Mapping the genetic architecture of gene expression in human liver

Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order disease traits. Therefore, identifying the molecular phenotypes that vary in response to changes in DNA and that also associate with changes in disease traits has the potential to provide the functional information required to not only identify and validate the susceptibility genes that are directly affected by changes in DNA, but also to understand the molecular networks in which such genes operate and how changes in these networks lead to changes in disease traits. Toward that end, we profiled more than 39,000 transcripts and we genotyped 782,476 unique single nucleotide polymorphisms (SNPs) in more than 400 human liver samples to characterize the genetic architecture of gene expression in the human liver, a metabolically active tissue that is important in a number of common human diseases, including obesity, diabetes, and atherosclerosis. This genome-wide association study of gene expression resulted in the detection of more than 6,000 associations between SNP genotypes and liver gene expression traits, where many of the corresponding genes identified have already been implicated in a number of human diseases. The utility of these data for elucidating the causes of common human diseases is demonstrated by integrating them with genotypic and expression data from other human and mouse populations. This provides much-needed functional support for the candidate susceptibility genes being identified at a growing number of genetic loci that have been identified as key drivers of disease from genome-wide association studies of disease. By using an integrative genomics approach, we highlight how the gene RPS26 and not ERBB3 is supported by our data as the most likely susceptibility gene for a novel type 1 diabetes locus recently identified in a large-scale, genome-wide association study. We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process. © 2008 Schadt et al

Malignant peritoneal mesothelioma presenting as recurrent adhesion obstruction in general surgery: a case report

<p>Abstract</p> <p>Introduction</p> <p>Malignant peritoneal mesothelioma is a well-described entity in many reports in the literature in which it has been associated with asbestosis. However, there is no information describing the gross appearance and cardinal features seen during laparotomy, hence it is easy for the unwary surgeon to miss the diagnosis of this rare condition.</p> <p>Case presentation</p> <p>A 49-year-old man of African descent presented to our hospital with a three-month history of weight loss, anorexia, abdominal distension, and general signs of cachexia and ascites on second presentation. At first presentation one year prior to this, he had undergone a laparotomy at our institution by a different team for intestinal obstruction secondary to adhesions with no biopsy taken. The patient's condition subsequently progressively deteriorated, and investigations including upper and lower gastrointestinal endoscopies and computed tomography of the abdomen were inconclusive, except for some free fluid in the peritoneal cavity and diffuse, mild thickening of the gut wall and mesentery. A second-look exploratory laparotomy revealed widespread nodular thickening of the visceral peritoneum with a striking, uniformly diffuse, erythematous, and velvety appearance. The peritoneal biopsy histology showed that the patient had malignant peritoneal mesothelioma. His condition deteriorated rapidly, and he died eight weeks after surgery.</p> <p>Conclusion</p> <p>Our report aims to increase the diagnosing clinician's awareness of the cardinal features of malignant peritoneal mesothelioma and thus reduce diagnostic errors and delays in treatment.</p

Bilateral Assessment of Functional Tasks for Robot-assisted Therapy Applications

This article presents a novel evaluation system along with methods to evaluate bilateral coordination of arm function on activities of daily living tasks before and after robot-assisted therapy. An affordable bilateral assessment system (BiAS) consisting of two mini-passive measuring units modeled as three degree of freedom robots is described. The process for evaluating functional tasks using the BiAS is presented and we demonstrate its ability to measure wrist kinematic trajectories. Three metrics, phase difference, movement overlap, and task completion time, are used to evaluate the BiAS system on a bilateral symmetric (bi-drink) and a bilateral asymmetric (bi-pour) functional task. Wrist position and velocity trajectories are evaluated using these metrics to provide insight into temporal and spatial bilateral deficits after stroke. The BiAS system quantified movements of the wrists during functional tasks and detected differences in impaired and unimpaired arm movements. Case studies showed that stroke patients compared to healthy subjects move slower and are less likely to use their arm simultaneously even when the functional task requires simultaneous movement. After robot-assisted therapy, interlimb coordination spatial deficits moved toward normal coordination on functional tasks

