Technical Note: Field experiences using UV/VIS sensors for high-resolution monitoring of nitrate in groundwater

peer-reviewedTwo different in situ spectrophotometers are compared that were used in the field to determine nitrate-nitrogen (NO3-N) concentrations at two distinct spring discharge sites. One sensor was a double wavelength spectrophotometer (DWS) and the other a multiple wavelength spectrophotometer (MWS). The objective of the study was to review the hardware options, determine ease of calibration, accuracy, influence of additional substances and to assess positive and negative aspects of the two sensors as well as troubleshooting and trade-offs. Both sensors are sufficient to monitor highly time-resolved NO3-N concentrations in emergent groundwater. However, the chosen path length of the sensors had a significant influence on the sensitivity and the range of detectable NO3-N. The accuracy of the calculated NO3-N concentrations of the sensors can be affected if the content of additional substances such as turbidity, organic matter, nitrite or hydrogen carbonate significantly varies after the sensors have been calibrated to a particular water matrix. The MWS offers more possibilities for calibration and error detection but requires more expertise compared with the DWS.The authors would like to acknowledge the Teagasc Walsh Fellowship scheme for funding the study in Ireland, and the German federal Ministry of Education and Research (BMBF) for sponsoring the SMART-project (grant no. 02WM1079-1086, 02WM1211-1212) for the study in Jordan.Teagasc Walsh Fellowship Programm

Significant abundance of cis configurations of coding variants in diploid human genomes

To fully understand human genetic variation and its functional consequences, the specific distribution of variants between the two chromosomal homologues of genes must be known. The 'phase' of variants can significantly impact gene function and phenotype. To assess patterns of phase at large scale, we have analyzed 18 121 autosomal genes in 1092 statistically phased genomes from the 1000 Genomes Project and 184 experimentally phased genomes from the Personal Genome Project. Here we show that genes with cis-configurations of coding variants are more frequent than genes with trans-configurations in a genome, with global cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all genomes in all populations. Moreover, we identified a large group of genes exhibiting cis-configurations of protein-changing variants in excess, so-called 'cis-abundant genes', and a smaller group of 'trans-abundant genes'. These two gene categories were functionally distinguishable, and exhibited strikingly different distributional patterns of protein-changing variants. Underlying these phenomena was a shared set of phase-sensitive genes of importance for adaptation and evolution. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their functional significance, highlighting the importance of phase for the interpretation of protein-coding genetic variation and gene function

Probable multiple system atrophy in a German family. J Neurol Neurosurg Psychiatry 75: 924–925

Abstract: Mutations in LRRK2 were first reported as causing Parkinson's disease (PD) in late 2004. Since then, approximately a dozen LRRK2 substitutions have been identified that are believed to be pathogenic mutations. The substitution of adenine for guanine at nucleotide 4541 (4541G>A) in LRRK2 was recently reported. This substitution resulted in the replacement of an arginine at position 1514 with a glutamine (R1514Q). Although this substitution was not found in a large cohort of controls, its pathogenicity could not be verified. We have now genotyped the R1514Q substitution in a sample of 954 PD patients from 429 multiplex PD families. This substitution was identified in 1.8% of the PD patients; however, the majority of the PD sibships segregating this substitution were discordant for this putative mutation. In addition, the R1514Q substitution was detected in 1.4% of neurologically evaluated, control individuals. These data suggest that the R1514Q variant is not a pathogenic LRRK2 mutation. We believe it is imperative that the causative nature of any newly identified genetic variant be determined before it is included in any panel for diagnostic testing. © 2006 Movement Disorder Society Key words: Parkinson's disease; genetics; LRRK2; mutation Parkinson's disease (PD) is the second most common neurodegenerative disorder. Clinical features of PD include resting tremor, rigidity, bradykinesia, and postural instability. Although quite variable, the average age of onset is 60 years. In addition, there is a slight preponderance of affected men. Pathologically, PD is characterized by the presence of Lewy bodies and progressive degeneration of neurons in the substantia nigra, pars compacta, and other brain regions. In our ongoing effort to identify additional PD susceptibility genes, we have recruited a large cohort of PD families. The control sample was collected through three sources and provided appropriate written informed consent. One sample of controls (n ϭ 52) was ascertained in Indiana, and all control subjects were examined by a single Parkinson Study Group movement disorder specialist. These control subjects completed the identical clinical evaluation as the PD sample. Individuals were considered controls if they met the following criteria: did not have a diagnosis or symptoms of PD, Alzheimer's disease (AD), stroke, or other neurological disorder; no tremor; no other first-degree family members reported to be diagnosed with PD; and no history of polio. The average age at examination of these first control subjects was 68.3 years, with a range of 55 to 82 years. All individuals were non-Hispanic Caucasians. A second control sample (n ϭ 40) was obtained from the National Cell Repository for Alzheimer's Disease. The subjects were recruited as part of an ongoing genetic initiative to make available to the research community a sample of rigorously evaluated individuals without any evidence of neurological disease. All control subjects were evaluated, and there was no evidence for either PD or dementia. The average age at examination of the second control cohort was 76.9 years, with a range of 58 to 91 years. As was the case with the first control set, all subjects from the second control set were non-Hispanic Caucasians. DNA was prepared from peripheral blood samples collected from the PD families and control subjects. The third control sample (n ϭ 276) is composed of three neurologically normal Caucasian control panels (NDPT002, NDPT006, NDPT009) obtained from the NINDS Human Genetics Resource Center at the Coriell Institute Coriell Cell Repositories (Camden, NJ). This third control sample contains 132 males and 144 females. The average age at examination of the subjects was 69.7 years, with a range of 55 to 88 years. In total, 368 neurologically normal control samples were evaluated. The guanine to adenine substitution at nucleotide 4541 of the LRRK2 cDNA that results in the R1514Q Lrrk2 (dardarin) protein variant was screened for using a newly developed TaqMan allelic-discrimination assay (Applied Biosystems). The assay was performed with 30 ng of genomic DNA from each PD subject and control individual using conditions recommended by the manufacturer and an Applied Biosystems 7300 Real Time PCR System. Of 954 affected individuals from 12 different families, 16 (1.8%) were shown to be heterozygous carriers of the R1514Q variant. In addition, 5 (1.4%) of 368 control subjects were also found to be heterozygous for the same variant similar to the frequency observed by Zimprich and associates. Discordance for the mutation among affected individuals was observed in 10 of the 13 families in which the variant was segregating. Of the 28 affected individuals in these 12 families for whom DNA was available for study, 12 of them do not carry the R1514Q variant. This finding suggests that the R1514Q variant is not segregating with PD in these families. No statistically significant difference between the R1514Q carrier group (16) and the noncarrier group (938) was detected in our analyses of numerous parameters, including age of disease onset (61.75 years in R1514Q carriers vs. 60.9 years in noncarriers), disease duration (7.18 years carriers vs. 9.53 years noncarriers), Mini-Mental State Examination score (25.62 carriers vs. 26.48 noncarriers), Blessed Functional Activity Scale (3.66 carriers vs. 4.41 noncarriers), Hoehn & Yahr (2.2 carriers vs. 2.48 noncarriers), and ethnicity. Taken together, these data suggest that the R1514Q variant is likely a nonpathogenic variant in Lrrk2 that does not contribute to the development of Parkinson disease, confirming the report of Zimprich and coworkers

