Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

Although more than 2,400 genes have been shown to contain variants that cause Mendelian disease, there are still several thousand such diseases yet to be molecularly defined. The ability of new whole-genome sequencing technologies to rapidly indentify most of the genetic variants in any given genome opens an exciting opportunity to identify these disease genes. Here we sequenced the whole genome of a single patient with the dominant Mendelian disease, metachondromatosis (OMIM 156250), and used partial linkage data from her small family to focus our search for the responsible variant. In the proband, we identified an 11 bp deletion in exon four of PTPN11, which alters frame, results in premature translation termination, and co-segregates with the phenotype. In a second metachondromatosis family, we confirmed our result by identifying a nonsense mutation in exon 4 of PTPN11 that also co-segregates with the phenotype. Sequencing PTPN11 exon 4 in 469 controls showed no such protein truncating variants, supporting the pathogenicity of these two mutations. This combination of a new technology and a classical genetic approach provides a powerful strategy to discover the genes responsible for unexplained Mendelian disorders.     

Osteopathic manipulative treatment for pneumonia

The pneumonias due to infection continue to be a meaningful threat to the health and viability of persons, particularly those in high risk groups: children, the aged and the debilitated. Noll and colleagues provide us with the results of a well-designed and well-executed multi-institutional controlled clinical trial to evaluate the efficacy of osteopathic manipulative treatment (OMT) in the treatment of pneumonia. The data obtained indicate that by intention-to-treat analysis, the addition of OMT to conventional care did not improve the designated outcomes when compared to conventional care only. A disappointing but important finding. However, by per-protocol analysis, the addition of OMT or of light touch decreased length of hospital stay, the duration of intravenous antibiotics and the incidence of respiratory failure and death relative to conventional care only. Further study is called for to explain these surprising results. Meeting the need for randomized clinical trials of the role and efficacy of OMT is a responsibility of high priority for the osteopathic profession in this age of evidence-based medicine. The American Osteopathic Association (AOA) needs to consider reinstating a dues-generated financial set-aside both to increase its support of osteopathic research and to initiate a program of physician-investigator career development awards to recruit and help establish osteopathic clinical investigators in a career in translational and clinical research.     

God Versus the Human Genome Inside the Human Genome: A Case for Non-Intelligent Design, by John C. Avise. Oxford: Oxford University Press, 2010. Pp. xi + 222. H/b $19.95.

The University of Arizona’s Tree of Life Web Project organizes information about the biological taxa on the model of the tree of life itself. This creates intuitive and informative pathways for browsing. The Project has a well-articulated protocol for checking on the quality of information published on the site, which is evaluated a number of times as it is added to the site. This paper is intended to be an entreé to the site for teachers at all levels and the general public.     

Molecular motors: from one motor many tails to one motor many tales

Kinesin and dynein molecular motor proteins generate the movement of a wide variety of materials in cells. Such movements are crucial for many different cellular and developmental functions, including organelle movement, localization of developmental determinants, mitosis, meiosis and possibly long-range signaling in neurons. Kinesins that control the dynamics of microtubules have also been discovered. Recent work has begun to identify processes in which defective molecular motor function can cause human disease.     

Is hemiepiphytism an adaptation to high irradiance? Testing seedling responses to light levels and drought in hemiepiphytic and non‐hemiepiphytic Ficus

The epiphytic growth habit in many Ficus species during their juvenile stages has commonly been hypothesized to be an adaptation for avoiding deep shade in the forest understory, but this has never been tested experimentally. We examined growth and ecophysiology in seedlings of three hemiepiphytic (Hs) and three non‐hemiepiphytic (NHs) Ficus species grown under different irradiance levels. Both Hs and NHs exhibited characteristics of high light requiring species, such as high plasticity to growth irradiance and relatively high maximum photosynthetic assimilation rates. Diurnal measurements of leaf gas exchange showed that Hs have much shorter active photosynthetic periods than NHs; moreover, leaves of Hs have lower xylem hydraulic conductivity but stronger drought tolerance as indicated by much lower rates of leaf diebacks during the drought treatment. Seedlings of NHs had 3.3‐ and 13.3‐fold greater height and biomass than those of Hs species after growing in the nursery for 5 months, indicating a trade‐off between growth and drought tolerance due to the conflicting requirements for xylem conductivity and cavitation resistance. This study does not support the shade‐avoidance hypothesis; rather, it suggests that the canopy regeneration in Hs is an adaptation to avoid alternative terrestrial growth‐related risks imposed to tiny Ficus seedlings. The NHs with terrestrial regeneration reduce these risks by having an initial burst of growth to rapidly gain relatively large seedling sizes, while in Hs seedlings more conservative water use and greater drought tolerance for surviving the canopy environment are intrinsically associated with slow growth.     

SVA: software for annotating and visualizing sequenced human genomes

SUMMARY: Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits. We illustrate the annotation features of SVA using two simple examples of sequenced genomes that harbor Mendelian mutations. Availability and implementation: Freely available on the web at http://www.svaproject.org.     

An age-specific CD8+ T cell pathway that impairs the effectiveness of strategies to prolong allograft survival

Age-related decline in immunity can impair cell-mediated responses during an infection, malignancy, and acute allograft rejection. Although much research has been allocated to understand the immune responses that impact the former two conditions, the cellular mechanisms by which aging impacts the immune acceptance of organ allografts are not completely clear. In this study, we examined how recipient age impacts the efficacy of therapies that modulate immune recognition of allografts using an immunogenic murine skin transplant model. We found that costimulatory blockade-based treatment failed to extend allograft survival in older recipients to the same extent as that observed in younger recipients. CD8(+) T cells were critical for the inability of aged recipients to achieve maximal allograft survival. Although aged mice displayed a larger number of effector memory T cells prior to transplantation, these cells did not exhibit enhanced alloreactivity compared with young memory T cells. In contrast, naive aged CD8(+) T cells exhibited enhanced IFN-γ production to allostimulation compared with young naive T cells. Our results provide evidence that aging enhances CD8(+) T cell alloreactivity. This could impair the ability of costimulatory blockade-based therapies to prolong allograft survival. Thus, targeting CD8(+) T cells in humans may be a way to improve outcomes in older patients requiring immune modulatory therapy.