The gene genie: good fairy or wicked witch?

The so-called genetics revolution rests on a history which at its least can be described as controversial. Modern genetics needs to bear this history in mind. In particular, as with the past, the area of reproductive choice seems particularly vulnerable to potential abuse. Courts in the UK and elsewhere have already shown themselves willing to interfere with the choices of women in the management of their pregnancies. Medical advance, perhaps particularly the capacity to visualise the developing foetus, has added complexity to the question of whether the health care provider has one patient (the woman) or two patients (the woman and the foetus). Additionally, pregnancy is thoroughly monitored in modern medical practice and genetics may provide a further impetus or incentive to mandate increased policing of pregnancy. Gene therapy, once offered, will add further to the desire to ensure that women make the ‘right’ choice, especially when the invasion required is relatively minimal. Further, genetic information is at best predictive, but may, because of its scientific nature, appear to those receiving it to be certain. Thus, the provision of genetic information may reduce rather than enhance choice, unless carefully and sensitively provided. A mature and sophisticated debate about the role of genetics in reproduction is required—engaging rather than bypassing the public—if the real potential of genetics is to be vindicated.     

The Tarsius gamma-globin gene: pseudogene or active gene?

We sequenced the approximately 5-kb long gamma-globin gene locus from Tarsius bancanus and compared it to the published gamma-globin gene sequence from the related species Tarsius syrichta. The T. syrichta gene's promoter lacks the distal CCAAT box and has a point mutation in the functionally important proximal CCAAT box (CCgAT). This previous finding had suggested that in tarsiers the gamma-globin gene might be a nonexpressed pseudogene. The two tarsier species show the same point mutation at the third nucleotide of the proximal CCAAT element and absence of the distal CCAAT element. Nevertheless, our results indicate that in tarsiers the gamma-globin gene is active, since all three coding regions show only synonymous substitutions and a much lower level of divergence than the noncoding regions. This is significantly different from what would be expected for a silent gene evading stabilizing selection. Thus, we hypothesize that the tarsier's gamma-globin gene locus is expressed even with the mutation in the proximal CCAAT box.     

Identity crisis? The need for systematic gene IDs

Recent years have seen an explosion in the availability of protozoan pathogen genome sequences. Although data regarding the underlying genome sequence remain relatively stable after the initial draft, understanding of specific gene function is increasing rapidly. This dichotomy is reflected in the relative stability of systematic gene identifiers (SysIDs(*)) in genome sequence databases, as compared to evolving and/or conflicting gene and gene product names. GenBank/EMBL/DDBJ accession numbers are important, but most protozoan parasite researchers use organism-based databases such as EuPathDB or GeneDB as their immediate resource for gene-based information because they not only provide sequence information but also functional information and links to references. Reference to SysIDs therefore provides a valuable bridge to this repository of information.     

The Arabidopsis gene ATST4a is?not a typical brassinosteroids catabolic gene

Brassinosteroid (BR) homeostasis is maintained in part by this hormone’s catabolism. The presence of multiple BR-catabolic pathways in Arabidopsis demonstrates the importance of this process in growth and development. Previous biochemical analyses suggest that ATST4a has BR catalytic activity. We have used both overexpression and loss-of-function genetic approaches to further explore the role of ATST4a in Arabidopsis. Up to 1000-fold overexpression of the ATST4a gene did not result in any characteristic BR-deficient phenotypes. In addition, the T-DNA insertion null mutant atst4a1–1 did not display enhanced seedling hypocotyl growth in the presence or absence of the active BR brassinolide when grown in white light. This lack of hallmark characteristics for BR-inacitivion genes suggests that ATST4a encodes an atypical BR catabolic enzyme.     

The low-density lipoprotein receptor gene family: a cellular Swiss army knife?

