Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori using short oligonucleotide probes containing repetitive sequences

The ability of oligonucleotide probes containing short repetitive sequence motifs to differentiate between isolates of Helicobacter pylori was investigated. Genomic DNA preparations from H. pylori were digested with the restriction enzyme Hind III, electrophoresed in agarose gels and transferred to nylon filters. Five separate oligonucleotide probes were tested for hybridization sequentially to fingerprint the digested DNA from a panel of 29 clinical isolates and one type strain of H. pylori , and their relative discriminatory abilities were assessed. Four probes, (GACA)₄, (GT)₈, (GTG)₅ and (GGAT)₄, were each shown to yield highly informative hybridization band profiles allowing differentiation of H. pylori isolates. The DNA fingerprints of individual isolates obtained with each probe were distinct and reproducible. Direct comparison with ribotyping revealed that oligonucleotide fingerprinting had far superior discriminatory power. Computer-assisted similarity analysis of (GGAT)₄-generated hybridization profiles of pairwise combinations of H. pylori isolates revealed that there was no correlation between ribotype and oligonucleotide fingerprint patterns. The results of this study demonstrate that oligonucleotide probes containing microsatellite sequences provide a new and powerful tool for isolate discrimination of H. pylori .     

Cryptomyrus: a new genus of Mormyridae (Teleostei,Osteoglossomorpha) with two new species from Gabon,West-Central Africa

We use mitochondrial and nuclear sequence data to show that three weakly electric mormyrid fish specimens collected at three widely separated localities in Gabon, Africa over a 13-year period represent an unrecognized lineage within the subfamily Mormyrinae and determine its phylogenetic position with respect to other taxa. We describe these three specimens as a new genus containing two new species. Cryptomyrus, new genus, is readily distinguished from all other mormyrid genera by a combination of features of squamation, morphometrics, and dental attributes. Cryptomyrus ogoouensis, new species, is differentiated from its single congener, Cryptomyrus ona, new species, by the possession of an anal-fin origin located well in advance of the dorsal fin, a narrow caudal peduncle and caudal-fin lobes nearly as long as the peduncle. In Cryptomyrus ona, the anal-fin origin is located only slightly in advance of the dorsal fin, the caudal peduncle is deep and the caudal-fin lobes considerably shorter than the peduncle. Continued discovery of new taxa within the “Lower Guinea Clade” of Mormyridae highlights the incompleteness of our knowledge of fish diversity in West-Central Africa. We present a revised key to the mormyrid genera of Lower Guinea.     

Phosphorus speciation and micro-scale spatial distribution in North-American temperate agricultural soils from micro X-ray fluorescence and X-ray absorption near-edge spectroscopy

Background and Aims

Phosphorus (P) is an essential nutrient for plants but its low availability often necessitates amendments for agronomical issues. Objectives were to determine P spatial distribution and speciation that remain poorly understood in cultivated soils.

Methods

Aquic Argiudoll soil samples developed on a calcareous loam glacial till were collected from experimental plots submitted to contrasting crop rotations and amendments. Micro-X-ray fluorescence (μ-XRF) maps were collected on undisturbed samples. X-ray absorption near edge structure (XANES) spectra were collected on bulk samples and on fractions thereof, and on points of interests selected from μ-XRF maps. Results were compared with chemical analyses and extraction techniques results.

Results

Chemical analyses show variations in total and exchangeable P contents depending on the samples but no significant difference is observed in terms of P distribution and speciation. P distribution is dominated by a low-concentration diffuse background with a minor contribution from minute hot spots. P speciation is dominated by phosphate groups bound to clay-humic complexes. No modification of P distribution and speciation is observed close to roots.

Conclusions

This study evidenced minor effect of cropping and fertilizing practices on P speciation in cultivated soils. Despite analytical challenges, the combined use of μ-XRF and XANES provides relevant information on P speciation in heterogeneous soil media.

