RecQ helicases: lessons from model organisms

RecQ DNA helicases function during DNA replication and are essential for the maintenance of genome stability. There is increasing evidence that spontaneous genomic instability occurs primarily during DNA replication, and that proteins involved in the S-phase checkpoint are a principal defence against such instability. Cells that lack functional RecQ helicases exhibit phenotypes consistent with an inability to fully resume replication fork progress after encountering DNA damage or fork arrest. In this review we will concentrate on the various functions of RecQ helicases during S phase in model organisms.     

Stress and prions: lessons from the yeast model

Yeast self-perpetuating amyloids (prions) provide a convenient model for studying the cellular control of highly ordered aggregates involved in mammalian protein assembly disorders. The very ability of an amyloid to propagate a prion state in yeast is determined by its interactions with the stress-inducible chaperone Hsp104. Prion formation and propagation are also influenced by other stress-related chaperones (Hsp70 and Hsp40), and by alterations of the protein trafficking and degradation networks. Some stress conditions induce prion formation or loss. It is proposed that prions arise as byproducts of the reversible assembly of highly ordered complexes, protecting certain proteins during unfavorable conditions.     

Engaging the community in research: lessons learned from the malaria vaccine trial

When staff of the Papua New Guinea Institute of Medical Research first went into Wosera in 1979, to try and interest the community into participating in malaria research, the traditional warning sign of crossed bamboo sticks constantly blocked their path as they tried to enter the villages. In 2003, the site is a thriving research centre, with many projects under its belt, a successfully executed malaria vaccine trial to its credit, and approximately 13000 people from 29 villages currently participating in demographic surveillance and various research projects. It has been a long road from community suspicion to sustainable community participation, and the field workers have learned many important lessons along the way that can be applicable to research programs in other disease-endemic areas.     

Type I IFN as a natural adjuvant for a protective immune response: lessons from the influenza vaccine model

The identification of natural adjuvants capable of selectively promoting an efficient immune response against infectious agents would represent an important advance in immunology, with direct implications for vaccine development, whose progress is generally hampered by the difficulties in defining powerful synthetic adjuvants suitable for clinical use. Here, we demonstrate that endogenous type I IFN is necessary for the Th1 type of immune response induced by typical adjuvants in mice and that IFN itself is an unexpectedly powerful adjuvant when administered with the human influenza vaccine, for inducing IgG2a and IgA production and conferring protection from virus challenge. The finding that these cytokines, currently used in patients, are necessary for full expression of adjuvant activity and are sufficient for the generation of a protective immune response opens new perspectives in understanding the basis of immunity and in vaccine development.     

Presymptomatic testing for late-onset genetic disorders: lessons from Huntington's disease.

Huntington's disease is an inherited, neurodegenerative disorder, usually of adult onset. Since the identification of linked markers, more than 1000 presymptomatic tests have been performed worldwide and multiple ethical issues have been encountered in relation to informed consent, testing of children, exclusion testing during pregnancy, and confidentiality. Further ethical problems are anticipated after identification of the causal mutation (or mutations). As Huntington's disease is a model for other disorders of adult onset for which testing is becoming possible, the successful resolution of these ethical issues is of great importance. A failure to do so might discredit genetic testing as a whole.     

The PLP cofactor: lessons from studies on model reactions

Experimental probes of the acidity of weak carbon acids have been developed and used to determine the carbon acid pK(a)s of glycine, glycine derivatives and iminium ion adducts of glycine to the carbonyl group, including 5'-deoxypyridoxal (DPL). The high reactivity of the DPL-stabilized glycyl carbanion towards nucleophilic addition to both DPL and the glycine-DPL iminium ion favors the formation of Claisen condensation products at enzyme active sites. The formation of the iminium ion between glycine and DPL is accompanied by a 12-unit decrease in the pK(a) of 29 for glycine. The complicated effects of formation of glycine iminium ions to DPL and other aromatic and aliphatic aldehydes and ketones on carbon acid pK(a) are discussed. These data provide insight into the contribution of the individual pyridine ring substituents to the catalytic efficiency of DPL. It is suggested that the 5'-phosphodianion group of PLP may play an important role in enzymatic catalysis of carbon deprotonation by providing up to 12 kcal/mol of binding energy that is utilized to stabilize the transition state for the enzymatic reaction. This article is part of a Special Issue entitled: Pyridoxal Phospate Enzymology.     

