A Fast and Scalable Kymograph Alignment Algorithm for Nanochannel-Based Optical DNA Mappings

Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge for this technique is thermal motion of the DNA as it undergoes imaging; this blurs fluorescent patterns along the DNA and results in information loss. Correcting for this effect (a process referred to as kymograph alignment) is a common preprocessing step in nanochannel-based optical mapping workflows, and we present here a highly efficient algorithm to accomplish this via pattern recognition. We compare our method with the one previous approach, and we find that our method is orders of magnitude faster while producing data of similar quality. We demonstrate proof of principle of our approach on experimental data consisting of melt mapped bacteriophage DNA.     

Climate and climatic variability at Lake Myvatn

The climate of the Lake Myvatn region is examined through the use of weather station data, using the years from 1971 to 2000 as a reference period. Variations in mean monthly temperature and precipitation at Reykjahlid (Myvatn) are compared with variations at seven other weather stations in north east Iceland. The area is drier and colder than coastal stations and exhibits a seasonal cycle in temperature that is larger than found at the coast. The temperature is significantly influenced by the number of sunlight hours only during the summer months. During summer, the influence of a sea breeze circulation can be clearly identified.The variability of climate since 1936 is also examined in comparison with the seven other weather stations. It is found that temperature variations at the different stations are highly correlated, but for precipitation the correlation is significant but much weaker.The influence of the large scale atmospheric circulation on temperature and precipitation at Lake Myvatn is also examined. It is found that the air temperature at Lake Myvatn is most sensitive to an east-west dipole in the large scale sea surface pressure field, i.e. to a pattern that is very different from the spatial pattern associated with the North Atlantic Oscillation (NAO). Precipitation at Lake Myvatn is to some degree influenced by the NAO, but generally precipitation is associated with northerly winds and cold temperatures whereas southerly winds at Lake Myvatn are likely to be drier.     

Growth hormone-induced effects on mortality, energy status and growth: a field study on Brown Trout (Salmo trutta)

1. Growth hormone (GH) treatment increases the growth rate and competitive ability of salmonids under laboratory conditions. Since fast growth should increase fitness, why is endogenous secretion of GH not higher in wild fish? To address this question, three hypotheses were suggested. H₁: high GH levels reduce antipredator responses and may therefore increase mortality from predation. H₂: high GH levels reduce long-term (e.g. over winter) survival by reducing allocation to critical energy reserves. H₃: GH is not beneficial for growth under natural conditions.
2. To test these hypotheses, the performance of GH-treated juvenile Brown Trout ( Salmo trutta ) and control (placebo) trout was compared in an enclosed stream section subjected to natural predation. Four experiments were conducted during winter, spring, summer and autumn, respectively.
3. Mortality rates were not significantly different between GH-treated and control trout in any of the four experiments so H₁ was not supported. Energy reserves were generally lower in GH-treated fish, which is consistent with H₂, whereas growth rates in mass were higher in GH-treated fish than in controls so H₃ was not supported. This suggests that GH promotes growth at the expense of investment in maintenance.
4. Judging from growth and mortality rates, the fitness of GH-treated and control trout appeared similar. Thus, escaped GH-manipulated fish may compete successfully with wild fish.
5. Hatchery-raised trout with higher initial condition index suffered higher mortality rates than more slender fish. This novel finding may be explained by reduced escape ability related to body morphology, reduced behavioural responses towards predators by high-condition trout, or predator preferences for high-condition fish.     

Peripherally administered growth hormone increases brain dopaminergic activity and swimming in rainbow trout

