Mutation analysis of the CDKN2A promoter in Australian melanoma families

Approximately 50% of all melanoma families worldwide show linkage to 9p21-22, but only about half of these have been shown to contain germ line CDKN2A mutations. It has been hypothesized that a proportion of these families carry mutations in the noncoding regions of CDKN2A. Several Canadian families have been reported to carry a mutation in the 5' UTR, at position -34 relative to the start site, which gives rise to a novel AUG translation initiation codon that markedly decreases translation from the wild-type AUG (Liu et al., 1999). Haplotype sharing in these Canadian families suggested that this mutation is of British origin. We sequenced 1,327 base pairs (bp) of CDKN2A, making up 1,116 bp of the 5' UTR and promoter, all of exon 1, and 61 bp of intron 1, in at least one melanoma case from 110 Australian families with three or more affected members known not to carry mutations within the p16 coding region. In addition, 431 bp upstream of the start codon was sequenced in an additional 253 affected probands from two-case melanoma families for which the CDKN2A mutation status was unknown. Several known polymorphisms at positions -33, -191, -493, and -735 were detected, in addition to four novel variants at positions 120, -252, -347, and -981 relative to the start codon. One of the probands from a two-case family was found to have the previously reported Q50R mutation. No family member was found to carry the mutation at position -34 or any other disease-associated mutation. For further investigation of noncoding CDKN2A mutations that may affect transcription, allele-specific expression analysis was carried out in 31 of the families with at least three affected members who showed either complete or "indeterminate" 9p haplotype sharing without CDKN2A exonic mutations. Reverse transcription polymerase chain reaction and automated sequencing showed expression of both CDKN2A alleles in all family members tested. The lack of CDKN2A promoter mutations and the absence of transcriptional silencing in the germ line of this cohort of families suggest that mutations in the promoter and 5' UTR play a very limited role in melanoma predisposition.

Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism

We used in vivo (biological), in silico (computational structure prediction), and in vitro (model sequence folding) analyses of single-stranded DNA sequences to show that nucleic acid folding conservation is the selective principle behind a high-frequency single-nucleotide reversion observed in a three-nucleotide mutated motif of the Maize streak virus replication associated protein (Rep) gene. In silico and in vitro studies showed that the three-nucleotide mutation adversely affected Rep nucleic acid folding, and that the single-nucleotide reversion [C(601)A] restored wild-type-like folding. In vivo support came from infecting maize with mutant viruses: those with Rep genes containing nucleotide changes predicted to restore a wild-type-like fold [A(601)/G(601)] preferentially accumulated over those predicted to fold differently [C(601)/T(601)], which frequently reverted to A(601) and displaced the original population. We propose that the selection of native nucleic acid folding is an epigenetic effect, which might have broad implications in the evolution of plants and their viruses.

A mouse with an N-ethyl-N-nitrosourea (ENU) induced Trp589Arg Galnt3 mutation represents a model for hyperphosphataemic familial tumoural calcinosis

Mutations of UDP-N-acetyl-alpha-D-galactosamine polypeptide N-acetyl galactosaminyl transferase 3 (GALNT3) result in familial tumoural calcinosis (FTC) and the hyperostosis-hyperphosphataemia syndrome (HHS), which are autosomal recessive disorders characterised by soft-tissue calcification and hyperphosphataemia. To facilitate in vivo studies of these heritable disorders of phosphate homeostasis, we embarked on establishing a mouse model by assessing progeny of mice treated with the chemical mutagen N-ethyl-N-nitrosourea (ENU), and identified a mutant mouse, TCAL, with autosomal recessive inheritance of ectopic calcification, which involved multiple tissues, and hyperphosphataemia; the phenotype was designated TCAL and the locus, Tcal. TCAL males were infertile with loss of Sertoli cells and spermatozoa, and increased testicular apoptosis. Genetic mapping localized Tcal to chromosome 2 (62.64-71.11 Mb) which contained the Galnt3. DNA sequence analysis identified a Galnt3 missense mutation (Trp589Arg) in TCAL mice. Transient transfection of wild-type and mutant Galnt3-enhanced green fluorescent protein (EGFP) constructs in COS-7 cells revealed endoplasmic reticulum retention of the Trp589Arg mutant and Western blot analysis of kidney homogenates demonstrated defective glycosylation of Galnt3 in Tcal/Tcal mice. Tcal/Tcal mice had normal plasma calcium and parathyroid hormone concentrations; decreased alkaline phosphatase activity and intact Fgf23 concentrations; and elevation of circulating 1,25-dihydroxyvitamin D. Quantitative reverse transcriptase-PCR (qRT-PCR) revealed that Tcal/Tcal mice had increased expression of Galnt3 and Fgf23 in bone, but that renal expression of Klotho, 25-hydroxyvitamin D-1α-hydroxylase (Cyp27b1), and the sodium-phosphate co-transporters type-IIa and -IIc was similar to that in wild-type mice. Thus, TCAL mice have the phenotypic features of FTC and HHS, and provide a model for these disorders of phosphate metabolism. © 2012 Esapa et al.

