Identification of novel chromosomal regions associated with airway hyperresponsiveness in recombinant congenic strains of mice

Airway responsiveness is the ability of the airways to respond to bronchoconstricting stimuli by reducing their diameter. Airway hyperresponsiveness has been associated with asthma susceptibility in both humans and murine models, and it has been shown to be a complex and heritable trait. In particular, the A/J mouse strain is known to have hyperresponsive airways, while the C57BL/6 strain is known to be relatively refractory to bronchoconstricting stimuli. We analyzed recombinant congenic strains (RCS) of mice generated from these hyper- and hyporesponsive parental strains to identify genetic loci underlying the trait of airway responsiveness in response to methacholine as assessed by whole-body plethysmography. Our screen identified 16 chromosomal regions significantly associated with airway hyperresponsiveness (genome-wide P ≤ 0.05): 8 are supported by independent and previously published reports while 8 are entirely novel. Regions that overlap with previous reports include two regions on chromosome 2, three on chromosome 6, one on chromosome 15, and two on chromosome 17. The 8 novel regions are located on chromosome 1 (92–100 cM), chromosome 5 (>73 cM), chromosome 7 (>63 cM), chromosome 8 (52–67 cM), chromosome 10 (3–7 cM and >68 cM), and chromosome 12 (25–38 cM and >52 cM). Our data identify several likely candidate genes from the 16 regions, including Ddr2, Hc, Fbn1, Flt3, Utrn, Enpp2, and Tsc.     

MicA sRNA links the PhoP regulon to cell envelope stress

Numerous small RNAs regulators of gene expression exist in bacteria. A large class of them binds to the RNA chaperone Hfq and act by base pairing interactions with their target mRNA, thereby affecting their translation and/or stability. They often have multiple direct targets, some of which may be regulators themselves, and production of a single sRNA can therefore affect the expression of dozens of genes. We show in this study that the synthesis of the Escherichia coli pleiotropic PhoPQ two‐component system is repressed by MicA, a σ^E‐dependent sRNA regulator of porin biogenesis. MicA directly pairs with phoPQ mRNA in the translation initiation region of phoP and presumably inhibits translation by competing with ribosome binding. Consequently, MicA downregulates several members of the PhoPQ regulon. By linking PhoPQ to σ^E, our findings suggest that major cellular processes such as Mg²⁺ transport, virulence, LPS modification or resistance to antimicrobial peptides are modulated in response to envelope stress. In addition, we found that Hfq strongly affects the expression of phoP independently of MicA, raising the possibility that even more sRNAs, which remain to be identified, could regulate PhoPQ synthesis.     

Efficient age determination: how freezing affects eye lens weight of the small rodent species Arvicola terrestris

Age determination of animals by measuring the weight of their eye lenses is a widely used method in wildlife biology. In general, it is recommended to prepare lenses immediately after trapping to avoid errors in the age estimation due to decomposition of lens tissue. However, in many field studies, large numbers of animals need to be trapped over long periods of time in huge areas and by many different field workers. Therefore, the immediate preparation of eye lenses imposes a considerable logistic constraint that could be avoided by prior freezing of trapped animals. To assess the impact of freezing, weights of lens of frozen and unfrozen eyes of 114 Arvicola terrestris were compared pair wise. The frozen lenses weighed at average 3.3% (95% CI: 2.4–4.1%) more than the unfrozen ones from the same animals. Freezing time, weight of lenses and mean temperature of the trapping day as an indicator of decomposition speed did not affect the freezing-induced weight increase. Age estimates based on weights of unfrozen lenses varied between 24 and 445 days. Estimates based on frozen lenses were systematically higher. Applying a constant correction factor of 1.033⁻¹ for the weight of frozen lenses corrects this overestimation of age. We conclude that age determination with frozen lenses of small rodents can yield valid age estimates if a correction factor for freezing is applied. Thus, age determination can be organised much more efficiently in field studies, which is highly advantageous for many ecological, agricultural and epidemiological research projects.     

Modulation of cellulosome composition in Clostridium cellulolyticum: Adaptation to the polysaccharide environment revealed by proteomic and carbohydrate‐active enzyme analyses

Clostridium cellulolyticum is a model mesophilic anaerobic bacterium that efficiently degrades plant cell walls. The recent genome release offers the opportunity to analyse its complete degradation system. A total of 148 putative carbohydrate‐active enzymes were identified, and their modular structures and activities were predicted. Among them, 62 dockerin‐containing proteins bear catalytic modules from numerous carbohydrate‐active enzymes' families and whose diversity reflects the chemical and structural complexity of the plant carbohydrate. The composition of the cellulosomes produced by C. cellulolyticum upon growth on different substrates (cellulose, xylan, and wheat straw) was investigated by LC MS/MS. The majority of the proteins encoded by the cip‐cel operon, essential for cellulose degradation, were detected in all cellulosome preparations. In the presence of wheat straw, the natural and most complex of the substrates studied, additional proteins predicted to be involved in hemicellulose degradation were produced. A 32‐kb gene cluster encodes the majority of these proteins, all harbouring carbohydrate‐binding module 6 or carbohydrate‐binding module 22 xylan‐binding modules along dockerins. This newly identified xyl‐doc gene cluster, specialised in hemicellulose degradation, comes in addition of the cip‐cel operon for plant cell wall degradation. Hydrolysis efficiencies determined on the different substrates corroborates the finding that cellulosome composition is adapted to the growth substrate.     