The low-density lipoprotein receptor gene family is an evolutionarily conserved group of cell-surface receptors produced by mammals and other organisms. Initially thought to be endocytic receptors that mediate the uptake of lipoproteins, recent findings have shown that these receptors have other roles in a range of cellular processes. Among other activities, members of this family act as signal transducers in neuronal migration processes, regulate synaptic plasticity or control vitamin homeostasis. Such multifunctionality is achieved by interaction with diverse cell-surface proteins including glycolipid-anchored receptors, G-protein-coupled receptors and ion channels. Here, we review the molecular interactions of this protein family with other cell-surface proteins that provide specificity and versatility - a versatility that may be reminiscent of a cellular Swiss army knife.     

The α-glucuronidase-encoding gene of Trichoderma reesei

The Trichoderma reesei cDNA coding for α-glucuronidase (GLRI), which releases glucuronic acid attached to xylose units of xylan, was cloned and sequenced. The deduced N-terminal amino acid (aa) sequence of the protein was verified by sequencing of the purified GLRI. The aa sequence of the GLRI displayed no similarity with any aa sequence available in the data bases.     

The Great Wall of China: a physical barrier to gene flow?

One population from each of six plant species along both sides of the Juyong-guan Great Wall, together with one population from each of five species along both sides of a path on a mountain top near Juyong-guan, were selected to study the effect of the Great Wall as a barrier on genetic differentiation between two subpopulations using RAPD markers. Significant genetic differentiation was found between the subpopulations on both sides of the Great Wall. A wind-pollinated woody species, Ulmus pumila, showed less genetic differentiation than four insect-pollinated species: Prunus armeniaca, Ziziphus jujuba, Vitex negundo, and Heteropappus hispidus. Cleistogenes caespitosa, a wind-pollinated perennial herb, displayed more genetic differentiation between subpopulations than the insect-pollinated species because of its propagation strategy. Although AMOVA analysis showed that subpopulations divided by a mountain path had diverged genetically, the variance component between the subpopulations on both sides of the Great Wall was significantly larger than that between the subpopulations at the control site. Therefore, it is reasonable to deduce that the Juyong-guan Great Wall has served as a physical barrier to gene flow between subpopulations separated for more than 600 years.     

The J gene of ?X174: Isolation and characterization of a J gene mutant

Summary The J gene protein of bacteriophage X174 is a component of the mature phage. The previous lack of J gene mutants has prevented an in vivo analysis of J protein functions. A X174 mutant was constructed by inserting an 11 nucleotide sequence into the J gene. This mutant, designated insJ, was viable only in the presence of a wild-type J gene carried on a plasmid that could provide J protein. An analysis of DNA synthesis during insJ mutant infection under non-permissive conditions confirmed that the J protein is not required for viral DNA synthesis.     

The future is now - will the real disease gene please stand up?

The transmission/disequilibrium test (TDT) [Spielman et al.: Am J Hum Genet 1993;52:506-516] has been postulated as the future of gene mapping for complex diseases, provided one is able to genotype a dense enough map of markers across the genome. Risch and Merikangas [Science 1996;273:1516-1517] suggested a million-marker screen in affected sibpair (ASP) families, demonstrating that the TDT is a more powerful test of linkage than traditional linkage tests based on allele-sharing when there is also association between marker and disease alleles. While the future of genotyping has arrived, successes in family-based association studies have been modest. This is often attributed to excessive false positives in candidate gene studies. This problem is only exacerbated by the increasing numbers of whole genome association (WGA) screens. When applied in ASPs, the TDT statistic, which assumes transmissions to siblings are independent, is not expected to have a constant variance in the presence of variable linkage. This results in generally more extreme statistics, hence will further aggravate the problem of having a large number of positive results to sort through. So an important question is how many positive TDT results will show up on a chromosome containing a disease gene due only to linkage, and will they obfuscate the true disease gene location. To answer this question we combined theory and computer simulations. These studies show that in ASPs the normal version of the TDT statistic has a mean of 0 and a variance of 1 in unlinked regions, but has a variance larger than 1 in linked regions. In contrast, the pedigree disequilibrium test (PDT) statistic adjusts for correlation between siblings due to linkage and maintains a constant variance of 1 at unassociated markers irrespective of linkage. The TDT statistic is generally larger than the PDT statistic across linked regions. This is true for unassociated as well as associated markers. To compare the two tests we ranked both statistics at the disease locus, or an associated marker, among statistics at all other markers. The TDT did better job than PDT placing the score of the associated marker near the top. Though, strictly speaking, the TDT in ASPs should be interpreted as a test of linkage and not a test of association, there is a good chance that if a marker stands out, the marker is associated as well as linked. In conclusion, our results suggest that TDT is an effective screening tool for WGA studies, especially in multiplex families.     