Shaping the niche: lessons from the Drosophila testis and other model systems

Stem cells are fascinating, as they supply the cells that construct our adult bodies and replenish, as we age, worn out, damaged, and diseased tissues. Stem cell regulation relies on intrinsic signals but also on inputs emanating from the neighbouring niche. The Drosophila testis provides an excellent system for studying such processes. Although recent advances have uncovered several signalling, cytoskeletal and other factors affecting niche homeostasis and testis differentiation, many aspects of niche regulation and maintenance remain unsolved. In this review, we discuss aspects of niche establishment and integrity not yet fully understood and we compare it to the current knowledge in other model systems such as vertebrates and plants. We also address specific questions on stem cell maintenance and niche regulation in the Drosophila testis under the control of Hox genes. Finally, we provide insights on the striking functional conservation of homologous genes in plants and animals and their respective stem cell niches. Elucidating conserved mechanisms of stem cell control in both lineages could reveal the importance underlying this conservation and justify the evolutionary pressure to adapt homologous molecules for performing the same task.     

Mosquito immune responses and malaria transmission: lessons from insect model systems and implications for vertebrate innate immunity and vaccine development

The introduction of novel biochemical, genetic, molecular and cell biology tools to the study of insect immunity has generated an information explosion in recent years. Due to the biodiversity of insects, complementary model systems have been developed. The conceptual framework built based on these systems is used to discuss our current understanding of mosquito immune responses and their implications for malaria transmission. The areas of insect and vertebrate innate immunity are merging as new information confirms the remarkable extent of the evolutionary conservation, at a molecular level, in the signaling pathways mediating these responses in such distant species. Our current understanding of the molecular language that allows the vertebrate innate immune system to identify parasites, such as malaria, and direct the acquired immune system to mount a protective immune response is very limited. Insect vectors of parasitic diseases, such as mosquitoes, could represent excellent models to understand the molecular responses of epithelial cells to parasite invasion. This information could broaden our understanding of vertebrate responses to parasitic infection and could have extensive implications for anti-malarial vaccine development.     

The blood-brain barrier and cerebral angiogenesis: lessons from the cold-injury model.

Brain injury is associated with an initial blood-brain barrier (BBB) breakdown, which can be life threatening. A second phase of BBB breakdown accompanies the angiogenesis occurring at the lesion margins. Studies of the molecular mechanisms involved in these processes are essential to determine targets for therapeutic intervention, as well as the time periods during which therapeutic intervention could ameliorate brain damage and thus improve the clinical outcome.     

A model for follicular selection and ovulation: lessons from superovulation

A model for selection of the preovulatory follicle during the normal ovarian cycle is proposed. During menstruation the concentration of FSH rises to a level high enough to "activate" a single small antral follicle (2-4 mm dia.) so that it can produce large amounts of oestradiol. As the follicle develops, the concentration of FSH is suppressed below this threshold level by the secretion of oestradiol and inhibin. The dominant follicle becomes increasingly sensitive to FSH so that it continues to develop in an environment which inhibits development of other follicles. Multiple ovulation can be achieved by extending the period during which the level of FSH remains above this threshold level (e.g. during treatment with clomiphene or gonadotrophins). Although multiple ovulation occurs when the gate is widened in this way, the follicles are never completely synchronous as they continue to grow at approximately the same rate. Current evidence suggests that ovulation occurs at random between the two ovaries in successive cycles and that the corpus luteum exerts an inhibitory effect on folliculogenesis by suppressing the secretion of FSH and LH. These observations are compatible with the hypothesis that while small antral follicles are recruited continuously, at all stages of reproductive life, selection of the dominant follicle requires the unique gonadotrophic environment which is only present in the early follicular phase. The follicle of the month is, therefore, selected by chance because it is at the right place at the right time.     

Isoprene synthesis in plants: lessons from a transgenic tobacco model

Isoprene is a highly reactive gas, and is emitted in such large quantities from the biosphere that it substantially affects the oxidizing potential of the atmosphere. Relatively little is known about the control of isoprene emission at the molecular level. Using transgenic tobacco lines harbouring a poplar isoprene synthase gene, we examined control of isoprene emission. Isoprene synthase required chloroplastic localization for catalytic activity, and isoprene was produced via the methyl erythritol (MEP) pathway from recently assimilated carbon. Emission patterns in transgenic tobacco plants were remarkably similar to naturally emitting plants under a wide variety of conditions. Emissions correlated with photosynthetic rates in developing and mature leaves, and with the amount of isoprene synthase protein in mature leaves. Isoprene synthase protein levels did not change under short-term increase in heat/light, despite an increase in emissions under these conditions. A robust circadian pattern could be observed in emissions from long-day plants. The data support the idea that substrate supply and changes in enzyme kinetics (rather than changes in isoprene synthase levels or post-translational regulation of activity) are the primary controls on isoprene emission in mature transgenic tobacco leaves.     

