Germline mosaicism and Duchenne muscular dystrophy mutations

Duchenne muscular dystrophy (DMD) is a severe X-linked neuromuscular disease with an incidence of approximately 1 in 3,500 newborn boys. The DMD locus has a high mutation frequency: one third of the cases is thought to result from a new mutation. Linkage studies using probes to detect restriction fragment length polymorphisms and DNA deletion studies have greatly improved DMD carrier detection and prenatal diagnosis. Here we report on two families in which a pERT87 (DXS164) deletion was transmitted to more than one offspring by women who showed no evidence for the mutation in their own somatic (white blood) cells. We also show that the deletion in both siblings in one of the families is identical, indicating that the deletion must have occurred during mitosis in early germline proliferation, leading to a germline mosaicism. This phenomenon may turn out to be a major factor contributing to the induction of DMD mutations, and has important implications for the counselling of DMD families.     

Myosin IXB variant increases the risk of celiac disease and points toward a primary intestinal barrier defect

Celiac disease is probably the best-understood immune-related disorder. The disease presents in the small intestine and results from the interplay between multiple genes and gluten, the triggering environmental factor. Although HLA class II genes explain 40% of the heritable risk, non-HLA genes accounting for most of the familial clustering have not yet been identified. Here we report significant and replicable association (P = 2.1 x 10(-6)) to a common variant located in intron 28 of the gene myosin IXB (MYO9B), which encodes an unconventional myosin molecule that has a role in actin remodeling of epithelial enterocytes. Individuals homozygous with respect to the at-risk allele have a 2.3-times higher risk of celiac disease (P = 1.55 x 10(-5)). This result is suggestive of a primary impairment of the intestinal barrier in the etiology of celiac disease, which may explain why immunogenic gluten peptides are able to pass through the epithelial barrier.     

Methanotrophic symbionts provide carbon for photosynthesis in peat bogs

Wetlands are the largest natural source of atmospheric methane, the second most important greenhouse gas. Methane flux to the atmosphere depends strongly on the climate; however, by far the largest part of the methane formed in wetland ecosystems is recycled and does not reach the atmosphere. The biogeochemical controls on the efficient oxidation of methane are still poorly understood. Here we show that submerged Sphagnum mosses, the dominant plants in some of these habitats, consume methane through symbiosis with partly endophytic methanotrophic bacteria, leading to highly effective in situ methane recycling. Molecular probes revealed the presence of the bacteria in the hyaline cells of the plant and on stem leaves. Incubation with (13)C-methane showed rapid in situ oxidation by these bacteria to carbon dioxide, which was subsequently fixed by Sphagnum, as shown by incorporation of (13)C-methane into plant sterols. In this way, methane acts as a significant (10-15%) carbon source for Sphagnum. The symbiosis explains both the efficient recycling of methane and the high organic carbon burial in these wetland ecosystems.     

Anaerobic ammonium oxidation by anammox bacteria in the Black Sea

The availability of fixed inorganic nitrogen (nitrate, nitrite and ammonium) limits primary productivity in many oceanic regions. The conversion of nitrate to N2 by heterotrophic bacteria (denitrification) is believed to be the only important sink for fixed inorganic nitrogen in the ocean. Here we provide evidence for bacteria that anaerobically oxidize ammonium with nitrite to N2 in the world's largest anoxic basin, the Black Sea. Phylogenetic analysis of 16S ribosomal RNA gene sequences shows that these bacteria are related to members of the order Planctomycetales performing the anammox (anaerobic ammonium oxidation) process in ammonium-removing bioreactors. Nutrient profiles, fluorescently labelled RNA probes, 15N tracer experiments and the distribution of specific 'ladderane' membrane lipids indicate that ammonium diffusing upwards from the anoxic deep water is consumed by anammox bacteria below the oxic zone. This is the first time that anammox bacteria have been identified and directly linked to the removal of fixed inorganic nitrogen in the environment. The widespread occurrence of ammonium consumption in suboxic marine settings indicates that anammox might be important in the oceanic nitrogen cycle.     

