DNA damage levels are raised in Barrett's oesophageal mucosa relative to the squamous epithelium of the oesophagus.

Barrett's oesophagus (BE) is a pre-malignant metaplastic tissue predisposing to oesophageal adenocarcinoma (EC), and gastro-oesophageal reflux is a risk factor for both conditions. Reflux of acid and bile can cause mucosal injury and initiate chronic inflammation. These processes can induce DNA damage, possibly via an oxidative stress mechanism, thus increasing the likelihood of progression from Barrett's metaplasia to dysplasia and finally carcinoma. The comet assay was optimized for the detection of DNA damage (strand breaks and alkali-labile sites) in oesophageal biopsies, including incorporation of the DNA repair enzyme Fapy-DNA glycosylase (Fpg). Fpg allows the detection of 8-hydroxy-2-deoxyguanosine (8-OHdG) sites, a known pro-mutagenic DNA lesion. BE patients were recruited from BE surveillance clinics and oesophageal biopsies collected at endoscopy. Comet analysis revealed significantly increased (p < 0.001) DNA damage in Barrett's epithelium compared with matched squamous epithelium, with median % tail DNA values of 25.1% (first to third quartile 21.7-29.6%) and 18.6% (first to third quartile 16.9-21.4%), respectively. The median % tail DNA was up to 70% higher in the matched BE tissue compared with squamous epithelium from the same patient. Fpg sensitive sites were demonstrated in both tissue types at similar levels. The raised level of DNA damage in the premalignant BE may contribute to the accumulation of genetic alterations occurring during progression to EC. Understanding these underlying mechanisms provides a basis for cancer prevention strategies in BE patients.     

The role of niche measures in explaining the abundance–distribution relationship in tropical lotic chironomids

In situ measurements of both community metabolism (primary production and respiration) and PAM fluorometry were conducted during emersion on intertidal sediments in the Mont Saint-Michel Bay, in areas where oysters and mussels were cultivated. Results highlighted a low benthic metabolism compared to other intertidal areas previously investigated with the same methods. Comparisons between gross community primary production and relative electron transport rates confirmed this statement. More specifically, primary productivity remained very low all over the year, whereas the associated microalgal biomass was estimated to be high. We suggest that the microphytobenthic community studied was characterized by a self-limitation of its primary productivity by its own biomass, as previously shown in Marennes-Oléron Bay for example. The almost permanent high biomass would represent a limiting factor for micromigration processes within the first millimetres of the sediment. This could be explained by very low resuspension processes occurring in the western part of the bay, enhanced by the occurrence of numerous aquaculture structures that could decrease tidal currents in the benthic boundary layer. Handling editor: N. Desroy     

Reactive Oxygen Species Production by Potato Tuber Mitochondria Is Modulated by Mitochondrially Bound Hexokinase Activity

