Reference-Free Validation of Short Read Data

Background

High-throughput DNA sequencing techniques offer the ability to rapidly and cheaply sequence material such as whole genomes. However, the short-read data produced by these techniques can be biased or compromised at several stages in the sequencing process; the sources and properties of some of these biases are not always known. Accurate assessment of bias is required for experimental quality control, genome assembly, and interpretation of coverage results. An additional challenge is that, for new genomes or material from an unidentified source, there may be no reference available against which the reads can be checked.

Results

We propose analytical methods for identifying biases in a collection of short reads, without recourse to a reference. These, in conjunction with existing approaches, comprise a methodology that can be used to quantify the quality of a set of reads. Our methods involve use of three different measures: analysis of base calls; analysis of k-mers; and analysis of distributions of k-mers. We apply our methodology to wide range of short read data and show that, surprisingly, strong biases appear to be present. These include gross overrepresentation of some poly-base sequences, per-position biases towards some bases, and apparent preferences for some starting positions over others.

Conclusions

The existence of biases in short read data is known, but they appear to be greater and more diverse than identified in previous literature. Statistical analysis of a set of short reads can help identify issues prior to assembly or resequencing, and should help guide chemical or statistical methods for bias rectification.     

Distribution and population characteristics of the alien talitrid amphipod Orchestia cavimana in relation to environmental conditions in the Northeastern Baltic Sea

The talitrid amphipods were found for the first time in the Northeastern Baltic Sea in 1999. Orchestia cavimana inhabited damp wracks cast up on shore within a 200 m area of Saaremaa Island. In the following year, the species expanded its range to a few kilometres. In 2002, six additional locations of O. cavimana were found in Saaremaa Island and two locations in the Northwestern part of Estonia. Abundances and biomasses were highest in the first year of the invasion. In the following years, the values stabilized on remarkably lower levels. Population characteristics of the species varied significantly between locations. The average biomass and abundance were 9 g dw m⁻² and 1975 ind m⁻², respectively. Wrack biomass and interaction between wrack biomass and exposure were the best predictors of the abundances and biomasses of O. cavimana. Humidity explained additional variability in biomasses. The size structure of the population of O. cavimana was mostly related to humidity and wrack biomass. The Southern coast of the Baltic Sea may be regarded as the initial donor region for the Estonian populations of O. cavimana. The vector of this invasion is most likely related to the natural dispersal of the drifting algae but human activities as a transport vector can not be excluded. The incredible speed of the invasion of O. cavimana and its high biomasses indicate that the species will very likely extend its distribution along the coast of the Northeastern Baltic Sea in the following years.     

Effects of Obesity and Weight Loss on Cardiac Function and Valvular Performance

KARASON, KRISTJAN, INGEMAR WALLENTIN, BO LARSSON, LARS SJOSTROM. Effects of obesity and weight loss on cardiac function and valvular performance. Obes Res. 1998;6:422–429. Objective : To study the consequences of long-standing obesity on myocardial function and valvular performance and to determine the effects of weight loss on these cardiovascular features. Research Methods and Procedures : We included 41 patients with obesity referred for weight-reducing gastroplasty, 31 patients with obesity who received dietary recommendations, and 43 lean subjects. Body weight and blood pressure were measured, and cardiac function and valvular performance were estimated echocardiographically. Left ventricular ejection fraction was used to assess systolic heart function, and the ratio of transmitral early to atrial (E/A) peak flow velocity was used as an estimate of diastolic filling. All three study groups were investigated at baseline, and the two groups with obesity were re-examined at 1-year follow-up. Results : Patients with obesity had higher blood pressure, greater cardiac output, lower ejection fraction, and reduced E/A ratio, compared with lean subjects (p<0.01). Surgical treatment of obesity led to significant decreases in body weight, whereas body weight remained unchanged in the group treated with dietary recommendations (p<0.001). In the weight loss group, blood pressure and cardiac output decreased and the E/A ratio increased (p<0.001). Left ventricular ejection fraction tended to increase in the weight loss group and decrease in the obese control group p<0.01). No significant valvular disease was observed in any of the subjects with obesity at baseline or after weight loss. Discussion : We conclude that weight reduction in subjects with obesity is associated with improvements in left ventricular diastolic filling and has favorable effects on left ventricular ejection fraction. Neither obesity nor weight loss seem to promote valvular heart disease.     

Seasonal Direct Light Availability Affects Mean Leaf Orientation in a Herbaceous Multi-Species Canopy

Abstract: Relationship between leaf orientation in natural or semi-natural herbaceous communities and the local abundance of direct light has rarely been investigated. We present evidence from a permanent plot experiment that seasonal direct light availability in 40 × 40 cm plots significantly affects mean leaf orientation in a semi-natural wooded meadow. In sunny years and in well-illuminated conditions, the leaf surface is exposed predominantly to the north, and vice versa . Two groups of species are responsible for such a response: of the variation in leaf orientation, 41 % is explainable through direct light availability for light-demanding species, and 26 % for graminoid species. In shade-tolerant species and in forbs there is no sign of a regression between leaf orientation and direct light abundance. Ability to plastically react to variation in seasonal and local direct light availability appears to be a trait under considerable selective pressure only in light-demanding plants, and more characteristic of species with graminoid growth form.     

