Whole-genome sequence assembly for mammalian genomes: Arachne 2

We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rejoined using several criteria, yielding a 64-fold increase in length (N50), and apparent elimination of all global misjoins; (2) gaps between contigs in supercontigs were filled (partially or completely) by insertion of reads, as suggested by pairing within the supercontig, increasing the N50 contig length by 50%; (3) memory usage was reduced fourfold. The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002).     

Inhibitory processes in adults with persistent childhood onset ADHD

The theory that attention-deficit/hyperactivity disorder (ADHD) stems from a deficit in an executive behavioral inhibition process has been little studied in adults, where the validity of ADHD is in debate. This study examined, in high-functioning young adults with persistent ADHD and a control group, 2 leading measures of inhibitory control: the antisaccad task and the negative priming task. ADHD adults showed weakened ability to effortfully stop a refle ve or anticipated oculomotor response but had normal ability to automatically suppress irrelevant information. Results suggest that an inhibitory deficit in ADHD is confined to effortful inhibition of motor response, that antisaccade and negative priming tasks index distinct inhibition systems, and that persistence of ADHD symptoms into adulthood is associated with persistence of executive motor inhibition deficits.     

The history of contraction of the wrist flexors can change cortical excitability

Many freshwater turtles in temperate climates may experience winter periods trapped under ice unable to breathe, in anoxic mud, or in water depleted of O₂. To survive, these animals must not only retain function while anoxic, but they must do so for extended periods of time. Two general physiological adaptive responses appear to underlie this capacity for long-term survival. The first is a coordinated depression of metabolic processes within the cells, both the glycolytic pathway that produces ATP and the cellular processes, such as ion pumping, that consume ATP. As a result, both the rate of substrate depletion and the rate of lactic acid production are slowed greatly. The second is an exploitation of the extensive buffering capacity of the turtle's shell and skeleton to neutralize the large amount of lactic acid that eventually accumulates. Two separate shell mechanisms are involved: release of carbonate buffers from the shell and uptake of lactic acid into the shell where it is buffered and sequestered. Together, the metabolic and buffering mechanisms permit animals to survive for 3–4 months at 3 °C with no O₂ and with circulating lactate levels of 150 mmol l⁻¹ or more.     

Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease

The inflammatory bowel diseases (IBDs), Crohn's disease (CD) and ulcerative colitis, are chronic inflammatory disorders of the digestive tract. The pathogenesis of IBD is complicated, and it is widely accepted that immunologic, environmental and genetic components contribute to its etiology. To identify genetic susceptibility factors in CD, we performed a genome-wide association study in Japanese patients and controls using nearly 80,000 gene-based single nucleotide polymorphism (SNP) markers and investigated the haplotype structure of the candidate locus in Japanese and European patients. We identified highly significant associations (P = 1.71 x 10(-14) with odds ratio of 2.17) of SNPs and haplotypes within the TNFSF15 (the gene encoding tumor necrosis factor superfamily, member 15) genes in Japanese CD patients. The association was confirmed in the study of two European IBD cohorts. Interestingly, a core TNFSF15 haplotype showing association with increased risk to the disease was common in the two ethnic groups. Our results suggest that the genetic variations in the TNFSF15 gene contribute to the susceptibility to IBD in the Japanese and European populations.     

An investigation of the disclosure process and support needs of BRCA1 and BRCA2 carriers

Disclosure of the results of a positive genetic mutation to offspring can be challenging. The purpose of this study was to investigate the content and process of disclosure from BRCA1/2 carriers to their offspring. A semi-structured questionnaire focused on the disclosure processes between parent and offspring. Thirty-one/40 mothers with BRCA1/2 mutations completed the cross-sectional survey. Sixteen carriers (51.6%) chose to disclose their results to all of their children, thirteen carriers (41.9%) chose not to disclose their results, and two carriers (6.5%) chose to disclose to some of their children. The age of a child appeared to be the most significant contributing factor in the decision to disclose. The mean age of the offspring who learned of the positive test result was 24.3 years with most carriers advocating the ideal age range for disclosure from 19 to 25 years. There was a discrepancy between actual and potential disclosure topics between those who had disclosed and those who had not disclosed at the time of the survey. Women who disclosed their result tended to do so alone, within a week of learning their own results, equally to male and female offspring and expressed that the relationships between themselves and their children had strengthened since revealing the presence of a genetic mutation in the family. Women who had not disclosed the results of their genetic test to offspring were significantly more interested in receiving additional individual counseling, educational videos, and email newsletters that focus on disclosure of this complex and life altering information compared to those who had already disclosed. Disclosure of BRCA1/2 results is determined primarily by age of offspring, is usually done by women alone, relatively soon after receiving results and appears to enhance the relationships between mothers and offspring. Both disclosed and non-disclosed carriers demonstrated significant interest in a variety of interventions to support the disclosure process.     

