Carbon dioxide balance of subarctic tundra from plot to regional scales

Peer reviewe

Methane dynamics in the subarctic tundra : combining stable isotope analyses, plot- and ecosystem-scale flux measurements

Methane (CH4) fluxes were investigated in a subarctic Russian tundra site in a multi-approach study combining plot-scale data, ecosystem-scale eddy covariance (EC) measurements, and a fine-resolution land cover classification scheme for regional upscaling. The flux data as measured by the two independent techniques resulted in a seasonal (May-October 2008) cumulative CH4 emission of 2.4 (EC) and 3.7 gCH(4) m(-2) (manual chambers) for the source area representative of the footprint of the EC instruments. Upon upscaling for the entire study region of 98.6 km(2), the chamber measured flux data yielded a regional flux estimate of 6.7 gCH(4) m(-2) yr(-1). Our upscaling efforts accounted for the large spatial variability in the distribution of the various land cover types (LCTs) predominant at our study site. Wetlands with emissions ranging from 34 to 53 gCH(4) m(-2) yr(-1) were the most dominant CH4-emitting surfaces. Emissions from thermokarst lakes were an order of magnitude lower, while the rest of the landscape (mineral tundra) was a weak sink for atmospheric methane. Vascular plant cover was a key factor in explaining the spatial variability of CH4 emissions among wetland types, as indicated by the positive correlation of emissions with the leaf area index (LAI). As elucidated through a stable isotope analysis, the dominant CH4 release pathway from wetlands to the atmosphere was plant-mediated diffusion through aerenchyma, a process that discriminates against C-13-CH4. The CH4 released to the atmosphere was lighter than that in the surface porewater, and delta C-13 in the emitted CH4 correlated negatively with the vascular plant cover (LAI). The mean value of delta C-13 obtained here for the emitted CH4, 68.2 +/- 2.0 %, is within the range of values from other wetlands, thus reinforcing the use of inverse modelling tools to better constrain the CH4 budget. Based on the IPCC A1B emission scenario, a temperature increase of 6.1 degrees C relative to the present day has been predicted for the European Russian tundra by the end of the 21st Century. A regional warming of this magnitude will have profound effects on the permafrost distribution leading to considerable changes in the regional landscape with a potential for an increase in the areal extent of CH4-emitting wet surfaces.Peer reviewe

Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy

Background Nephronophthisis associated ciliopathies (NPHP-AC) comprise a group of autosomal recessive cystic kidney diseases that includes nephronophthisis (NPHP), Senior-Loken syndrome (SLS), Joubert syndrome (JBTS), and Meckel-Gruber syndrome (MKS). To date, causative mutations in NPHP-AC have been described for 18 different genes, rendering mutation analysis tedious and expensive. To overcome the broad genetic locus heterogeneity, a strategy of DNA pooling with consecutive massively parallel resequencing (MPR) was devised.Methods In 120 patients with severe NPHP-AC phenotypes, five pools of genomic DNA with 24 patients each were prepared which were used as templates in order to PCR amplify all 376 exons of 18 NPHP-AC genes (NPHP1, INVS, NPHP3, NPHP4, IQCB1, CEP290, GLIS2, RPGRIP1L, NEK8, TMEM67, INPP5E, TMEM216, AHI1, ARL13B, CC2D2A, TTC21B, MKS1, and XPNPEP3). PCR products were then subjected to MPR on an Illumina Genome-Analyser and mutations were subsequently assigned to their respective mutation carrier via CEL I endonuclease based heteroduplex screening and confirmed by Sanger sequencing.Results For proof of principle, DNA from patients with known mutations was used and detection of 22 out of 24 different alleles (92% sensitivity) was demonstrated. MPR led to the molecular diagnosis in 30/120 patients (25%) and 54 pathogenic mutations (27 novel) were identified in seven different NPHP-AC genes. Additionally, in 24 patients only single heterozygous variants of unknown significance were found.Conclusions The combined approach of DNA pooling followed by MPR strongly facilitates mutation analysis in broadly heterogeneous single gene disorders. The lack of mutations in 75% of patients in this cohort indicates further extensive heterogeneity in NPHP-AC

Molecular Characterization and DNA Fingerprinting of Xanthomonas oryzae pv. oryzae Isolates from Climate Change Prone Areas in East Africa

Genomic DNA fingerprinting is a useful tool for effective and reliable identification and differentiation of Xanthomonas oryzae pv. oryzae (Xoo) pathogen from rice. The study aimed to conduct molecular characterization and DNA fingerprinting of 23 Xoo isolates from East Africa and two Xoo isolates from IRRI (Philippines) as control. PCR analysis was carryout on genomic DNA of 25 Xoo isolates using 6 Xoo specific primer pairs. Cluster analyses of genetic data obtained from 25 Xoo DNA fingerprints revealed two major genotypes (GrpA and GrpB) among the 25 Xoo isolates. GrpA has three subgroups (GrpA1; GrpA2; GrpA3) and GrpB (GrpB1; GrpB2; GrpB3). GrpA genotype consists of 20 Xoo isolates from Uganda, Rwanda and Philippines while GrpB genotype has 5 Xoo isolates from Rwanda. Some Xoo isolates were identical (PX-1, PX-2; UX621, RX2101; RX554, UX623, RX4113; UX211, UX213, UX214, RX4112, UX215). The emergence of subgroup genotypes could possibly be due to mutations and interactions among isolates and strains in host cells. Some Xoo isolates from Rwanda and Uganda were identical suggesting possible pathogen migration between these countries and long-term survival. Durable resistance rice cultivars would need to overcome both GrpA and GrpB Xoo genotypes in order to survive after their deployment into different rice ecologies in East Afric