The metabolic acclimation of Arabidopsis thaliana to arsenate is sensitized by the loss of mitochondrial LIPOAMIDE DEHYDROGENASE2, a key enzyme in oxidative metabolism

Mitochondrial lipoamide dehydrogenase is essential for the activity of four mitochondrial enzyme complexes central to oxidative metabolism. The reduction in protein amount and enzyme activity caused by disruption of mitochondrial LIPOAMIDE DEHYDROGENASE2 enhanced the arsenic sensitivity of Arabidopsis thaliana. Both arsenate and arsenite inhibited root elongation, decreased seedling size and increased anthocyanin production more profoundly in knockout mutants than in wild‐type seedlings. Arsenate also stimulated lateral root formation in the mutants. The activity of lipoamide dehydrogenase in isolated mitochondria was sensitive to arsenite, but not arsenate, indicating that arsenite could be the mediator of the observed phenotypes. Steady‐state metabolite abundances were only mildly affected by mutation of mitochondrial LIPOAMIDE DEHYDROGENASE2. In contrast, arsenate induced the remodelling of metabolite pools associated with oxidative metabolism in wild‐type seedlings, an effect that was enhanced in the mutant, especially around the enzyme complexes containing mitochondrial lipoamide dehydrogenase. These results indicate that mitochondrial lipoamide dehydrogenase is an important protein for determining the sensitivity of oxidative metabolism to arsenate in Arabidopsis.     

A fast,highly sensitive double‐nested PCR‐based method to screen fish immunobiomes

Efficient methods for constructing 16S tag amplicon libraries for pyrosequencing are needed for the rapid and thorough screening of infectious bacterial diversity from host tissue samples. Here we have developed a double‐nested PCR methodology that generates 16S tag amplicon libraries from very small amounts of bacteria/host samples. This methodology was tested for 133 kidney samples from the lake whitefish Coregonus clupeaformis (Salmonidae) sampled in five different lake populations. The double‐nested PCR efficiency was compared with two other PCR strategies: single primer pair amplification and simple nested PCR. The double‐nested PCR was the only amplification strategy to provide highly specific amplification of bacterial DNA. The resulting 16S amplicon libraries were synthesized and pyrosequenced using 454 FLX technology to analyse the variation of pathogenic bacteria abundance. The proportion of the community sequenced was very high (Good’s coverage estimator; mean = 95.4%). Furthermore, there were no significant differences of sequence coverage among samples. Finally, the occurrence of chimeric amplicons was very low. Therefore, the double‐nested PCR approach provides a rapid, informative and cost‐effective method for screening fish immunobiomes and most likely applicable to other low‐density microbiomes as well.     

Isolation and characterization of polymorphic microsatellite markers in the gray,short‐tailed opossum (Monodelphis domestica)

Twenty‐six polymorphic microsatellite markers were isolated from (AC)_n and (AG)_n microsatellite‐enhanced genomic libraries of the gray, short‐tailed opossum Monodelphis domestica. All 26 loci showed high allelic diversity, with allele numbers ranging from five to 11 in a subset of 35 animals. Normal Mendelian inheritance was confirmed for 24 loci by analysing allelic segregation in 10, two‐generation, families. Non‐amplifying (null) alleles were detected at two loci, which we recommend be used only if pedigree data are available. We conclude that all of these microsatellite markers would be useful for quantitative trait locus mapping and population genetic studies.     

The debate about drag and reconfiguration of freshwater macrophytes: comparing results obtained by three recently discussed approaches

1. The paper by Sand‐Jensen (2003 , Freshwater Biology, 48 , 271–283) on drag and reconfiguration of freshwater macrophytes stimulated comments and a reply about the use of variables in assessments of the drag coefficient (C_d) or the Reynolds number (Re) of such plants. Although the physical argument in this debate starts from the same equations, it diverges into approaches that address differently the dynamic behaviour of flexible plants in the boundary layer flow (the typical condition experienced by lotic macrophytes). 2. We compared three (potentially among many more) such different approaches using some preliminary experiments with Egeria densa by measuring drag (and other physical variables of interest) on (1) a single shoot exposed to varying flume flows; (2) a single shoot exposed to a constant flume flow, from which we subsequently pruned off pieces from the distal end; and (3) multiple shoots exposed to a constant flume flow after they had experienced replicated flow disturbances (causing shoot reconfiguration). 3. These experiments illustrated that the three approaches can produce opposite trends in the relationship between C_d and Re and that, for a given plant and flow, the C_d values obtained by these approaches can differ by about two orders of magnitude. Thus, conventions about the use of variables are required for experiments on drag and reconfiguration of freshwater macrophytes, otherwise the field will be plagued by a multitude of incomparable results.     

Simple predictions of instream habitat model outputs for target fish populations

1. Bottom-up approaches based on individual behaviour can help to identify key variables influencing populations at larger scales. Instream habitat models have been developed to predict the consequences, for populations in stream reaches, of fish preferences for particular hydraulic conditions observed at the scale of individuals. Conventional instream habitat models (e.g. PHABSIM) predict habitat values for species or life stages in reaches, and their changes with discharge. Despite their worldwide use, they have been subject to continuing criticism and have been mainly limited to site-specific case studies.
2. We ran conventional instream habitat models in 58 French stream reaches dominated by brown trout. Using non-linear mixed effect models, we demonstrated that the outputs of instream habitat models (habitat values for three trout life stages and five other species) are predictable from average characteristics of reaches (discharge, depth, width and bed particle size).
3. Our models closely reflect variations in habitat values within-reaches (with discharge) and between-reaches. Within-reach changes are linked to the Reynolds number of reaches, while between-reach changes depend mainly on the Froude number at median daily discharge. These two dimensionless variables combine discharge, mean depth and mean width of reaches. Independent model validations showed robust model predictions that are consistent with studies of habitat values for brown trout made in larger streams from western North America.
4. Our results contribute to identifying the main hydraulic variables governing estimates of fish habitat values. They should facilitate habitat studies in multiple streams, at the basin or larger scales, while reducing their cost. They should enhance the biological validation of habitat model predictions, which remains critical.     