The heterogeneity of bovine IgG2--V. Differences in the primary structure of bovine IgG2 allotypes.

The partial amino acid sequences of the gamma chains of the bovine IgG2a(A1) and IgG2a(A2) allotypes were determined. Sequence differences were found in the CH1 domain, the hinge region, and the CH3 domain. The hinge regions displayed only 71.4% similarity and all of the differences were of a radical nature. The A2 hinge has isoleucine instead of serine at 229, histidine for asparagine at 235, proline for histidine at 238, and cysteine instead of proline in position 234; the latter has the potential for forming an additional interheavy chain disulphide bridge. The occurrence of such a bridge could explain the presence of a pepsin fragment consisting of the hinge region and the Fc. A corresponding fragment is not obtained with the A1 allotype. Both allotypes have a shortened hinge region and a truncated CH2 domain. This feature is characteristic of all reported sequences of IgG2 proteins but not IgG1 in cattle and the goat. This structural feature may be important in subclass-specific recognition by Fc gamma receptors in ruminants. A surprising discovery was the occurrence of five substitutions in the CH3 domain of the IgG2a(A2) in comparison with the A1, which are shared with the CH3 of IgG1. These permit the occurrence of isoallotypic determinants and can explain the difficulty encountered in preparing A2-specific antisera during which adsorption with IgG1 is a routine procedure. The primary sequence data we report confirm the presence of major structural differences between the A allotypes of cattle that was suggested by previous work. The sequence of the A1 allotype most closely agrees with the two IgG2 sequences deduced from their nucleotide sequences whereas the sequence differences in the hinge and C-terminal CH3 make IgG2a(A2) unique. The structural differences between allotypes could have major consequences for such biological activities as phagocytosis, transepithelial transport, lymphocyte and complement activation.     

Characterization of porcine CD19 and anti-CD19 monoclonal antibodies

CD19 is an important pan B cell marker and co-stimulatory protein in humans and mice. Efforts to further characterize B cell ontogeny in swine have been hampered by the lack of monoclonal antibodies (mAb) to valuable surface markers like Vpre-B, CD19, CD34 and CD43. We report here on the complete nucleotide and deduced amino acid sequence of porcine CD19, the cross-reactivity of anti-human CD19 monoclonals and efforts to prepare anti-porcine CD19 mAb to bacterially-expressed products. Porcine CD19 is highly homologous to those in the few other species studied, i.e. human, mouse and guinea pig, but only in certain domains. Among the 14 CD19 exons, homology approaches 90% to human CD19 in exons 6, 9, 11 and 12 and is approximately 80% with other species in this region. The highly homologous C-terminal cytoplasmic region contains nine tyrosines including the YEND/E motif that binds the SH2 domain of Fyn. Two different porcine CD19 isoforms that differ in their 3' UTRs were identified just as in human CD19. Thus, the signaling properties of CD19 may be similar to those in humans. On the other hand, only 60% sequence similarity was seen in exons 1-5 that encode the N-terminal extracellullar region that is involved in ligand binding and is the target of CD19-specific mAb. This probably explains why only 1 of the 17 anti-human CD19 mAb tested recognized swine B cells. Furthermore, when the extracellular domains of CD19 were expressed in E. coli, mAbs to the bacterially-expressed product did not recognize CD19 on porcine B cells suggesting that carbohydrate-dependent conformation may determine antigenicity.