Base-calling of automated sequencer traces using phred. II. Error probabilities

Elimination of the data processing bottleneck in high-throughput sequencing will require both improved accuracy of data processing software and reliable measures of that accuracy. We have developed and implemented in our base-calling program phred the ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data. These error probabilities are shown here to be valid (correspond to actual error rates) and to have high power to discriminate correct base-calls from incorrect ones, for read data collected under several different chemistries and electrophoretic conditions. They play a critical role in our assembly program phrap and our finishing program consed.

Consed: a graphical tool for sequence finishing

Sequencing of large clones or small genomes is generally done by the shotgun approach (Anderson et al. 1982). This has two phases: (1) a shotgun phase in which a number of reads are generated from random subclones and assembled into contigs, followed by (2) a directed, or finishing phase in which the assembly is inspected for correctness and for various kinds of data anomalies (such as contaminant reads, unremoved vector sequence, and chimeric or deleted reads), additional data are collected to close gaps and resolve low quality regions, and editing is performed to correct assembly or base-calling errors. Finishing is currently a bottleneck in large-scale sequencing efforts, and throughput gains will depend both on reducing the need for human intervention and making it as efficient as possible. We have developed a finishing tool, consed, which attempts to implement these principles. A distinguishing feature relative to other programs is the use of error probabilities from our programs phred and phrap as an objective criterion to guide the entire finishing process. More information is available at http:// www.genome.washington.edu/consed/consed. html.

Base-calling of automated sequencer traces using phred. I. Accuracy assessment

The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-scale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required to obtain the 3-billion-base human genome sequence by the target date of 2005. To reach this goal, improved automation will be essential, and it is particularly important that human involvement in sequence data processing be significantly reduced or eliminated. Progress in this respect will require both improved accuracy of the data processing software and reliable accuracy measures to reduce the need for human involvement in error correction and make human review more efficient. Here, we describe one step toward that goal: a base-calling program for automated sequencer traces, phred, with improved accuracy. phred appears to be the first base-calling program to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.

The 131-amino-acid repeat region of the essential 39-kilodalton core protein of fowlpox virus FP9, equivalent to vaccinia virus A4L protein, is nonessential and highly immunogenic

The immunodominant, 39,000-molecular weight core protein (39K protein) of fowlpox virus (FP9 strain), equivalent to the vaccinia virus A4L gene product, contains highly charged domains at each end of the protein and multiple copies of a 12-amino-acid serine-rich repeat sequence in the middle of the protein. Similar repeats were also detected in other fowlpox virus strains, suggesting that they might confer a selective advantage to the virus. The molloscum contagiosum virus homolog (MC107L) also contains repeats, unlike the vaccinia virus protein. The number of repeats in the fowlpox virus protein does not seem to be crucial, since some strains have a different number of repeats, as shown by the difference in the size of the protein in these strains. The repeat region could be deleted, indicating that it is not essential for replication in vitro. It was not possible to delete the entire 39K protein, indicating that it was essential (transcriptional control signals for the flanking genes were left intact). The repeat region is partly responsible for the immunodominance of the protein, but the C-terminal part of the protein also contains highly antigenic linear epitopes. A role for the 39K protein in immune system modulation is discussed.

A novel approach for inhibiting growth factor signalling in murine tooth development. Inhibition of FGF's

Growth factors belonging to the FGF and TGF-beta families, together with other secreted factors such as Sonic hedgehog, have been shown to be spatially and temporally regulated during tooth development. Providing evidence of the functions of these molecules has, however, proved difficult. We have developed a novel strategy for investigating the role of secreted molecules in tooth development using soluble forms of membrane bound receptors to sequester ligands. Chimeric fusion proteins of receptor extracellular domains were cloned into the eukaryotic expression vector pIG-1 and transfected into COS cells. Fusion proteins secreted by the COS cells were purified using Protein A Sepharose. A soluble form of the FGF receptor FGF-1IIIc, which preferentially binds FGF-2 and FGF-4, was produced using this technique and added to mouse mandible cultures. Addition of the soluble receptors to E13 cultures resulted in down-regulation of Sonic hedgehog expression in molar enamel knots, consistent with inhibition of FGF-4 signalling.