Potato tuber (Solanum tuberosum) mitochondria (PTM) have a mitochondrially bound hexokinase (HK) activity that exhibits a pronounced sensitivity to ADP inhibition. Here we investigated the role of mitochondrial HK activity in PTM reactive oxygen species generation. Mitochondrial HK has a 10-fold higher affinity for glucose (Glc) than for fructose (K_MGlc = 140 μm versus K_MFrc = 1,375 μm). Activation of PTM respiration by succinate led to an increase in hydrogen peroxide (H₂O₂) release that was abrogated by mitochondrial HK activation. Mitochondrial HK activity caused a decrease in the mitochondrial membrane potential and an increase in oxygen consumption by PTM. Inhibition of Glc phosphorylation by mannoheptulose or GlcNAc induced a rapid increase in H₂O₂ release. The blockage of H₂O₂ release sustained by Glc was reverted by oligomycin and atractyloside, indicating that ADP recycles through the adenine nucleotide translocator and F₀F₁ATP synthase is operative during the mitochondrial HK reaction. Inhibition of mitochondrial HK activity by 60% to 70% caused an increase of 50% in the maximal rate of H₂O₂ release. Inhibition in H₂O₂ release by mitochondrial HK activity was comparable to, or even more potent, than that observed for StUCP (S. tuberosum uncoupling protein) activity. The inhibition of H₂O₂ release in PTM was two orders of magnitude more selective for the ADP produced from the mitochondrial HK reaction than for that derived from soluble yeast (Saccharomyces cerevisiae) HK. Modulation of H₂O₂ release and oxygen consumption by Glc and mitochondrial HK inhibitors in potato tuber slices shows that hexoses and mitochondrial HK may act as a potent preventive antioxidant mechanism in potato tubers.Production of reactive oxygen species (ROS) is an unavoidable consequence of aerobic respiration (Chance et al., 1979). The mitochondrial electron transport system (ETS) is the major site of ROS production in mammalian and nonphotosynthesizing plant cells (Puntarulo et al., 1991; Halliwell and Gutteridge, 2007). Depending on the mitochondrial respiratory states, a small portion of the consumable oxygen is partially reduced to generate ROS (Skulachev, 1996; Liu, 1997; Turrens, 1997; Møller, 2001; Considine et al., 2003; Smith et al., 2004). In plants, the monoelectronic reduction of oxygen by ETS leads to the production of superoxide radicals (O₂^·−) that can be dismutated by SOD, producing hydrogen peroxide (H₂O₂), and further decomposed by catalase and/or ascorbate-glutathione peroxidase cycles (Møller, 2001). An imbalance between the ROS production and antioxidant defenses can lead to an oxidative stress condition. Increased levels of ROS may be a consequence of the action of plant hormones, environmental stress, pathogens, or high levels of sugars and fatty acids (Bolwell et al., 2002; Couée et al., 2006; Gechev et al., 2006; Liu et al., 2007; Rhoads and Subbaiah, 2007). These conditions may lead to storage deterioration or impairment of seedling growth decreasing on crop yield. To avoid the harmful accumulation of ROS or to fine tune the steady-state levels of ROS, various enzymatic systems control the rate of ROS production in mitochondria (Schreck and Baeuerle, 1991; Møller, 2001).Mitochondrial ROS production is highly dependent on the membrane potential (ΔΨ_m) generated by the proton gradient formed across the inner mitochondrial membrane. High ΔΨ_m was shown to stimulate ROS production when the ETS is predominantly in a reduced state (i.e. when NADH, FADH₂, and O₂ are present in abundance but ADP or Pi levels are low). This condition is reached in resting metabolic states after a full oxidation of Glc or fatty acids. Stimulating electron flow by decreasing ΔΨ_m, either by the use of uncouplers or by coupling respiration to ATP synthesis, slows the ROS generation rate (Boveris and Chance, 1973; Korshunov et al., 1997). It has been observed that in isolated potato tuber (Solanum tuberosum) mitochondria (PTM) the uncoupling protein (referred to as PUMP in plants, or UCP in animals) causes a small decrease in ΔΨ_m when this proton carrier protein is activated by the presence of anionic fatty acids, a condition that blocks ROS generation (Vercesi et al., 1995, 2006). Nucleotides, such as ATP, antagonize this