The ATM gene and breast cancer: is it really a risk factor?

The genetic determinants for most breast cancer cases remain elusive. Whilst mutations in BRCA1 and BRCA2 significantly contribute to familial breast cancer risk, their contribution to sporadic breast cancer is low. In such cases genes frequently altered in the general population, such as the gene mutated in Ataxia telangiectasia (AT), ATM may be important risk factors. The initial interest in studying ATM heterozygosity in breast cancer arose from the findings of epidemiological studies of AT families in which AT heterozygote women had an increased risk of breast cancer and estimations that 1% of the population are AT heterozygotes. One of the clinical features of AT patients is extreme cellular sensitivity to ionising radiation. This observation, together with the finding that a significant proportion of breast cancer patients show an exaggerated acute or late normal tissue reactions after radiotherapy, has lead to the suggestion that AT heterozygosity plays a role in radiosensitivity and breast cancer development. Loss of heterozygosity in the region of the ATM gene on chromosome 11, has been found in about 40% of sporadic breast tumours. However, screening for ATM mutations in sporadic breast cancer cases, showing or not adverse effects to radiotherapy, has not revealed the magnitude of involvement of the ATM gene expected. Their size and the use of the protein truncation test to identify mutations limit many of these studies. This latter parameter is critical as the profile of mutations in AT patients may not be representative of the ATM mutations in other diseases. The potential role of rare sequence variants within the ATM gene, sometimes reported as polymorphisms, also needs to be fully assessed in larger cohorts of breast cancer patients and controls in order to determine whether they represent cancer and/or radiation sensitivity predisposing mutations.     

The ATM gene and breast cancer: is it really a risk factor?

The genetic determinants for most breast cancer cases remain elusive. Whilst mutations in BRCA1 and BRCA2 significantly contribute to familial breast cancer risk, their contribution to sporadic breast cancer is low. In such cases genes frequently altered in the general population, such as the gene mutated in Ataxia telangiectasia (AT), ATM may be important risk factors. The initial interest in studying ATM heterozygosity in breast cancer arose from the findings of epidemiological studies of AT families in which AT heterozygote women had an increased risk of breast cancer and estimations that 1% of the population are AT heterozygotes. One of the clinical features of AT patients is extreme cellular sensitivity to ionising radiation. This observation, together with the finding that a significant proportion of breast cancer patients show an exaggerated acute or late normal tissue reactions after radiotherapy, has lead to the suggestion that AT heterozygosity plays a role in radiosensitivity and breast cancer development. Loss of heterozygosity in the region of the ATM gene on chromosome 11, has been found in about 40% of sporadic breast tumours. However, screening for ATM mutations in sporadic breast cancer cases, showing or not adverse effects to radiotherapy, has not revealed the magnitude of involvement of the ATM gene expected. Their size and the use of the protein truncation test to identify mutations limit many of these studies. This latter parameter is critical as the profile of mutations in AT patients may not be representative of the ATM mutations in other diseases. The potential role of rare sequence variants within the ATM gene, sometimes reported as polymorphisms, also needs to be fully assessed in larger cohorts of breast cancer patients and controls in order to determine whether they represent cancer and/or radiation sensitivity predisposing mutations.