A pilot study evaluating use of a computer-assisted neurorehabilitation platform for upper-extremity stroke assessment

<p>Abstract</p> <p>Background</p> <p>There is a need to develop cost-effective, sensitive stroke assessment instruments. One approach is examining kinematic measures derived from goal-directed tasks, which can potentially be sensitive to the subtle changes in the stroke rehabilitation process. This paper presents the findings from a pilot study that uses a computer-assisted neurorehabilitation platform, interfaced with a conventional force-reflecting joystick, to examine the assessment capability of the system by various types of goal-directed tasks.</p> <p>Methods</p> <p>Both stroke subjects with hemiparesis and able-bodied subjects used the force-reflecting joystick to complete a suite of goal-directed tasks under various task settings. Kinematic metrics, developed for specific types of goal-directed tasks, were used to assess various aspects of upper-extremity motor performance across subjects.</p> <p>Results</p> <p>A number of metrics based on kinematic performance were able to differentiate subjects with different impairment levels, with metrics associated with accuracy, steadiness and speed consistency showing the best capability. Significant differences were also shown on these metrics between various force field settings.</p> <p>Conclusion</p> <p>The results support the potential of using UniTherapy software with a conventional joystick system as an upper-extremity assessment instrument. We demonstrated the ability of using various types of goal-directed tasks to distinguish between subjects with different impairment levels. In addition, we were able to show that different force fields have a significant effect on the performance across subjects with different impairment levels in the trajectory tracking task. These results provide motivation for studies with a larger sample size that can more completely span the impairment space, and can use insights presented here to refine considerations of various task settings so as to generalize and extend our conclusions.</p

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Technology-assisted training of arm-hand skills in stroke: concepts on reacquisition of motor control and therapist guidelines for rehabilitation technology design

<p>Abstract</p> <p>Background</p> <p>It is the purpose of this article to identify and review criteria that rehabilitation technology should meet in order to offer arm-hand training to stroke patients, based on recent principles of motor learning.</p> <p>Methods</p> <p>A literature search was conducted in PubMed, MEDLINE, CINAHL, and EMBASE (1997–2007).</p> <p>Results</p> <p>One hundred and eighty seven scientific papers/book references were identified as being relevant. Rehabilitation approaches for upper limb training after stroke show to have shifted in the last decade from being analytical towards being focussed on environmentally contextual skill training (task-oriented training). Training programmes for enhancing motor skills use patient and goal-tailored exercise schedules and individual feedback on exercise performance. Therapist criteria for upper limb rehabilitation technology are suggested which are used to evaluate the strengths and weaknesses of a number of current technological systems.</p> <p>Conclusion</p> <p>This review shows that technology for supporting upper limb training after stroke needs to align with the evolution in rehabilitation training approaches of the last decade. A major challenge for related technological developments is to provide engaging patient-tailored task oriented arm-hand training in natural environments with patient-tailored feedback to support (re) learning of motor skills.</p

The Role of Glypicans in Wnt Inhibitory Factor-1 Activity and the Structural Basis of Wif1's Effects on Wnt and Hedgehog Signaling

Proper assignment of cellular fates relies on correct interpretation of Wnt and Hedgehog (Hh) signals. Members of the Wnt Inhibitory Factor-1 (WIF1) family are secreted modulators of these extracellular signaling pathways. Vertebrate WIF1 binds Wnts and inhibits their signaling, but its Drosophila melanogaster ortholog Shifted (Shf) binds Hh and extends the range of Hh activity in the developing D. melanogaster wing. Shf activity is thought to depend on reinforcing interactions between Hh and glypican HSPGs. Using zebrafish embryos and the heterologous system provided by D. melanogaster wing, we report on the contribution of glypican HSPGs to the Wnt-inhibiting activity of zebrafish Wif1 and on the protein domains responsible for the differences in Wif1 and Shf specificity. We show that Wif1 strengthens interactions between Wnt and glypicans, modulating the biphasic action of glypicans towards Wnt inhibition; conversely, glypicans and the glypican-binding “EGF-like” domains of Wif1 are required for Wif1's full Wnt-inhibiting activity. Chimeric constructs between Wif1 and Shf were used to investigate their specificities for Wnt and Hh signaling. Full Wnt inhibition required the “WIF” domain of Wif1, and the HSPG-binding EGF-like domains of either Wif1 or Shf. Full promotion of Hh signaling requires both the EGF-like domains of Shf and the WIF domains of either Wif1 or Shf. That the Wif1 WIF domain can increase the Hh promoting activity of Shf's EGF domains suggests it is capable of interacting with Hh. In fact, full-length Wif1 affected distribution and signaling of Hh in D. melanogaster, albeit weakly, suggesting a possible role for Wif1 as a modulator of vertebrate Hh signaling