effect (Considine et al., 2003; Vercesi et al., 2006). On the other hand, fluctuations in free hexose levels due to environmental or developmental conditions (Morrell and ap Rees, 1986; Geigenberger and Stitt, 1993; Renz and Stitt, 1993) lead to variations in the oxygen consumption rate in heterotrophic tissues of plant (Brouquisse et al., 1991; Dieuaide et al., 1992). As a result, ROS-producing pathways may be either stimulated or repressed (Couée et al., 2006). Unlike PUMP activity, which is activated by an excess of free fatty acids, a specific mechanism for mitochondrial ROS production caused by an excess of hexose remains elusive.The metabolism of free hexoses begins by their phosphorylation in a reaction catalyzed by the hexokinase (HK):HK is a ubiquitous enzyme found in many organisms. In plants, the binding mechanism of HK to the outer mitochondrial membrane is not fully established, but some reports indicate that it may differ considerably from those properties described for mammal cells (Dry et al., 1983; Miernyk and Dennis, 1983; Rezende et al., 2006). It has been shown that in several mature and developing plant tissues, multiple HK isoforms are expressed with different kinetic properties and subcellular localizations. The HKs are found in cytosol, bound to the mitochondrial membrane, or in stroma of plastids in plant cells (Miernyk and Dennis, 1983; Galina et al., 1995; Damari-Weissler et al., 2007). Beyond its obvious role in glycolysis regulation, HK activity may also function as a sugar sensor, triggering a signal transduction pathway in plants (Rolland et al., 2006).In mammals, HK types I and II are associated with the mitochondrial outer membrane through the voltage-dependent anion channel (VDAC) and adenine nucleotide transporter (ANT). These associations were found in tissues with a high energy demand, such as heart, brain, and tumor cells (Arora and Pedersen, 1988; BeltrandelRio and Wilson, 1992; Wilson, 2003). In addition, recent evidence in mammalian cells has shown that binding of HK to VDAC located at the outer mitochondrial membrane is somehow involved in the protection against proapoptotic stimuli (Nakashima et al., 1986; Gottlob et al., 2001; Vander Heiden et al., 2001; Pastorino et al., 2002; Cesar and Wilson, 2004). Similar observations were reported for tobacco (Nicotiana tabacum) plant mitochondrial HK (mt-HK; Kim et al., 2006). However, it has been shown that drugs such as the fungicide clotrimazole and the anesthetic thiopental, which promptly disrupt the association between mt-HK and VDAC in mammalian mitochondria, are unable to promote this effect in maize (Zea mays) root mitochondria (Rezende et al., 2006). These observations suggest a different type of association of mt-HK with plant mitochondria. The binding of mt-HK with mitochondria in many plants involves a common N-terminal hydrophobic membrane anchor domain of about 24 amino acids that is related to the membrane targeting, but the exact mechanism of association is unknown (Damari-Weissler et al., 2007).Recently, our group demonstrated that mt-HK activity plays a key preventive antioxidant role by reducing mitochondrial ROS generation through a steady-state ADP recycling mechanism in rat brain neurons. The mitochondrial ADP recycling leads to a decrease in the ΔΨ_m coupled to the synthesis of ATP by oxidative phosphorylation (da-Silva et al., 2004; Meyer et al., 2006).Although plant HK is recognized to fulfill a catalytic function, the role of mt-HK activity in the regulation of both mitochondrial respiration and ROS production in plants is unknown. Recently, an authentic HK activity was detected in PTM (Graham et al., 2007) and its involvement in potato tuber glycolysis suggested, but its involvement in PTM ROS generation was not explored. We then raise the hypothesis that HK bound to PTM would contribute to produce a steady-state ADP recycling that regulates ROS formation. However, whether this association is capable of controlling the rate of ROS generation in plant mitochondria is unknown. Here, we aim to investigate the role of mt-HK activity in PTM physiology. The data indicate that mt-HK activity plays a key role as a regulator of ROS levels in respiring plant tissues exposed to high hexose levels.     