The Case for a Hybrid P2P Search Infrastructure

Popular P2P file-sharing systems like Gnutella and Kazaa use unstructured network designs. These networks typically adopt flooding-based search techniques to locate files. While flooding-based techniques are effective for locating highly replicated items, they are poorly suited for locating rare items. As an alternative, a wide variety of structured P2P networks such as distributed hash tables (DHTs) have been recently proposed. Structured networks can efficiently locate rare items, but they incur significantly higher overheads than unstructured P2P networks for popular files. Through extensive measurements of the Gnutella network from multiple vantage points, we argue for a hybrid search solution, where structured search techniques are used to index and locate rare items, and flooding techniques are used for locating highly replicated content. To illustrate, we present experimental results of a prototype implementation that runs at multiple sites on PlanetLab and participates live on the Gnutella network

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

To fully understand human biology and link genotype to phenotype, the phase of DNA variants must be known. Here we present a comprehensive analysis of haplotype-resolved genomes to assess the nature and variation of haplotypes and their pairs, diplotypes, in European population samples. We use a set of 14 haplotype-resolved genomes generated by fosmid clone-based sequencing, complemented and expanded by up to 372 statistically resolved genomes from the 1000 Genomes Project. We find immense diversity of both haploid and diploid gene forms, up to 4.1 and 3.9 million corresponding to 249 and 235 per gene on average. Less than 15% of autosomal genes have a predominant form. We describe a ‘common diplotypic proteome’, a set of 4,269 genes encoding two different proteins in over 30% of genomes. We show moreover an abundance of cis configurations of mutations in the 386 genomes with an average cis/trans ratio of 60:40, and distinguishable classes of cis- versus trans-abundant genes. This work identifies key features characterizing the diplotypic nature of human genomes and provides a conceptual and analytical framework, rich resources and novel hypotheses on the functional importance of diploidy

Querying at Internet Scale

We are developing a distributed query processor called PIER, which is designed to run on the scale of the entire Internet. PIER utilizes a Distributed Hash Table (DHT) as its communication substrate in order to achieve scalability, reliability, decentralized control, and load balancing. PIER enhances DHTs with declarative and algebraic query interfaces, and underneath those interfaces implements multihop, in-network versions of joins, aggregation, recursion, and query/result dissemination. PIER is currently being used for diverse applications, including network monitoring, keyword-based filesharing search, and network topology mapping. We will demonstrate PIER\u27s functionality by showing system monitoring queries running on PlanetLab, a testbed of over 300 machines distributed across the globe

The state of peer-to-peer network simulators

Networking research often relies on simulation in order to test and evaluate new ideas. An important requirement of this process is that results must be reproducible so that other researchers can replicate, validate and extend existing work. We look at the landscape of simulators for research in peer-to-peer (P2P) networks by conducting a survey of a combined total of over 280 papers from before and after 2007 (the year of the last survey in this area), and comment on the large quantity of research using bespoke, closed-source simulators. We propose a set of criteria that P2P simulators should meet, and poll the P2P research community for their agreement. We aim to drive the community towards performing their experiments on simulators that allow for others to validate their results