Photoperiod gene control over partitioning between reproductive and vegetative growth

Summary The hypothesis tested was that lack of photoperiod gene activity allows inherent partitioning of photosynthate to continued growth of the earliest potential buds, flowers, pods, and seeds (the organs that give rise to the yield). Alternatively, and competitively, photoperiod gene activity causes the photosynthate to be partitioned predominantly toward continued growth of new vegetative organs plus later initiation of more reproductive (yield) organs. This hypothesis was tested by comparing an insensitive and a photoperiod-sensitive bean (Phaseolus vulgaris L.) cultivar and their F₁ with F₂ segregates of undetermined genotype. Randomly derived homozygous F₈ segregates were also compared. The F₈ generation included one photoperiod-insensitive and one photoperiod-sensitive genotype in a 1:1 ratio, which verified control by one photoperiod gene. Under long daylength (LD), in addition to early versus late flowering and maturity, the two genotypes expressed opposite levels of 23 other traits that would be changed by competitive partitioning of the photosynthate. In contrast, under short daylength (SD), both genotypes flowered and matured early, and both expressed the levels for all 25 traits that the photoperiod-insensitive genotype expressed in both SD and LD. The photoperiod gene interacted with daylength to control the levels of all three major physiological components of yield: the aerial biomass, harvest index, and days to maturity. Included among the other traits with levels altered by daylength-modulated photoperiod gene activity were: the number of branches, nodes, leaves and leaf area, the rate of yield accumulation, and sink activity.Department of Plant Breeding and Biometry paper no. 758     

Expression and regulation of α1β1 integrin in Schwann cells

The interaction of cells with the extracellular matrix plays a critical role in morphogenesis and cell differentiation. To define how Schwann cells might interact with the extracellular matrix, we chose to study the expression of the laminin/collagen receptor α1β1 integrin during nerve development in the rat from embryonic day 14 to maturity. We found that this integrin is expressed predominantly on mature non-myelin-forming cells and only at very low levels on myelin-forming cells. Significant levels of this integrin were not detected on Schwann cell precursors or embryonic Schwann cells in vivo. Experiments using transected and crushed sciatic nerve showed that α1β1 integrin expression is regulated at least in part by axonal contact. Furthermore, Schwann cell culture experiments showed that α1β1 integrin levels are strongly upregulated by transforming growth factor-βs and phorbol esters. © 1997 John Wiley & Sons, Inc. J Neurobiol 33: 914–928, 1997     

Inhibition of the Production of Phenolic Compounds in Brassica napus 2-Amino-oxyacetic Acid

Phenolic compounds precipitated with caffeine were more widelydistributed in the cytoplasm and nucleus in the outermost layerof the columella of germinating Brassica napus root than inthe other layers. Amino-oxyacetic acid, an inhibitor of thebiosynthesis of the C₆C₃ part of phenolic compounds, inhibitedthe biosynthesis of phenolics, and made dark deposits less numerousin all three of the outermost layers of the columella. The firstlayer was the most responsive, because symptoms of inhibitionwere already visible after 3 h. After 24 h the inhibition inthe second and third layers was proportional to the concentration.The first layer contained less deposits than the control, butmore than the second and third layers, suggesting that manyof these compounds in the first layer were present at the outset.Copyright1995, 1999 Academic Press Phenolics, 2-amino-oxyacetic acid, Brassica, germination, cytoplasm, nucleus     

Symptomatic relief precedes improvement of myocardial blood flow in patients under spinal cord stimulation

Background

Spinal cord electrical stimulation (SCS) has shown to be a treatment option for patients suffering from angina pectoris CCS III-IV although being on optimal medication and not suitable for conventional treatment strategies, e.g. CABG or PTCA. Although many studies demonstrated a clear symptomatic relief under SCS therapy, there are only a few short-term studies that investigated alterations in cardiac ischemia. Therefore doubts remain whether SCS has a direct effect on myocardial perfusion.

Methods

A prospective study to investigate the short- and long-term effect of spinal cord stimulation (SCS) on myocardial ischemia in patients with refractory angina pectoris and coronary multivessel disease was designed. Myocardial ischemia was measured by MIBI-SPECT scintigraphy 3 months and 12 months after the beginning of neurostimulation. To further examine the relation between cardiac perfusion and functional status of the patients we measured exercise capacity (bicycle ergometry and 6-minute walk test), symptoms and quality of life (Seattle Angina Questionnaire [SAQ]), as well.

Results

31 patients (65 ± 11 SEM years; 25 male, 6 female) were included into the study. The average consumption of short acting nitrates (SAN) decreased rapidly from 12 ± 1.6 times to 3 ± 1 times per week. The walking distance and the maximum workload increased from 143 ± 22 to 225 ± 24 meters and 68 ± 7 to 96 ± 12 watt after 3 months. Quality of life increased (SAQ) significantly after 3 month compared to baseline, as well. No further improvement was observed after one year of treament. Despite the symptomatic relief and the improvement in maximal workload computer based analysis (Emory Cardiac Toolbox) of the MIBI-SPECT studies after 3 months of treatment did not show significant alterations of myocardial ischemia compared to baseline (16 patients idem, 7 with increase and 6 with decrease of ischemia, 2 patients dropped out during initial test phase). Interestingly, in the long-term follow up after one year 16 patients (of 27 who completed the one year follow up) showed a clear decrease of myocardial ischemia and only one patient still had an increase of ischemia compared to baseline.

Conclusion

Thus, spinal cord stimulation not only relieves symptoms, but reduces myocardial ischemia as well. However, since improvement in symptoms and exercise capacity starts much earlier, decreased myocardial ischemia might not be a direct effect of neurostimulation but rather be due to a better coronary collateralisation because of an enhanced physical activity of the patients.