Structure and spatial pattern of the sensilla of the body segments of insect larvae

We describe the types and patterns of sensilla present on the thorax and abdomen of newly hatched larvae of representative species of several insect orders, among them Saltatoria, Mantodea, Blattaria, Heteroptera, Lepidoptera, and Diptera. Sensilla of non-Dipteran species almost exclusively comprise mechanoreceptive hairs or bristles (trichoid sensilla) of various sizes and numbers. In higher Dipterans, peg sensilla (sensilla basiconica, sensilla coeloconica) and so-called papilla sensilla predominate. The pattern of early larval sensilla falls into three main classes, which can be described as 1) fixed pattern, 2) variable pattern, and 3) variable pattern with fixed elements. In larvae exhibiting a fixed sensillum pattern (found in all Dipteran species investigated), sensilla are invariant in number; they are precisely placed in relationship to each other and typically form a single row behind the middle of each segment. A variable pattern (common in most insect groups) typically consists of several rows of relatively evenly spaced sensilla encircling the middle of each segment. In animals with a variable pattern including fixed elements, some sensilla, recognizable by their size or shape, are precisely placed, whereas other sensilla surrounding them are variable.

Complex regulatory region mediating tailless expression in early embryonic patterning and brain development

tailless encodes a transcription factor expressed in multiple domains in the developing embryo. Early and transient expression at the posterior pole is required to establish a domain from which the eighth abdominal segment, telson and posterior gut arise. Just a few nuclear cycles later, a brain-specific domain is initiated at the anterior; expression in this domain is maintained with complex modulations throughout embryogenesis. Expression of tailless in this domain is required to establish the most anterior region of the brain. To understand the function and regulation of these different domains of expression, we provide a detailed description of tailless expression in brain neuroblasts and show that this expression is not detectably regulated by the head gap genes buttonhead or orthodenticle, by the proneural gene lethal of scute or by tailless itself. We show that approximately 6 kb of sequenced upstream regulatory DNA can drive lacZ expression in a pattern that mimics the full tailless embryonic expression pattern. Within this sequence we identify multiple modules responsible for different aspects of the tailless pattern. In addition to identifying additional torso response elements that mediate early blastoderm polar expression, we show that the complex brain expression pattern is driven by a combination of modules; thus expression at a low level throughout the brain and at a high level in the dorsal medial portion of the brain and in the optic lobe, as well as neuroblast-specific repression are mediated by different DNA regions.

Hiding worries from One's spouse: associations between coping via protective buffering and distress in male post-myocardial infarction patients and their wives

The relationship between protective buffering, a style of coping in which the individual hides his/her concerns from spouse, and level of distress was studied among post-myocardial infarction (MI) patients and their spouses. Forty-three male married MI survivors and their wives completed measures of psychological distress and protective buffering at 4 weeks and 6 months post-hospital discharge. At both time periods, a greater propensity for protective buffering by the patient was related to higher levels of patient distress. Protective buffering by wife was also associated with higher levels of wife distress. In addition, patient buffering at 4 weeks predicted increased patient distress at 6 months. The results suggest that male MI patients who conceal their worries from their spouses adjust more poorly over time.

Replenishment of docosahexaenoic acid in n-3 fatty acid-deficient fetal rats by intraamniotic ethyl-docosahexaenoate administration

A procedure for intraamniotic ethyl-docosahexaenoate (Et-DHA) administration was used to restore the docosahexaenoic acid (DHA; 22:6 n-3) levels in n-3-deficient fetal rats. The state of deficiency, characterized by a 34% and 60% decrease in DHA content of fetal brain and liver, respectively, was attained by feeding the pregnant dams from day 8 and up to 20 days gestation, with an n-3 linolenic acid-deprived diet. After a single intraamniotic administration of Et-DHA on day 18 or 19, a rapid increase in both fetal brain and liver DHA was achieved. This increase was accompanied by a decrease in the docosapentaenoic acid (DPA; 22:5 n-6) level. After 48 hr following Et-DHA administration, the major phospholipids (PLs) phosphatidylserine (PS), phosphatidylethanolamine (PE), and phosphatidylcholine (PC), together accounting for more than 90% of total lipid phosphorus in sunflower oil (SFO)-treated animals, regained the DHA content to levels similar to control animals in both fetal brain and liver tissues. Unlike brain, however, most of the DHA content in liver PLs was restored by 24 hr, suggesting that the fetal liver may have a higher metabolic turnover. The DHA/DPA ratio was used to assess the degree of DHA correction. Fetal brain PS, PC, and PE ratios following Et-DHA administration grew steadily over a period of 48 hr but reached only approximately 60% of the control levels. Liver PS regained a value similar to the control, while those of PC and PE were 33% and 46% lower than the controls, respectively. Alterations in the PL polar head-group composition were observed following the dietary manipulations and Et-DHA administration. Although the intraamniotic injection is an invasive approach, the ability to rapidly enhance DHA acylation during intrauterine life may hold potential clinical value whenever an indication for DHA deficiency exists.