Analysis of human immunodeficiency virus type 1 drug resistance in children receiving nucleoside analogue reverse-transcriptase inhibitors plus nevirapine, nelfinavir, or ritonavir (Pediatric AIDS Clinical Trials Group 377)

In Pediatric AIDS Clinical Trials Group 377, antiretroviral therapy-experienced children were randomized to 4 treatment arms that included different combinations of stavudine, lamivudine (3TC), nevirapine (Nvp), nelfinavir (Nfv), and ritonavir (Rtv). Previous treatment with zidovudine (Zdv), didanosine (ddI), or zalcitabine (ddC) was acceptable. Drug resistance ((R)) mutations were assessed before study treatment (baseline) and at virologic failure. Zdv(R), ddI(R), and ddC(R) mutations were detected frequently at baseline but were not associated with virologic failure. Children with drug resistance mutations at baseline had greater reductions in virus load over time than did children who did not. Nvp(R) and 3TC(R) mutations were detected frequently at virologic failure, and Nvp(R) mutations were more common among children receiving 3-drug versus 4-drug Nvp-containing regimens. Children who were maintained on their study regimen after virologic failure accumulated additional Nvp(R) and 3TC(R) mutations plus Rtv(R) and Nfv(R) mutations. However, Rtv(R) and Nfv(R) mutations were detected at unexpectedly low rates.

Mutation frequency of non-ESBL phenotype SENTRY (Asia-Pacific) isolates of Klebsiella pneumoniae conversion to an ESBL positive phenotype

Extended spectrum β-lactamases or ESBLs, which are derived from non-ESBL precursors by point mutation of β-lactamase genes (bla), are spreading rapidly all over the world and have caused considerable problems in the treatment of infections caused by bacteria which harbour them. The mechanism of this resistance is not fully understood and a better understanding of these mechanisms might significantly impact on choosing proper diagnostic and treatment strategies. Previous work on SHV β-lactamase gene, blaSHV, has shown that only Klebsiella pneumoniae strains which contain plasmid-borne blaSHV are able to mutate to phenotypically ESBL-positive strains and there was also evidence of an increase in blaSHV copy number. Therefore, it was hypothesised that although specific point mutation is essential for acquisition of ESBL activity, it is not yet enough, and blaSHV copy number amplification is also essential for an ESBL-positive phenotype, with homologous recombination being the likely mechanism of blaSHV copy number expansion. In this study, we investigated the mutation rate of non-ESBL expressing K. pneumoniae isolates to an ESBL-positive status by using the MSS-maximum likelihood method. Our data showed that blaSHV mutation rate of a non-ESBL expressing isolate is lower than the mutation rate of the other single base changes on the chromosome, even with a plasmid-borne blaSHV gene. On the other hand, mutation rate from a low MIC ESBL-positive (≤ 8 µg/mL for cefotaxime) to high MIC ESBL-positive (≥16 µg/mL for cefotaxime) is very high. This is because only gene copy number increase is needed which is probably mediated by homologous recombination that typically takes place at a much higher frequencies than point mutations. Using a subinhibitory concentration of novobiocin, as a homologous recombination inhibitor, revealed that this is the case.

