Legislative and Administrative Processes. By Hans A. Linde and George Bunn; Introduction to the American Public Law System: Cases and Materials. By Jerry L. Mashaw and Richard A. Merrill

Background: Genome and transcriptome sequencing applications that rely on variation in sequence depth can be negatively affected if there are systematic biases in coverage. We have investigated patterns of local variation in sequencing coverage by utilising ultra-deep sequencing (>100,000X) of mtDNA obtained during sequencing of two vertebrate genomes, wolverine (Gulo gulo) and collared flycatcher (Ficedula albicollis). With such extreme depth, stochastic variation in coverage should be negligible, which allows us to provide a very detailed, fine-scale picture of sequence dependent coverage variation and sequencing error rates. Results: Sequencing coverage showed up to six-fold variation across the complete mtDNA and this variation was highly repeatable in sequencing of multiple individuals of the same species. Moreover, coverage in orthologous regions was correlated between the two species and was negatively correlated with GC content. We also found a negative correlation between the site-specific sequencing error rate and coverage, with certain sequence motifs "CCNGCC" being particularly prone to high rates of error and low coverage. Conclusions: Our results demonstrate that inherent sequence characteristics govern variation in coverage and suggest that some of this variation, like GC content, should be controlled for in, for example, RNA-Seq and detection of copy number variation

Is genetic diversity really higher in large populations?

Analyses of mitochondrial DNA (mtDNA) have challenged the concept that genetic diversity within populations is governed by effective population size and mutation rate. A recent study in BMC Evolutionary Biology shows that variation in the rate of mutation rather than in population size is the main explanation for variations in mtDNA diversity observed among bird species

Insertion-deletion polymorphisms (indels) as genetic markers in natural populations

<p>Abstract</p> <p>Background</p> <p>We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations.</p> <p>Results</p> <p>Sequence reads from light shot-gun sequencing efforts of different dog breeds were aligned to the dog genome reference sequence and gaps corresponding to indels were identified. One hundred candidate markers (4-bp indels) were selected and genotyped in unrelated dogs (n = 7) and wolves (n = 18). Eighty-one and 76 out of 94 could be validated as polymorphic loci in the respective sample. Mean indel heterozygosity in a diverse set of wolves was 19%, and 74% of the loci had a minor allele frequency of >10%. Indels found to be polymorphic in wolves were subsequently genotyped in a highly bottlenecked Scandinavian wolf population. Fifty-one loci turned out to be polymorphic, showing their utility even in a population with low genetic diversity. In this population, individual heterozygosity measured at indel and microsatellite loci were highly correlated.</p> <p>Conclusion</p> <p>With an increasing amount of sequence information gathered from non-model organisms, we suggest that indels will come to form an important source of genetic markers, easy and cheap to genotype, for studies of natural populations.</p

The unique genomic properties of sex-biased genes: Insights from avian microarray data

In order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and heart tissue

Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population

Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%–24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf populationpublishedVersio

Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population

Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%-24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population

Polymerase chain reaction amplified markers for bird sexing

Female birds are heterogametic (Z/W), while males are homogametic (Z/Z). PCR assays are often useful in sexing avian species, especially at hatch or in ovo. Two previously described assays are based on differences between the Z and W copy of the chicken chromodomain-helicase DNA-binding protein gene (CHD1Z and CHD1W). Applicability of these assays were tested in five other galliforms: red junglefowl, turkey, peafowl, bobwhite quail and common quail, and one waterfowl, mallard. Using primers described by Fridolfsson and Ellegren (1999), males of all galliform species studied displayed one 450-bp, Z-specific fragment, whereas females showed both CHD1Z (450-bp) and CHD1W (600-bp) fragments. Both mallard sexes yielded a single product of 600 bp. Using primers designed by Kahn and Quinn (1999), three species, red junglefowl, turkey and peafowl, displayed one Z-specific fragment (240 bp) in males and two fragments (240 and 265 bp) in females. Only a single fragment was obtained, irrespective of sex, in bobwhite quail (250 bp), common quail (275 bp) and mallard (240 bp). By screening a chicken BAC library with a CHD1W genomic fragment, two overlapping BAC inserts were obtained that, by PCR analysis, appear to contain the chicken CHD1Z gene. To date, we have been unable to identify a CHD1W-containing BAC in our library. Additional BAC analysis is underway

Tunkeutumisenesto ja havainnointi käytönvalvontajärjestelmissä

Tässä insinöörityössä tutkittiin tunkeutumisenesto- ja havainnointijärjestelmien soveltuvuutta nykyaikaisiin käytönvalvontajärjestelmiin. Työ tehtiin Helsingin Energialle, joka on merkittävä energiapalveluita tarjoava yritys Suomessa. Työssä perehdyttiin ensin teoreettisella tasolla käytönvalvontajärjestelmien arkkitehtuuriin, komponentteihin ja tietoturvavaatimuksiin. Lisäksi tutustuttiin yleisimpiin käytössä oleviin käytönvalvontaprotokolliin ja niiden rakenteisiin. Tämän jälkeen työssä selvitettiin tunkeutumisenesto- ja havainnointitekniikoiden toimintaa sekä suunnittelun perusteita. Tämä insinöörityö tuotti myös käytönvalvontajärjestelmiin suunnitellun tunkeutumisenesto- ja havainnointijärjestelmän vaatimusmäärittelyn ja toteutussuunnitelman. Työn tuloksena todettiin tunkeutumisenesto- ja havainnointijärjestelmien protokollakuvauksien tarjonnan olevan niukkaa Pohjoismaissa käytetyille käytönvalvontaprotokollille. Lisäksi kuvausten käyttöönottoon tulee suhtautua varauksella järjestelmien kriittisyyden vuoksi. IDPS-järjestelmien todettiin kuitenkin nostavan käytönvalvontajärjestelmien tieto-turvatasoa muilla ominaisuuksillaan. Työssä painotettiin lisäksi tunkeutumisenesto- ja havainnointijärjestelmän integroinnin tärkeyttä ylläpito- ja hallintaprosesseihin, sekä elinkaaresta huolehtimista.The purpose of this study was to research possibilities for implementing intrusion prevention and detection systems into modern SCADA networks. This study was carried out for Helsinki Energy, a significant energy service provider in Finland. The first part discusses the architecture of SCADA networks, its components and data security requirements on a theoretical level, as well as the most common SCADA protocols and structures. The second part studies the function of intrusion prevention and detection and the basis for its design. This study also defined the requirements as well as laid out an implementation plan for intrusion prevention and detection in SCADA networks. The results of this study show that the supply of intrusion prevention and detection protocol filters is insufficient for SCADA networks used in the Nordic countries. Furthermore, the implementation of protocol filters must be viewed critically. Nevertheless, the IDPS systems still seem to raise the data security level of SCADA networks. It was concluded that the integration of intrusion prevention and detection into maintenance and management practice is as important as the lifecycle. This study was successful in defining the requirements as well as in creating an implementation plan for intrusion prevention and detection in SCADA networks