Immediate outcomes of substance use treatment within a state psychiatric hospital

Outcomes of an integrated inpatient treatment program for persons with serious mental illness and substance use disorders are examined in relationship to five stages of treatment--stabilization, engagement, persuasion/awareness, active treatment, and relapse prevention. The study used a randomized design with participants assigned to an integrated mental health and substance abuse treatment program or standard psychiatric hospital treatment. At discharge, participants in the integrated treatment program indicated more active engagement in treatment and greater awareness of mental health issues, substance use issues, and the 12-step program than those who received standard hospital treatment. Participants in the integrated treatment program also saw their treatment as being more effective and had more motivation to stay healthy and sober. The integrated treatment program was not equally effective at each treatment stage with all participants. The implications of the program's success overall and at each treatment stage are discussed.

Control of early neurogenesis of the Drosophila brain by the head gap genes tll, otd, ems, and btd

The progenitors of the Drosophila central nervous system (CNS), called neuroblasts, segregate from the neurectoderm of the early embryo in a stereotyped pattern. The neuroblasts that give rise to the brain segregate from the procephalic neurectoderm and form three neuromeres, called protocerebrum, deuterocerebrum, and tritocerebrum. The expression of the proneural genes of the achaete-scute complex (AS-C) is required for neurectodermal cells to acquire the competency to form neuroblasts. We show here that the expression of the proneural gene lethal of scute (l'sc) is required for the development of the majority of the procephalic neuroblasts. l'sc expression in the procephalic neurectoderm is controlled by the head gap genes tailless (tll), orthodenticle (otd), buttonhead (btd), and empty spiracles (ems), which are expressed in partially overlapping domains of the head neurectoderm. Loss of function of a given head gap gene results in the absence of l'sc expression in its domain, followed by the absence of neuroblasts that would normally segregate from this domain. Loss of tll function results in the absence of all protocerebral neuroblasts, otd functions in a domain that includes a large part of the protocerebrum and a smaller part of the adjacent deuterocerebrum. Both ems and btd are required in partially overlapping subsets of neuroblasts of the deuterocerebrum and tritocerebrum.

Two chimaeric transcription units result from an inversion breaking intron 1 of the factor VIII gene and a region reportedly affected by reciprocal translocations in T-cell leukaemia

Analysis of mRNA in two haemophilic monozygotic twins offers novel information on the organisation of expressed sequences distal to the coagulation factor VIII gene. These patients show an inversion that, in contrast to the common inversions responsible for 1/5 of all haemophilia A, affects the first rather than intron 22 of the gene. This displaces the most telomeric of the factor VIII exons (exon 1) by approximately 100 kb towards the telomere, and close to the region of the C6.1A gene. This novel inversion creates two hybrid transcription units: one formed by the promoter and first exon of the factor VIII gene followed by a widely expressed sequence; the other by the promoter and coding region of the C6.1A gene plus most of the factor VIII gene (part of intron 1 and exons 2-26). Investigation of this transcription unit reveals that the C6.1A gene has an unsuspected intron in the region coding for the previously described 3'-untranslated tail of the message. Furthermore, exons located beyond the known C6.1A sequence and present in normal transcripts precede exons 2-26 of the factor VIII gene in the hybrid mRNA of the haemophilic twins. The factor VIII sequences in this hybrid mRNA are not expected to be expressed because they lack the first exon, encoding the prepeptide, and follow a translation stop in the C6.1A gene. Leukaemia-related translocations in the C6.1A region suggest that this region may be somewhat unstable.

Fatty acid composition of late embryonic and early postnatal rat brain

The fatty acid (FA) composition and distribution in a variety of phospholipids (PL) and neutral lipids (NL) at two discrete stages during the embryonic rat brain development were investigated. Over 96% of the FA were acylated into fetal brain PL at embryonic day 17 after the peak of neuronal proliferation and at embryonic day 20, one day prior to delivery. Phosphatidylcholine constituted approximately 60% of the total PL pool, phosphatidylethanolamine (PE) 30%, phosphatidylserine (PS) 6%, and phosphatidylinositol (PI) 4%. The diacylglycerols and triacylglycerols constituted 1-2% of the fetal brain lipids. alpha-Linolenic acid (18:3n-3) and linoleic acid (18:2n-6) were found in very low amounts in all fetal brain PL and NL. The percentage of the n-6 polyunsaturated FA, consisting of arachidonic acid (AA), 22:4n-6 and 22:5n-6, remained unchanged in all the fractions, except in PI, in which the proportion of AA increased. The concentration of docosahexaenoic acid (DHA) increased with age in all the fractions, with the bulk of accumulation accounted for by its increase in PE and, to a lesser extent, in PS. This finding suggests a "DHA accretion spurt" during the last three days of pregnancy.