgrounds including academia, government, industry, and non-for-profit organisations. It specifically aims to create a space for discussion and design of innovative approaches to understanding and cultivating sustainable food practices via human-computer-interaction (HCI) as well as addressing the wider opportunities for the HCI community to engage with food as a key issue for sustainability The workshop addresses environmental, health, and social domains of sustainability in particular, by looking at various conceptual and design approaches in orchestrating sustainable interaction of people and food in and through dynamic techno-social networks.

Modelling the activation of words in human memory : the spreading activation, spooky-activation-at-a-distance and the entanglement models compared

Modelling how a word is activated in human memory is an important requirement for determining the probability of recall of a word in an extra-list cueing experiment. The spreading activation, spooky-action-at-a-distance and entanglement models have all been used to model the activation of a word. Recently a hypothesis was put forward that the mean activation levels of the respective models are as follows: Spreading � Entanglment � Spooking-action-at-a-distance This article investigates this hypothesis by means of a substantial empirical analysis of each model using the University of South Florida word association, rhyme and word norms.

Effects of varied ionic calcium and phosphate on the proliferation, osteogenic differentiation and mineralization of human periodontal ligament cells in vitro

Background and Objective: A number of bone filling materials containing calcium (Ca++) and phosphate (P) ions have been used in the repair of periodontal bone defects; however, the effect that local release of Ca++ and P ions have on biological reactions is not fully understood. In this study, we investigated the effects of various levels of Ca++ and P ions on the proliferation, osteogenic differentiation, and mineralization of human periodontal ligament cells (hPDLCs). Materials and Methods: hPDLCs were obtained using an explant culture method. Defined concentrations and ratios of ionic Ca++ to inorganic P were added to standard culture and osteogenic induction media. The ability of hPDLCs to proliferate in these growth media was assayed using the Cell Counting Kit-8 (CCK-8). Cell apoptosis was evaluated by FITC-Annexin V/PI double staining method. Osteogenic differentiation and mineralization were investigated by morphological observations, alkaline phosphatase (ALP) activity, and Alizarin red S/von Kossa staining. The mRNA expression of osteogenic related markers was analyzed using a reverse transcriptase polymerase chain reaction (RT-PCR). Results: Within the ranges of Ca++ and P ions concentrations tested, we observed that increased concentrations of Ca++ and P ions enhanced cell proliferation and formation of mineralized matrix nodules; whereas ALP activity was reduced. The RT-PCR results showed that elevated concentrations of Ca++ and P ions led to a general increase of Runx2 mRNA expression and decreased ALP mRNA expression, but gave no clear trend on OCN mRNA levels. Conclusion: The concentrations and ratios of Ca++ and P ions could significantly influence proliferation, differentiation, and mineralization of hPDLCs. Within the range of concentrations tested, we found that the combination of 9.0 mM Ca++ ions and 4.5 mM P ions were the optimum concentrations for proliferation, differentiation, and mineralization in hPDLCs.

The right to be green: using human rights law to achieve environmental protection

The relationship between the environment and human rights has long been recognised. It is now largely accepted that a ‘good’ environment is a necessary precondition for the enjoyment of a wide range of human rights, including the right to health, the right to an adequate standard of living, and even the right to life. It has even been suggested that as humans we all possess a right to live in an environment of a certain standard, based on the intrinsic value of the natural world to all human beings. In this context much has been written regarding the important role that the environment plays in human lives. This paper looks at the flip-side of this discussion, and examines what human rights can do for the environment. It is argued that, while there are valid criticisms for linking environmental protection too strongly to human needs, there is nonetheless much to be gained from using human rights law as a framework to achieve environmental protection.

The role of human rights in environmental governance : the challenge of climate change

The role of human rights in environmental governance is increasingly gaining attention. This is particularly the case in relation to the challenge of climate change, where there is growing recognition of a real threat to human rights. This chapter argues in favour of greater reference to human rights principles in environmental governance. It refers to the experiences of Torres Strait Islanders to demonstrate the impact of climate change on human rights, and the many benefits which can be gained from a greater consideration of human rights norms in the development of strategies to combat climate change. The chapter also argues that a human rights perspective can help address the underlying injustice of climate change: that it is the people who have contributed least to the problem who will bear the heaviest burden of its effects.

Human rights and environmental wrongs : achieving environmental justice through human rights law

The links between the environment and human rights are well established internationally. It is accepted that environmental problems impact on individuals’ and communities’ enjoyment of rights which are guaranteed to them under international human rights law. Environmental issues also impact on governments’ capacity to protect and fulfil the rights of their citizens. In addition to these links between the environment and human rights, it is argued that human rights principles offer a strategy for addressing environmental injustice. The justice implications of environmental problems are well documented, with many examples where pollution, deforestation or other degradation disproportionately impacts upon poorer neighbourhoods or areas populated by minority groups. On the international level, there are environmental injustices which exist between developed and developing states. Further, there are also potential injustices for future generations. This paper investigates the role of human rights principles in addressing these instances of environmental injustice, and argues that the framework of human rights norms provides an approach to environmental governance which can help to minimise injustice and promote the interests of those groups who are most adversely affected. Further, it suggests that the human rights enforcement mechanisms which exist at international law could be utilised to lend more weight to claims for more equitable environmental policies.