Reverse immigration

This book (256 pages, written in Korean) is a critical essay that reviews, questions, and criticises Korean and Eastern immigrants’ thinking and behaviour styles in Australia from their cultural perspectives, and discuss and proposes a creative cultural dimension for their better life in a multicultural context. Multiculturalism is not supportive of Eastern cultures because of individualistic collection of cultures, while transculturalism facilitates nurture of their culture in a community-oriented way within multicultural circumstances. Korean and Eastern immigrants, sharing oriental cultural systems and values, should approach to the Australian multicultural context with transculturalism which allows creating new cultural values in collaboration with and by participation into local communities. ------------------------------------------------------------ Many Eastern immigrants live in their own ethnic communities without or less interacting with Australian (communities). The author defines this phenomenon as “reverse immigration”. Reverse immigration refers to re-immigrating to their ethnic community in Australia or to their birth country despite they did not anticipate that this would happen to them before immigration to Australia. The author argues that Easterners’ collectivistic culture often devalues individuality and vice versa. Cultural clash between West and East often forces the immigrants to choose reverse immigration because of their lack of understanding of Western culture and their cultural characteristics such as low individuality, high power distance, and high uncertainty avoidance. For example, a vague boundary between individualist and collectivist in a collectivistic context (within their ethnic group) often leads to maladjustment to local communities and enhancement of cultural conservatism. The author proposes that the cultural clash can be overcome by cross-cultural activities named “transculturalism”. To Eastern immigrants, transculturalism can be achieved by acculturation of their two predominant cultures, the third-person perspective and generalised others. In a multicultural context, the former refers to the ability to share another person's feelings and emotions as if they were your own, and the latter does the ability to manage community and public expectations. When both cultural values are used for quality interactions between East and West, they allow Eastern immigrants to be more creative and critical and Australian to be more socially inclusive and culturally tolerant. With these discussions, the author discusses cultural differences throughout the book with four topics (chapters) and proposes transculturalism as a solution to the reverse immigration. ------------------------------------------------------------ Chapter 1 criticises Koreans’ attitudes and methods towards learning English that is less pragmatic and practical, but more likely to be a scholarly study. The author explains that Koreans’ non-pragmatic towards learning English has been firmly built based on their traditional systems and values that Koreans view English as a discipline and an aim of academic achievements rather than a means of communication. Within their cultural context, English can be perceived as more than a language, but something like vastly superior to their language and culture. Their collectivistic culture regards English as an unreachable and heterogeneous one that may threaten their cultural identity, so that “scholarly studying” is only the way to achieve (not learn) it. This discourages the immigrants to engage and involve in daily dialogues by “using” English as a second language. The author further advises the readers to be aware of Eastern collectivistic culture in communication and interaction that sometimes completely reverses private and public topics in a Western context. This leads them to feel that they have no content to talk to natives. ------------------------------------------------------------ Chapter 2 compares between Korea and Australia in terms of their educational systems and values, and proposes how Eastern overseas students can achieve critical and creative thinking within a Western educational setting. Interestingly, this chapter includes an explanation of why Eastern overseas students easily fail assessments including essay writing, oral presentations and discussions. One of the reasons the author explains is that Eastern students are not familiar to criticise others and think creatively, especially when they recognise that their words and ideas may harm the collectivistic harmony. Western educational systems focuses on enhancement of individuality such as self-confidence, self-esteem, and self-expression, while Eastern educational systems foster group-oriented values such as interpersonal relationship, and strong moral and spiritual values. Yet, the author argues that the collectivistic approach to criticism and creativity is often more critical and creative than Western individuals when they know what they are supposed to do for a group (or a community). Therefore, Eastern students need to think their cultural merits and demerits by using an individual perspective rather than generalised others’ perspective. The latter often discourages individual participation in a community, and the generalised others in a Western culture is weaker than Eastern. Furthermore, Western educational systems do not educate students to transform (loose) their individuality to fit into a group or a community. Rather they cultivate individuality for community prosperity. ------------------------------------------------------------ Chapter 3 introduces various cases of reverse immigration in workplaces that many immigrants return to their country or their ethnic community after many trials for acculturation. Reverse immigration is unexpected and not planned before immigration, so that its emotional embarrassment increases such severe social loneliness. Most Eastern immigrant workers have tried to adjust themselves in this new cultural environment at the early stages of immigration. However, their cultural features of collectivism, high power distance, high uncertainty avoidance, and long-term oriented cultures suppress individual initiative and eliminate the space for experiments in ways of acculturation. The author argues that returning to their ethnic community (physically and psychologically) leads to two significant problems: their distorted parenting and becoming more conservatives. The former leads the first generation of immigrants to pressure their children to pursue extrinsic or materialist values, such as financial success, fame and physical appearance, rather than on intrinsic values, while the latter refers to their isolated conservative characters because of their remoteness from the changes of their own country. The author also warns that their ethnic and religious groups actively strengthens immigrants’ social loneliness and systematically discourages immigrants’ interests and desire to be involving into local communities. The ethnic communities and leaders have not been interacting with Australian local communities and, as a result, are eager to conserve outdated cultural systems values. Even they have a tendency to weed out those people who wish to settle down within Australian local communities. They believe that those people can threaten their community’s survival and continuity. ------------------------------------------------------------ Chapter 4 titled multiculturalism argues that Korean and Eastern immigrants should more precisely understand Australia as a multicultural society in a way of collaboratively creating new cultural values. The author introduces multiculturalism with its definitions and history in Australia and argues the limitations of multiculturalism from an Easterner’s perspective. With well known tragedies of the second generations of U.S. immigrants, Cho Seung-Hui, a university student, massacred 32 people on the Virginia Tech before committing suicide and Hidal Hassan, an Army psychiatrist, killed 13 people at Fort Hood and the responses of ethnic community, the author explains that their mental illness may be derived from their parents’ (or ethnic group) culturally isolated attitude and socially static viewpoint of U.S. (Western system and values). The author insists that multiculturalism may restrict Eastern immigrants’ engagement and involvement in local communities. Multiculturalism has been systematically and historically developed based on Western systems and cultural values. In other words, multiculturalism requires high self-confidence and self-esteem that Eastern immigrants less prioritise them. It has been generally known that Easterners put more weight on human relationship than Westerners, but the author claims that this is not true. Within an individualistic culture, Westerners are more interested in building person-to-person connections and relationships. While Easterners are more interested in how individuals can achieve a sense of belonging within a group and a community. Therefore, multiculturalism is an ideology which forces Eastern immigrants to discard their strong desire to be part of a group and does not give a sense of belonging. In a consequence, the author advises that Eastern immigrants should aim towards “transculturalism” which allows them to actively participate in and contribute to their multicultural community. Transculturalism does not ask Easterners to discard their cultural values, but enables them to be a collectivistic individualist (a community leader) who is capable of developing new cultural values in a more creative and productive way. Furthermore, transculturalism encourages Western Australians in a multicultural context to collaborate with ethnic minorities to build a better community.