A baboon model for endometriosis: implications for fertility

Endometriosis is one of the most common causes of chronic pelvic pain and infertility in women in the reproductive age group. Although the existence of this disease has been known for over 100 years our current knowledge of its pathogenesis and the pathophysiology of its related infertility remains unclear. Several reasons contribute to our lack of knowledge, the most critical being the difficulty in carrying out objective long-term studies in women. Thus, we and others have developed a model of this disease in the non-human primate, the baboon (Papio anubis). Intraperitoneal inoculation of autologous menstrual endometrium results in the development of endometriotic lesions with gross morphological characteristics similar to those seen in the human. Multiple factors have been implicated in endometriosis-associated infertility. We have described aberrant levels of factors involved in multiple pathways important in the establishment of pregnancy, in the endometrium of baboons induced with endometriosis. Specifically, we have observed dysregulation of proteins involved in invasion, angiogenesis, methylation, cell growth, immunomodulation, and steroid hormone action. These data suggest that, in an induced model of endometriosis in the baboon, an increased angiogenic capacity, decreased apoptotic potential, progesterone resistance, estrogen hyper-responsiveness, and an inability to respond appropriately to embryonic signals contribute to the reduced fecundity associated with this disease.     

Challenges of organizational LCA: lessons learned from road testing the guidance on organizational life cycle assessment

Purpose

The novelty of the O-LCA method and the existing differences with the established product LCA practice, as well as the unique structure each organization, pose a broad range of methodological and application challenges, in addition to the general methodological gaps in LCA. In order to provide practitioners with lessons learned for future applications and boost future method development efforts, the paper discusses those challenges.

Methods

The challenges included in this paper were mainly identified from a survey administered to the road testers and from experiences during the piloting process. These are complemented with case studies from literature. The focus of the paper is on challenges exclusive to the organizational approach, although some additional issues common to product LCA but intensified in organizational LCA are also included. Each issue is characterized and exemplified, recommendations of reference standards are analyzed, and possible solutions discussed.

Results and discussion

With the goal and scope of O-LCA, some challenging issues were to select part of an organization as the reporting organization, and the operability of the reporting flow. Regarding the system boundary, the challenges were which parts of the supply chain should be included in the study, problems when setting the system boundary for the service sector, how to include supporting activities, and how to prepare the right system boundary diagrams. Regarding the inventory stage, the discussion starts with alternatives to the categorization of the inventory into activities and the aggregation of those activities into groups. It includes an equivalence table for an easier transfer from other organizational frameworks (ISO 14069 and the GHG Protocol). Some challenges during impact assessment and interpretation were the assessment of local impacts, scoping performance tracking, and the use of O-LCA results for an organization’s strategy.

Conclusions

The review of challenges is not meant as a complete overview of all possible challenges—new challenges may arise in future case studies. Further application testing is needed, along with research to support a future revision of the O-LCA Guidance, in line with the issues highlighted in this paper and new challenges may arise in future case studies. O-LCA has the potential to contribute in the future implementation of the life cycle concept in environmental management systems, in the development of organizational footprint metrics for region-specific impacts, and in the social dimension of life cycle assessment.

     

Cystic fibrosis testing in a referral laboratory: results and lessons from a six-year period

Background

The recent introduction of high throughput sequencing technologies into clinical genetics has made it practical to simultaneously sequence many genes. In contrast, previous technologies limited sequencing based tests to only a handful of genes. While the ability to more accurately diagnose inherited diseases is a great benefit it introduces specific challenges. Interpretation of missense mutations continues to be challenging and the number of variants of uncertain significance continues to grow.

Results

We leveraged the data available at ARUP Laboratories, a major reference laboratory, for the CFTR gene to explore specific challenges related to variant interpretation, including a focus on understanding ethnic-specific variants and an evaluation of existing databases for clinical interpretation of variants. In this study we analyzed 555 patients representing eight different ethnic groups. We observed 184 different variants, most of which were ethnic group specific. Eighty-five percent of these variants were present in the Cystic Fibrosis Mutation Database, whereas the Human Mutation Database and dbSNP/1000 Genomes had far fewer of the observed variants. Finally, 21 of the variants were novel and we report these variants and their clinical classifications.

Conclusions

Based on our analyses of data from six years of CFTR testing at ARUP Laboratories a more comprehensive, clinical grade database is needed for the accurate interpretation of observed variants. Furthermore, there is a particular need for more and better information regarding variants from individuals of non-Caucasian ethnicity.