     

Greater Abundance of <Emphasis Type="Italic">Betula nana</Emphasis> and Early Onset of the Growing Season Increase Ecosystem CO<Subscript>2</Subscript> Uptake in West Greenland

Expansion of deciduous shrubs is a common observation throughout the Arctic, with implications for carbon (C) cycling. Shrubs may increase net ecosystem C uptake through greater leaf area and gross ecosystem photosynthesis (GEP), and/or through cooler summer soils and reduced ecosystem respiration (ER). We used a space-for-time substitution combined with experimental warming at a Low Arctic site in West Greenland to examine the biophysical effects of increased temperature and Betula nana abundance on ecosystem CO₂ exchange. Communities dominated by Betula were much stronger C sinks than graminoid communities due to greater GEP and lower ER. The warming treatment had little effect on GEP, ER, or net ecosystem CO₂ exchange (NEE). The start of the growing season has been advancing at our study site, as indicated by long-term observations of plant phenology. In a retrospective analysis, we estimate that earlier onset of the growing season has increased the strength of the ecosystem C sink at rates of 1.3 and 2.1 g C m^?2 y^?1 in Betula and graminoid tundra, respectively, since 2002. However, earlier, and presumably longer, growing seasons may be associated with greater potential for drought stress. Our data suggest that mid-summer drought-induced GEP declines may partially offset C gains associated with an earlier start to the growing season. Our results suggest greater deciduous shrub abundance and longer growing seasons will likely lead to greater net C uptake in our study area, while highlighting important complexities associated with drought and plant community composition.     

Pleistocene Hominins as a Resource for Carnivores: A c. 500,000-Year-Old Human Femur Bearing Tooth-Marks in North Africa (Thomas Quarry I,Morocco)

In many Middle Pleistocene sites, the co-occurrence of hominins with carnivores, who both contributed to faunal accumulations, suggests competition for resources as well as for living spaces. Despite this, there is very little evidence of direct interaction between them to-date. Recently, a human femoral diaphysis has been recognized in South-West of Casablanca (Morocco), in the locality called Thomas Quarry I. This site is famous for its Middle Pleistocene fossil hominins considered representatives of Homo rhodesiensis. The bone was discovered in Unit 4 of the Grotte à Hominidés (GH), dated to c. 500 ky and was associated with Acheulean artefacts and a rich mammalian fauna. Anatomically, it fits well within the group of known early Middle Pleistocene Homo, but its chief point of interest is that the diaphyseal ends display numerous tooth marks showing that it had been consumed shortly after death by a large carnivore, probably a hyena. This bone represents the first evidence of consumption of human remains by carnivores in the cave. Whether predated or scavenged, this chewed femur indicates that humans were a resource for carnivores, underlining their close relationships during the Middle Pleistocene in Atlantic Morocco.     

De Novo Occurrence of a Variant in ARL3 and Apparent Autosomal Dominant Transmission of Retinitis Pigmentosa

Background

Retinitis pigmentosa is a phenotype with diverse genetic causes. Due to this genetic heterogeneity, genome-wide identification and analysis of protein-altering DNA variants by exome sequencing is a powerful tool for novel variant and disease gene discovery. In this study, exome sequencing analysis was used to search for potentially causal DNA variants in a two-generation pedigree with apparent dominant retinitis pigmentosa.

Methods

Variant identification and analysis of three affected members (mother and two affected offspring) was performed via exome sequencing. Parental samples of the index case were used to establish inheritance. Follow-up testing of 94 additional retinitis pigmentosa pedigrees was performed via retrospective analysis or Sanger sequencing.

Results and Conclusions

A total of 136 high quality coding variants in 123 genes were identified which are consistent with autosomal dominant disease. Of these, one of the strongest genetic and functional candidates is a c.269A>G (p.Tyr90Cys) variant in ARL3. Follow-up testing established that this variant occurred de novo in the index case. No additional putative causal variants in ARL3 were identified in the follow-up cohort, suggesting that if ARL3 variants can cause adRP it is an extremely rare phenomenon.