The association between MC1R genotype and BRAF mutation status in cutaneous melanoma : findings from an Australian population

There is increasing epidemiological and molecular evidence that cutaneous melanomas arise through multiple causal pathways. The purpose of this study was to explore the relationship between germline and somatic mutations in a population-based series of melanoma patients to reshape and refine the divergent pathway model for melanoma. Melanomas collected from 123 Australian patients were analyzed for melanocortin-1 receptor (MC1R) variants and mutations in the BRAF and NRAS genes. Detailed phenotypic and sun exposure data were systematically collected from all patients. We found that BRAF-mutant melanomas were significantly more likely from younger patients and those with high nevus counts, and were more likely in melanomas with adjacent neval remnants. Conversely, BRAF-mutant melanomas were significantly less likely in people with high levels of lifetime sun exposure. We observed no association between germline MC1R status and somatic BRAF mutations in melanomas from this population. BRAF-mutant melanomas have different origins from other cutaneous melanomas. These data support the divergent pathways hypothesis for melanoma, which may require a reappraisal of targeted cancer prevention activities.

Reverse engineering and finite element analysis of a 3-wheeler automotive structure

Auto rickshaws (3-wheelers) are the most sought after transport among the urban and rural poor in India. The assembly of the vehicle involves assemblies of several major components. The L-angle is the component that connects the front panel with the vehicle floor. Current L-angle part has been observed to experience permanent deformation failure over period of time. This paper studies the effect of the addition of stiffeners on the L-angle to increase the strength of the component. A physical model of the L-angle was reversed engineered and modelled in CAD before static loading analysis were carried out on the model using finite element analysis. The modified L-angle fitted with stiffeners was shown to be able to withstand more load compare to previous design.