Direct detection of more than 50% of the Duchenne muscular dystrophy mutations by field inversion gels

Duchenne muscular dystrophy (DMD) is an X-linked disorder affecting about 1 in 3,500 males. It is allelic with the milder Becker muscular dystrophy. The biochemical basis for both diseases is unknown and no effective treatment is available. Long-range physical mapping has shown that the DMD gene, localized in Xp21, is extremely large, exceeding 2 million base pairs. Until now, carrier detection and prenatal diagnosis has involved the use of linked restriction fragment length polymorphism markers which detect muscular dystrophy-associated deletions in about 10% of the cases. Field inversion gel electrophoresis (FIGE) allows the detection of structural rearrangements in 21 out of 39 of the DMD patients studied (54%), of which 14 (65%) were not detected by conventional methods. Large deletions seem to make up a much higher fraction of the DMD mutations than so far indicated by other methods. A region prone to deletion was located in the distal half of the gene. FIGE analysis could provide a valuable extension of information for carrier detection and prenatal diagnosis. The technique should be generally applicable to the study of diseases involving structural chromosomal rearrangements.     

High temperatures in the Late Cretaceous Arctic Ocean

To understand the climate dynamics of the warm, equable greenhouse world of the Late Cretaceous period, it is important to determine polar palaeotemperatures. The early palaeoceanographic history of the Arctic Ocean has, however, remained largely unknown, because the sea floor and underlying deposits are usually inaccessible beneath a cover of floating ice. A shallow piston core taken from a drifting ice island in 1970 fortuitously retrieved unconsolidated Upper Cretaceous organic-rich sediment from Alpha ridge, a submarine elevated feature of probable oceanic origin. A lack of carbonate in the sediments from this core has prevented the use of traditional oxygen-isotope palaeothermometry. Here we determine Arctic palaeotemperatures from these Upper Cretaceous deposits using TEX86, a new palaeothermometer that is based on the composition of membrane lipids derived from a ubiquitous component of marine plankton, Crenarchaeota. From these analyses we infer an average sea surface temperature of approximately 15 degrees C for the Arctic Ocean about 70 million years ago. This calibration point implies an Equator-to-pole gradient in sea surface temperatures of approximately 15 degrees C during this interval and, by extrapolation, we suggest that polar waters were generally warmer than 20 degrees C during the middle Cretaceous (approximately 90 million years ago).     

Dynamic resource allocation for efficient patient scheduling: A data-driven approach

Efficient staff rostering and patient scheduling to meet outpatient demand is a very complex and dynamic task. Due to fluctuations in demand and specialist availability, specialist allocation must be very flexible and non-myopic. Medical specialists are typically restricted in sub-specialization, serve several patient groups and are the key resource in a chain of patient visits to the clinic and operating room (OR). To overcome a myopic view of once-off appointment scheduling, we address the patient flow through a chain of patient appointments when allocating key resources to different patient groups. We present a new, data-driven algorithmic approach to automatic allocation of specialists to roster activities and patient groups. By their very nature, simplified mathematical models cannot capture the complexity that is characteristic to the system being modeled. In our approach, the allocation of specialists to their day-to-day activities is flexible and responsive to past and present key resource availability, as well as to past resource allocation. Variability in roster activities is actively minimized, in order to enhance the supply chain flow. With discrete-event simulation of the application case using empirical data, we illustrate how our approach improves patient Service Level (SL, percentage of patients served on-time) as well as Wait Time (days), without change in resource capacity.     

Integrated detection and population-genetic analysis of SNPs and copy number variation

Dissecting the genetic basis of disease risk requires measuring all forms of genetic variation, including SNPs and copy number variants (CNVs), and is enabled by accurate maps of their locations, frequencies and population-genetic properties. We designed a hybrid genotyping array (Affymetrix SNP 6.0) to simultaneously measure 906,600 SNPs and copy number at 1.8 million genomic locations. By characterizing 270 HapMap samples, we developed a map of human CNV (at 2-kb breakpoint resolution) informed by integer genotypes for 1,320 copy number polymorphisms (CNPs) that segregate at an allele frequency >1%. More than 80% of the sequence in previously reported CNV regions fell outside our estimated CNV boundaries, indicating that large (>100 kb) CNVs affect much less of the genome than initially reported. Approximately 80% of observed copy number differences between pairs of individuals were due to common CNPs with an allele frequency >5%, and more than 99% derived from inheritance rather than new mutation. Most common, diallelic CNPs were in strong linkage disequilibrium with SNPs, and most low-frequency CNVs segregated on specific SNP haplotypes.