Plant‐extract‐induced changes in the proteome of the soil‐borne pathogenic fungus Thielaviopsis basicola

Thielaviopsis basicola is a hemibiotroph fungus that causes black root rot disease in diverse plants with significant impact on cotton production in Australia. To elucidate how T. basicola growth and proteome are influenced by interactions with natural sources, this fungus was cultured in the presence of root extracts from non‐host (wheat, hairy vetch) and susceptible host (cotton, lupin) plants. We found that T. basicola growth was significantly favored in the presence of host extracts, while hierarchical clustering analysis of 2‐DE protein profiles of T. basicola showed plant species had a larger effect on the proteome than host/non‐host status. Analysis by LC‐MS/MS of unique and differentially expressed spots and identification using cross‐species similarity searching and de novo sequencing allowed successful identification of 41 spots. These proteins were principally involved in primary metabolism with smaller numbers implicated in other diverse functions. Identification of several “morpho” proteins suggested morphological differences that were further microscopically investigated. Identification of several highly expressed spots suggested that vitamin B₆ is important in the T. basicola response to components present in hairy vetch extract, and finally, three spots, induced in the presence of lupin extract, may correspond to malic enzyme and be involved in lipid accumulation.     

The Neandertal lower right deciduous second molar from Trou de l'Abîme at Couvin, Belgium

A human lower right deciduous second molar was discovered in 1984 at the entrance of Trou de l'Abîme at Couvin (Belgium). In subsequent years the interpretation of this fossil remained difficult for various reasons: (1) the lack of taxonomically diagnostic elements which would support its attribution to either Homo (sapiens) neanderthalensis or H. s. sapiens; (2) the absence of any reliable chronostratigraphic interpretation of the sedimentary sequence of the site; (3) the contradiction between archaeological interpretations, which attributed the lithic industry to a transitional facies between the Middle and Early Upper Palaeolithic, and the radiocarbon date of 46,820 ± 3,290 BP obtained from animal bone remains associated with the tooth and the flint tools.Thanks to recent progress regarding these three aspects, the tooth from Trou de l'Abîme may now be studied in detail. Analyses of the morphology and enamel thickness of the fossil yielded diagnostic characters consistent with an attribution to Neandertals. Re-examination of the lithic industry of Couvin shows that it corresponds to the late Middle Palaeolithic rather than a transitional facies. Furthermore, a new analysis of the site stratigraphy indicates that the unit situated above the archaeological layer in which the tooth was found is probably a palaeosol of brown soil type. Comparison with the regional cave sequences as well as with the reference sequence from the Belgian loess belt tends to show that the most recent palaeosol of this type is dated between 42,000 and 40,000 BP. This is consistent with both a recently obtained AMS result at 44,500 BP and the published conventional date.     

Knock-down of the COX3 and COX17 gene expression of cytochrome c oxidase in the unicellular green alga Chlamydomonas reinhardtii

The COX3 gene encodes a core subunit of mitochondrial cytochrome c oxidase (complex IV) whereas the COX17 gene encodes a chaperone delivering copper to the enzyme. Mutants of these two genes were isolated by RNA interference in the microalga Chlamydomonas. The COX3 mRNA was completely lacking in the cox3-RNAi mutant and no activity and assembly of complex IV were detected. The cox17-RNAi mutant presented a reduced level of COX17 mRNA, a reduced activity of the cytochrome c oxidase but no modification of its amount. The cox3-RNAi mutant had only 40% of the wild-type rate of dark respiration which was cyanide-insensitive. The mutant presented a 60% decrease of H₂O₂ production in the dark compared to wild type, which probably accounts for a reduced electron leakage by respiratory complexes III and IV. In contrast, the cox17-RNAi mutant showed no modification of respiration and of H₂O₂ production in the dark but a two to threefold increase of H₂O₂ in the light compared to wild type and the cox3-RNAi mutant. The cox17-RNAi mutant was more sensitive to cadmium than the wild-type and cox3-RNAi strains. This suggested that besides its role in complex IV assembly, Cox17 could have additional functions in the cell such as metal detoxification or Reactive Oxygen Species protection or signaling. Concerning Cox3, its role in Chlamydomonas complex IV is similar to that of other eukaryotes although this subunit is encoded in the nuclear genome in the alga contrary to the situation found in all other organisms.     

Has the final countdown to wildlife extinction in Northern Central African Republic begun?

The wildlife populations of Northern Central African Republic experienced precipitous declines during the 1970s and 1980s. While anecdotes coming out of the region indicate that the wildlife populations remain under serious threat, little is known about their status. An aerial sample count was carried out in the Northern Central African Republic at the end of the dry season in June 2005 and covered an 85,000 km² complex landscape containing national parks, hunting reserves and community hunting areas. Results show a dramatic decline of wildlife since the previous survey in 1985. In 20 years, large mammals’ numbers decreased by 65%, probably because of poaching and diseases brought by illegal cattle transhumance. Elephant (Loxodonta africana) and Buffon kob (Kobus kob) populations showed the greatest decline (over 80% each), while buffalo (Syncerus caffer), roan antelope (Hippotragus equinus) and Giant Lord’s Derby Eland (Taurotragus derbianus) populations seem stable or increasing over these last 20 years. The analysis of the wildlife population distribution by status of the different types of protected areas (national parks, hunting areas) showed that individual encounter rates of elephant and buffalo were lower in national parks than in neighbouring hunting areas, while those for roan, giraffe (Giraffa camelopardalis) and Buffon kob were higher in the national parks.