Genetic relatedness assessment through individual odour similarities in mice

Previous research has demonstrated that closer genetic relatedness between individuals (from kin to across species) is associated with greater similarity in the qualities of their individual odours ('odour-genes covariance'). This predictable relationship between individual genotypes and individual odours could enable animals to assess their degree of genetic relatedness to other individuals by comparing the degree of similarity between another individual's odour and their own odour. In two-choice tests with odours of unfamiliar mice from different populations and species, subjects from two species of wild mice, Mus spicilegus and M. musculus , that had been raised in mixed litters of both species spent significantly more time investigating the ano-genital odour of the more genetically similar individual. This differential interest was not affected by common rearing with heterospecifics. These responses are consistent with a self-referencing mechanism enabling differential responses across a wide spectrum of genetic relatedness from kin through populations to heterospecifics. These assessments depend on the degree of similarity between the donor's and the subject's odours rather than on differences between them. Such a parsimonious mechanism may provide a basis for differential responses to conspecifics as opposed to heterospecifics that may function as a premating isolating mechanism.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78, 595–603.     

Effect of Drought on Metabolism and Partitioning of Carbon in Two Wheat Varieties Differing in Drought-tolerance

A model was constructed to describe the partitioning of carbonon the third and seventh day from anthesis for well-wateredand droughted plants of two wheat varieties (Triticum aestivumL. cv. Warigal and Condor). The glasshouse-grown plants weredetillered so that a simplified model could be derived for themain stem. The 9-d drought treatment, imposed just after anthesisduring the period of cell division in the grains, reduced grainyield by 18 per cent in Warigal and 30 per cent in Condor. Netcarbon fixation was up to 60 per cent higher in Warigal thanCondor towards the end of the drought period and this correlatedwith better osmotic adjustment in the flag leaf. Carbon partitioningbetween plant organs responded to water deficit more rapidlythan net carbon fixation. On day 3, carbon allocation to theroots of droughted plants was maintained in Condor and increasedby 14 per cent in Warigal, whereas carbon allocation to theear decreased in both varieties. However the roots did not competewell with the ear when the water deficit became more severe.Warigal accumulated 3 times more stem reserves than Condor underdrought. In the roots, the pattern of carbon allocation betweenrespiration and carbon accumulation changed soon after impositionof drought. Although total root respiration decreased underdrought it became more energy efficient, particularly for Warigal,as less respiration took place via the alternative pathway.On day 3, the larger carbon allocation to the roots and thelower root respiration accounted for the 4-times larger sugaraccumulation in droughted roots of Warigal compared with thoseof Condor. Osmotic adjustment in mature leaves and roots maybe of importance for the maintenance of vital processes andfor recovery after drought. Triticum aestivum L., wheat, drought, carbon, partitioning     

ASSOCIATION OF SYNTAXIN WITH SNAP 25 AND VAMP (SYNAPTOBREVIN) IN TORPEDO SYNAPTOSOMES

Two proteins of the presynaptic plasma membrane, syntaxin and SNAP 25, and VAMP/synaptobrevin, a synaptic vesicle membrane protein, form stable protein complexes which are involved in the docking and fusion of synaptic vesicles at the mammalian brain presynaptic membrane. Similar protein complexes were revealed in an homogeneous population of cholinergic synaptosomes purified from Torpedo electric organ by combining velocity sedimentation and immunoprecipitation experiments. After CHAPS solubilization, virtually all the nerve terminal syntaxin was found in the form of large 16 S complexes, in association with 65% of SNAP 25 and 15% of VAMP. Upon Triton X100 solubilization, syntaxin was still recovered in association with SNAP 25 and VAMP but in smaller 8 S complexes. A small (2–5%) percentage of the nerve terminal 15 kDa proteolipid subunit of the v-H⁺ ATPase and of mediatophore was copurified with syntaxin, using two different antisyntaxin monoclonal antibodies. The use of an homogeneous population of peripheral cholinergic nerve terminals allowed us to extend results on the composition of the brain presynaptic protein complexes to the Torpedo electric organ synapse, a model of the rapid neuromuscular synapses. Copyright © 1996 Elsevier Science Ltd     

Systematics of African lowland rainforest Praomys (Rodentia, Muridae) based on molecular and craniometrical data

Representatives of the genus Praomys occur throughout the African intertropical zone. It is unclear how many species this genus contains, nor do we know the exact distribution ranges and phylogenetic relationships of these taxa. Using molecular (16S rRNA gene sequencing) and morphological (multivariate craniometry) analyses we clarify the taxonomy and phylogenetic relationships among the Praomys occurring in Africa's lowland tropical rainforests. We studied most species known from this area, based on specimens collected in seven countries (Guinea, Ivory Coast, Cameroon, Central African Republic, Gabon, Congo Republic and Democratic Republic of Congo). In our study, Praomys appears to be monophyletic. Our results identify two species complexes: the jacksoni complex includes at least two species ( P. jacksoni and P. mutoni ) and the tullbergi complex contains at least four species ( P. tullbergi , P. rostratus , P. misonnei , P. petteri ). Although the 16S rRNA gene appears insufficient to resolve the phylogenetic relationships among all the members of the tullbergi species complex, it is suitable for the identification of most of the studied species, and its use has allowed us to redefine the geographical limits of several species.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 145 , 539–553.