Does emotion modulate the blink reflex in human conditioning? Startle potentiation during pleasant and unpleasant cues in the picture-picture paradigm

Emotional processes modulate the size of the eyeblink startle reflex in a picture-viewing paradigm, but it is unclear whether emotional processes are responsible for blink modulation in human conditioning. Experiment 1 involved an aversive differential conditioning phase followed by an extinction phase in which acoustic startle probes were presented during CS+, CS-, and intertrial intervals. Valence ratings and affective priming showed the CS+ was unpleasant postacquisition. Blink startle magnitude was larger during CS+ than during CS-. Experiment 2 used the same design in two groups trained with pleasant or unpleasant pictorial USs. Ratings and affective priming indicated that the CS+ had become pleasant or unpleasant in the respective group. Regardless of CS valence, blink startle was larger during CS+ than CS- in both groups. Thus, startle was not modulated by CS valence.

Affect, attention, or anticipatory arousal? Human blink startle modulation in forward and backward affective conditioning

Affect modulates the blink startle reflex in the picture-viewing paradigm, however, the process responsible for reflex modulation during conditional stimuli (CSs) that have acquired valence through affective conditioning remains unclear. In Experiment 1, neutral shapes (CSs) and valenced or neutral pictures (USs) were paired in a forward (CS → US) manner. Pleasantness ratings supported affective learning of positive and negative valence. Post-acquisition, blink reflexes were larger during the pleasant and unpleasant CSs than during the neutral CS. Rather than affect, attention or anticipatory arousal were suggested as sources of startle modulation. Experiment 2 confirmed that affective learning in the picture–picture paradigm was not affected by whether the CS preceded the US. Pleasantness ratings and affective priming revealed similar extents of affective learning following forward, backward or simultaneous pairings of CSs and USs. Experiment 3 utilized a backward conditioning procedure (US → CS) to minimize effects of US anticipation. Again, blink reflexes were larger during CSs paired with valenced USs regardless of US valence implicating attention rather than anticipatory arousal or affect as the process modulating startle in this paradigm.

Impacts of traditional husbandry practices on exploitable levels of genetic diversity in cultured 'Tra' catfish (Pangasianodon hypophthalmus) in the Mekong Delta, Vietnam

Sutchi catfish (Pangasianodon hypophthalmus) – known more universally by the Vietnamese name ‘Tra’ is an economically important freshwater fish in the Mekong Delta in Vietnam that constitutes an important food resource. Artificial propagation technology for Tra catfish has only recently been developed along the main branches of the Mekong River where more than 60% of the local human population participate in fishing or aquaculture. Extensive support for catfish culture in general, and that of Tra (P. hypophthalmus) in particular, has been provided by the Vietnamese government to increase both the scale of production and to develop international export markets. In 2006, total Vietnamese catfish exports reached approximately 286,602 metric tons (MT) and were valued at 736.87 $M with a number of large new export destinations being developed. Total value of production from catfish culture has been predicted to increase to approximately USD 1 billion by 2020. While freshwater catfish culture in Vietnam has a promising future, concerns have been raised about long-term quality of fry and the effectiveness of current brood stock management practices, issues that have been largely neglected to date. In this study, four DNA markers (microsatellite loci: CB4, CB7, CB12 and CB13) that were developed specifically for Tra (P. hypophthalmus) in an earlier study were applied to examine the genetic quality of artificially propagated Tra fry in the Mekong Delta in Vietnam. The goals of the study were to assess: (i) how well available levels of genetic variation in Tra brood stock used for artificial propagation in the Mekong Delta of Vietnam (breeders from three private hatcheries and Research Institute of Aquaculture No2 (RIA2) founders) has been conserved; and (ii) whether or not genetic diversity had declined significantly over time in a stock improvement program for Tra catfish at RIA2. A secondary issue addressed was how genetic markers could best be used to assist industry development. DNA was extracted from fins of catfish collected from the two main branches of the Mekong River inf Vietnam, three private hatcheries and samples from the Tra improvement program at RIA2. Study outcomes: i) Genetic diversity estimates for Tra brood stock samples were similar to, and slightly higher than, wild reference samples. In addition, the relative contribution by breeders to fry in commercial private hatcheries strongly suggest that the true Ne is likely to be significantly less than the breeder numbers used; ii) in a stock improvement program for Tra catfish at RIA2, no significant differences were detected in gene frequencies among generations (FST=0.021, P=0.036>0.002 after Bonferroni correction); and only small differences were observed in alleles frequencies among sample populations. To date, genetic markers have not been applied in the Tra catfish industry, but in the current project they were used to evaluate the levels of genetic variation in the Tra catfish selective breeding program at RIA2 and to undertake genetic correlations between genetic marker and trait variation. While no associations were detected using only four loci, they analysis provided training in the practical applications of the use of molecular markers in aquaculture in general, and in Tra culture, in particular.

A human capital framework : designed for convergence

The 21" century business environment is dominated by unprecedented change across a broad spectrum of social, economic, technological and cultural factors (Nowotny, Scott & Gibbons 2001). Among these, two broad trends -economic globalisation and rising knowledge intensity (Hart 2006)have come to distinguish organisational life. Under the weight of these transformational influences, the developed world, it seems, has arrived at a transformational moment. The far-reaching effects of the global financial crisis and its shadowy twin: the threat of a double dip recession, continue to exert an unsteadying influence on global and corporate finances. Growth in developed economies has slumped, share prices have declined, the market value of corporations has slipped and unemployment rates, in the vast majority of developed economies, have risen. Gross domestic product (GDP) growth has retreated from the strong growth experienced in the late 1990s to negative growth in 2009 and a sluggish and unsteady recovery in 2010. In response, the reach of Government in terms of its participation in markets has been extended, bringing with it the need to transition to new governance and regulatory arrangements. Ongoing concerns regarding the pace and sustainability of the recovery remains a front-of-mind concern with bailouts, buybacks, borrowings and BP dominating news services: 'We are witnessing the reweaving of the social, political and economic fabric that binds our planet, with long-term consequences that are as or more profound than those of the industrial era' (Tapscott & Williams 2006, p. 59).