The dynamic ups and downs of genome size evolution in Brassicaceae

Crucifers (Brassicaceae, Cruciferae) are a large family comprisingsome 338 genera and c. 3,700 species. The family includes importantcrops as well as several model species in various fields ofplant research. This paper reports new genome size (GS) datafor more than 100 cruciferous species in addition to previouslypublished C-values (the DNA amount in the unreplicated gameticnuclei) to give a data set comprising 185 Brassicaceae taxa,including all but 1 of the 25 tribes currently recognized. Evolutionof GS was analyzed within a phylogenetic framework based ongene trees built from five data sets (matK, chs, adh, trnLF,and ITS). Despite the 16.2-fold variation across the family,most Brassicaceae species are characterized by very small genomeswith a mean 1C-value of 0.63 pg. The ancestral genome size (ancGS)for Brassicaceae was reconstructed as ^anc1C = 0.50 pg. Approximately50% of crucifer taxa analyzed showed a decrease in GS comparedwith the ancGS. The remaining species showed an increase inGS although this was generally moderate, with significant increasesin C-value found only in the tribes Anchonieae and Physarieae.Using statistical approaches to analyze GS, evolutionary gainsor losses in GS were seen to have accumulated disproportionatelyfaster within longer branches. However, we also found that GShas not changed substantially through time and most likely evolvespassively (i.e., a tempo that cannot be distinguished betweenneutral evolution and weak forms of selection). The data revealan apparent paradox between the narrow range of small GSs overlong evolutionary time periods despite evidence of dynamic genomicprocesses that have the potential to lead to genome obesity(e.g., transposable element amplification and polyploidy). Toresolve this, it is suggested that mechanisms to suppress amplificationand to eliminate amplified DNA must be active in Brassicaceaealthough their control and mode of operation are still poorlyunderstood.     

Drosophila Transposon Insertions as Unknowns for Structured Inquiry Recombination Mapping Exercises in an Undergraduate Genetics Course

Structured inquiry approaches, in which students receive a Drosophila strain of unknown genotype to analyze and map the constituent mutations, are a common feature of many genetics teaching laboratories. The required crosses frustrate many students because they are aware that they are participating in a fundamentally trivial exercise, as the map locations of the genes are already established and have been recalculated thousands of times by generations of students. We modified the traditional structured inquiry approach to include a novel research experience for the students in our undergraduate genetics laboratories. Students conducted crosses with Drosophila strains carrying P[lacW] transposon insertions in genes without documented recombination map positions, representing a large number of unique, but equivalent genetic unknowns. Using the eye color phenotypes associated with the inserts as visible markers, it is straightforward to calculate recombination map positions for the interrupted loci. Collectively, our students mapped 95 genetic loci on chromosomes 2 and 3. In most cases, the calculated 95% confidence interval for meiotic map location overlapped with the predicted map position based on cytology. The research experience evoked positive student responses and helped students better understand the nature of scientific research for little additional cost or instructor effort.INQUIRY-BASED learning in which students are engaged in open-ended, student-centered, hands-on activities is an important tool for training undergraduates to think like scientists (Colburn 2000; Handelsman et al. 2004). With this approach, students learn scientific subjects by interpreting and discussing experimental results in a fashion similar to that used by scientific researchers (NRC 2003). There are three main approaches to instruction via inquiry. In open inquiry, students formulate their own problem, as well as the procedures to investigate the problem. In guided inquiry, the instructor provides the problem and necessary materials, but the students devise an experimental procedure to investigate the problem. Finally, in structured inquiry, the instructor provides the problem, the materials, and the procedure, but the students are required to gather and interpret the experimental data independently, coming to their own conclusions (Welch et al. 2006). In each case, the instructor does not provide “the answer” to the problem. In the ideal case, the instructor does not even know what the answer will be prior to the student experiment, forcing the students to grapple with the information themselves. Inquiry-based laboratories can even be extended so that students are participating in novel research as part of their coursework (DebBurman 2002; Buckner et al. 2007), which been shown to improve undergraduate retention and student performance in biology lecture courses (Marcus et al. 2009).The process of inquiry has been identified as central to training students to understand fundamental approaches used in the field of genetics such as the design of controlled crosses and interpretation of experimental data (Cartier and Stewart 2000). Pukkila (2004) discusses effective methods by which inquiry-based learning can be incorporated into undergraduate genetics lecture courses with large enrollments and into recitation sections. However, the implementation of inquiry-based approaches in undergraduate genetics laboratories has not been discussed extensively.Teaching laboratories offer some advantages for inquiry learning because they generally contain small groups of students, facilitating a flexible and intimate learning environment with many interactions between students and the instructor, as well as among classmates. However, teaching laboratories associated with large lecture courses also offer some challenges, in particular how to deliver substantially similar experiences to laboratory sections taught by multiple instructors, as well as how to provide inquiry-based learning in a logistically manageable and cost-effective manner. For these reasons, most inquiry-based genetics laboratory exercises have used the structured inquiry approach, for example, using many Drosophila melanogaster strains with similar mutant phenotypes (e.g., white eyes and black bodies), but a variety of genotypes, in a series of standardized genetic mapping crosses to familiarize students with the collection and interpretation of classical genetic data (MacIntyre 1974; Pye 1980). The difficulty with contrived genetic unknowns carrying well-mapped genetic mutations is that many students become frustrated that their hard work evaluating the crosses over a period of several months is devoted to a fundamentally trivial exercise, as the recombination map locations of the genes are already established in the scientific literature and have been recalculated thousands of times by generations of genetics students.We have expanded upon the structured inquiry approach to genetics to include novel research experiences for the students in our undergraduate genetics laboratories. They conduct mapping crosses with Drosophila strains carrying P-element transposon insertions in genes without documented recombination map positions. The stock centers maintain very large collections of P-element transposon stocks with known insertion sites on the cytological and genome maps (Spradling et al. 1999). However, in spite of the cytology to recombination map equivalence table available in FlyBase (2009), very few of the transposon inserts have been formally placed on the recombination map. By using the eye color phenotypes associated with many transposon inserts as visible markers in genetic crosses (Marcus 2003), it is straightforward to calculate recombination map positions for the interrupted loci. The stock collections contain many stocks with identical transposons inserted at different chromosomal locations, providing a large number of unique, but equivalent genetic unknowns that can be used for recombination mapping exercises. At the same time, this approach provides students with the opportunity to map genes that have never been mapped before, allowing them to make small but useful contributions to the field of Drosophila genetics.     