There is increasing evidence that growth hormone (GH) has important behavioral effects in fish, but the underlying mechanisms are not well understood. To investigate if peripherally administered GH influences the monoaminergic activity of the brain, and how this is correlated to behavior, juvenile rainbow trout were implanted intraperitoneally with ovine GH. Fish were either kept isolated or in groups of five. The physical activity and food intake of the isolated fish were observed after 1 and 7 days, when brains were also sampled. The content of serotonin, dopamine, and noradrenaline and their metabolites in hypothalamus, telencephalon, optic tectum, and brain stem was then analyzed. For fish kept isolated for 7 days following implant, GH increased swimming activity and the levels of the dopamine metabolite 3, 4-hydroxy-phenylacetic acid (DOPAC) were higher in all brain parts examined. In the optic tectum, the levels of the dopamine metabolite homovanillic acid (HVA) were lowered by the GH treatment. One-day GH implant did not affect behavior or monoamine levels of isolated fish. In the fish kept in groups, a 7-day GH implant increased the hypothalamic levels of DOPAC, but not in the other brain parts examined, which may indicate an effect on the brain dopaminergic system from social interactions. It can be concluded that peripherally administered GH may function as a neuromodulator, affecting the dopaminergic activity of the rainbow trout brain, and this is associated with increased swimming activity.     

Cis control of gene expression in E.coli by ribosome queuing at an inefficient translational stop signal

An UGA stop codon context which is inefficient because of the 3'-flanking context and the last two amino acids in the gene protein product has a negative effect on gene expression, as shown using a model protein A' gene. This is particularly true at low mRNA levels, corresponding to a high intracellular ribosome/mRNA ratio. The negative effect is smaller if this ratio is decreased, or if the distance between the initiation and termination signals is increased. The results suggest that an inefficient termination codon can cause ribosomal pausing and queuing along the upstream mRNA region, thus blocking translation initiation of short genes. This cis control effect is dependent on the stop codon context, including the C-terminal amino acids in the gene product, the translation initiation signal strength, the ribosome/mRNA ratio and the size of the mRNA coding region. A large proportion of poorly expressed natural Escherichia coli genes are small, and the weak termination codon UGA is under-represented in small, highly expressed E.coli genes as compared with the efficient stop codon UAA.     

Bacteriophage strain typing by rapid single molecule analysis

Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the method by labelling the genomes of λ and T7 bacteriophages, resulting in a consistent, unique AM profile for each genome. These profiles are also successfully used for identification of the phages from a background phage library. Our method may provide a facile route for screening and typing of various organisms and has potential applications in metagenomics studies of various ecosystems.     

Bioconversion of industrial hemp to ethanol and methane: the benefits of steam pretreatment and co-production

Several scenarios for ethanol production, methane production (by anaerobic digestion) and co-production of these, using autumn harvested hemp as substrate, were investigated and compared in terms of gross energy output. Steam pretreatment improved the methane production rate compared with mechanical grinding. The methane yield of steam pretreated stems was similar both with and without pre-hydrolysis with cellulolytic enzymes. Co-production of ethanol and methane from steam pretreated stems gave a high yield of transportation fuel, 11.1-11.7 MJ/kg processed stem dry matter (DM); more than twice that of ethanol production alone from hexoses, 4.4-5.1 MJ/kg processed stem DM. Co-production from the whole hemp plant would give 2600-3000 L ethanol and 2800-2900 m(3) methane, in total 171-180 GJ per 10,000 m(2) of agricultural land, based on a biomass yield of 16 Mg DM. Of this, the yeast and enzymes from ethanol production were estimated to contribute 700 m(3) (27 GJ) of methane.     

Genomewide scan for hand osteoarthritis: a novel mutation in matrilin-3

Osteoarthritis (OA) is the most common human joint disease, characterized by loss and/or remodeling of joint synovium, cartilage, and bone. Here, we describe a genomewide linkage analysis of patients with idiopathic hand OA who were carefully phenotyped for involvement of either or both the distal interphalangeal (DIP) joints and the first carpometacarpal (CMC1) joints. The best linkage peaks were on chromosomes 4q and 3p and on the short arm of chromosome 2. Genomewide significance was reached for a locus on chromosome 2 for patients with affected CMC1 joints (LOD = 4.97); this locus was also significant for patients with OA in both CMC1 and DIP joints (LOD = 4.44). The peak LOD score at this locus coincides with a gene, MATN3, encoding the noncollagenous cartilage extracellular matrix protein, matrilin-3. Subsequent screening of the genomic sequence revealed a missense mutation, of a conserved amino acid codon, changing threonine to methionine in the epidermal growth factor-like domain in matrilin-3. The missense mutation cosegregates with hand OA in several families. The mutation frequency is slightly more than 2% in patients with hand OA in the Icelandic population and has a relative risk of 2.1.