Antibody-mediated enhancement aggravates chikungunya virus infection and disease severity

The arthropod-transmitted chikungunya virus (CHIKV) causes a flu-like disease that is characterized by incapacitating arthralgia. The re-emergence of CHIKV and the continual risk of new epidemics have reignited research in CHIKV pathogenesis. Virus-specific antibodies have been shown to control virus clearance, but antibodies present at sub-neutralizing concentrations can also augment virus infection that exacerbates disease severity. To explore this occurrence, CHIKV infection was investigated in the presence of CHIKV-specific antibodies in both primary human cells and a murine macrophage cell line, RAW264.7. Enhanced attachment of CHIKV to the primary human monocytes and B cells was observed while increased viral replication was detected in RAW264.7 cells. Blocking of specific Fc receptors (FcγRs) led to the abrogation of these observations. Furthermore, experimental infection in adult mice showed that animals had higher viral RNA loads and endured more severe joint inflammation in the presence of sub-neutralizing concentrations of CHIKV-specific antibodies. In addition, CHIKV infection in 11 days old mice under enhancing condition resulted in higher muscles viral RNA load detected and death. These observations provide the first evidence of antibody-mediated enhancement in CHIKV infection and pathogenesis and could also be relevant for other important arboviruses such as Zika virus

Cerebellar-dependent delay eyeblink conditioning in adolescents with Specific Language Impairment

Cerebellar impairments have been hypothesized as part of the pathogenesis of Specific Language Impairment (SLI), although direct evidence of cerebellar involvement is sparse. Eyeblink Conditioning (EBC) is a learning task with well documented cerebellar pathways. This is the first study of EBC in affected adolescents and controls. 16 adolescent controls, 15 adolescents with SLI, and 12 adult controls participated in a delay EBC task. Affected children had low general language performance, grammatical deficits but no speech impairments. The affected group did not differ from the control adolescent or control adult group, showing intact cerebellar functioning on the EBC task. This study did not support cerebellar impairment at the level of basic learning pathways as part of the pathogenesis of SLI. Outcomes do not rule out cerebellar influences on speech impairment, or possible other forms of cerebellar functioning as contributing to SLI

A Generic Program for Multistate Protein Design

Some protein design tasks cannot be modeled by the traditional single state design strategy of finding a sequence that is optimal for a single fixed backbone. Such cases require multistate design, where a single sequence is threaded onto multiple backbones (states) and evaluated for its strengths and weaknesses on each backbone. For example, to design a protein that can switch between two specific conformations, it is necessary to to find a sequence that is compatible with both backbone conformations. We present in this paper a generic implementation of multistate design that is suited for a wide range of protein design tasks and demonstrate in silico its capabilities at two design tasks: one of redesigning an obligate homodimer into an obligate heterodimer such that the new monomers would not homodimerize, and one of redesigning a promiscuous interface to bind to only a single partner and to no longer bind the rest of its partners. Both tasks contained negative design in that multistate design was asked to find sequences that would produce high energies for several of the states being modeled. Success at negative design was assessed by computationally redocking the undesired protein-pair interactions; we found that multistate design's accuracy improved as the diversity of conformations for the undesired protein-pair interactions increased. The paper concludes with a discussion of the pitfalls of negative design, which has proven considerably more challenging than positive design