A Claudin-9–Based Ion Permeability Barrier Is Essential for Hearing

Hereditary hearing loss is one of the most common birth defects, yet the majority of genes required for audition is thought to remain unidentified. Ethylnitrosourea (ENU)–mutagenesis has been a valuable approach for generating new animal models of deafness and discovering previously unrecognized gene functions. Here we report on the characterization of a new ENU–induced mouse mutant (nmf329) that exhibits recessively inherited deafness. We found a widespread loss of sensory hair cells in the hearing organs of nmf329 mice after the second week of life. Positional cloning revealed that the nmf329 strain carries a missense mutation in the claudin-9 gene, which encodes a tight junction protein with unknown biological function. In an epithelial cell line, heterologous expression of wild-type claudin-9 reduced the paracellular permeability to Na⁺ and K⁺, and the nmf329 mutation eliminated this ion barrier function without affecting the plasma membrane localization of claudin-9. In the nmf329 mouse line, the perilymphatic K⁺ concentration was found to be elevated, suggesting that the cochlear tight junctions were dysfunctional. Furthermore, the hair-cell loss in the claudin-9–defective cochlea was rescued in vitro when the explanted hearing organs were cultured in a low-K⁺ milieu and in vivo when the endocochlear K⁺-driving force was diminished by deletion of the pou3f4 gene. Overall, our data indicate that claudin-9 is required for the preservation of sensory cells in the hearing organ because claudin-9–defective tight junctions fail to shield the basolateral side of hair cells from the K⁺-rich endolymph. In the tight-junction complexes of hair cells, claudin-9 is localized specifically to a subdomain that is underneath more apical tight-junction strands formed by other claudins. Thus, the analysis of claudin-9 mutant mice suggests that even the deeper (subapical) tight-junction strands have biologically important ion barrier function.