Cortical Dysfunction Underlies the Development of the Split-Hand in Amyotrophic Lateral Sclerosis

The split-hand phenomenon, a specific feature of amyotrophic lateral sclerosis (ALS), refers to preferential wasting of abductor pollicis brevis (APB) and first dorsal interosseous (FDI) with relative preservation of abductor digiti minimi (ADM). The pathophysiological mechanisms underlying the split-hand phenomenon remain elusive and resolution of this issue would provide unique insights into ALS pathophysiology. Consequently, the present study dissected out the relative contribution of cortical and peripheral processes in development of the split-hand phenomenon in ALS. Cortical and axonal excitability studies were undertaken on 26 ALS patients, with motor responses recorded over the APB, FDI and ADM muscles. Results were compared to 21 controls. Short interval intracortical inhibition (SICI), a biomarker of cortical excitability, was significantly reduced across the range of intrinsic hand muscles (APB_{SICI ALS} 0.3±2.0%, APB_{SICI controls} 16.0±1.9%, P<0.0001; FDI_{SICI ALS} 2.7±1.7%, FDI _{SICI controls} 14.8±1.9%, P<0.0001; ADM_{SICI ALS} 2.6±1.5%, ADM _{SICI controls} 9.7±2.2%, P<0.001), although the reduction was most prominent when recorded over APB/FDI. Changes in SICI were accompanied by a significant increase in motor evoked potential amplitude and reduction of cortical silent period duration, all indicative of cortical hyperexcitability, and these were most prominent from the APB/FDI. At a peripheral level, a significant increase in strength-duration time constant and reduction in depolarising threshold electrotonus were evident in ALS, although these changes did not follow a split-hand distribution. Cortical dysfunction contributed to development of the split-hand in ALS, thereby implying an importance of cortical hyperexcitability in ALS pathogenesis.     

Hexazonium pararosaniline as a fixative for animal tissues.

Hexazonium pararosaniline is a valuable reagent that has been used in enzyme activity histochemistry for 50 years. It is an aqueous solution containing the tris-diazonium ion derived from pararosaniline, an aminotriarylmethane dye, and it contains an excess of nitrous acid that was not consumed in the diazotization reaction. Other investigators have found that immersion for 2 min in an acidic (pH 3.5) 0.0015 M hexazonium pararosaniline solution can protect cryostat sections of unfixed animal tissues from the deleterious effects of aqueous reagents such as buffered solutions used in immunohistochemistry, while preserving specific affinities for antibodies. In the present investigation hexazonium pararosaniline protected lymphoid tissue and striated muscle against the damaging effects of water or saline. The same protection was conferred on unfixed sections treated with dilute nitrous or hydrochloric acid in concentrations similar to those in hexazonium pararosaniline solutions. Model tissues (solutions, gels or films containing gelatin and/or bovine albumin) responded predictably to well known cross-linking (formaldehyde) or coagulant (mercuric chloride) fixatives. Hexazonium pararosaniline solutions prevented the dissolution of protein gels in water only after 9 or more days of contact, during which time considerable swelling occurred. It is concluded that there is no evidence for a "fixative" action of hexazonium pararosaniline. The protective effect on frozen sections of unfixed tissue is attributable probably to the low pH of the solution.     

Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase

Background

Orthology is a central tenet of comparative genomics and ortholog identification is instrumental to protein function prediction. Major advances have been made to determine orthology relations among a set of homologous proteins. However, they depend on the comparison of individual sequences and do not take into account divergent orthologs.

Results

We have developed an iterative orthology prediction method, Ortho-Profile, that uses reciprocal best hits at the level of sequence profiles to infer orthology. It increases ortholog detection by 20% compared to sequence-to-sequence comparisons. Ortho-Profile predicts 598 human orthologs of mitochondrial proteins from Saccharomyces cerevisiae and Schizosaccharomyces pombe with 94% accuracy. Of these, 181 were not known to localize to mitochondria in mammals. Among the predictions of the Ortho-Profile method are 11 human cytochrome c oxidase (COX) assembly proteins that are implicated in mitochondrial function and disease. Their co-expression patterns, experimentally verified subcellular localization, and co-purification with human COX-associated proteins support these predictions. For the human gene C12orf62, the ortholog of S. cerevisiae COX14, we specifically confirm its role in negative regulation of the translation of cytochrome c oxidase.

Conclusions

Divergent homologs can often only be detected by comparing sequence profiles and profile-based hidden Markov models. The Ortho-Profile method takes advantage of these techniques in the quest for orthologs.     

New resources for functional analysis of omics data for the genus <Emphasis Type="Italic">Aspergillus</Emphasis>

Background

Detailed and comprehensive genome annotation can be considered a prerequisite for effective analysis and interpretation of omics data. As such, Gene Ontology (GO) annotation has become a well accepted framework for functional annotation. The genus Aspergillus comprises fungal species that are important model organisms, plant and human pathogens as well as industrial workhorses. However, GO annotation based on both computational predictions and extended manual curation has so far only been available for one of its species, namely A. nidulans.

Results

Based on protein homology, we mapped 97% of the 3,498 GO annotated A. nidulans genes to at least one of seven other Aspergillus species: A. niger, A. fumigatus, A. flavus, A. clavatus, A. terreus, A. oryzae and Neosartorya fischeri. GO annotation files compatible with diverse publicly available tools have been generated and deposited online. To further improve their accessibility, we developed a web application for GO enrichment analysis named FetGOat and integrated GO annotations for all Aspergillus species with public genome sequences. Both the annotation files and the web application FetGOat are accessible via the Broad Institute's website (http://www.broadinstitute.org/fetgoat/index.html). To demonstrate the value of those new resources for functional analysis of omics data for the genus Aspergillus, we performed two case studies analyzing microarray data recently published for A. nidulans, A. niger and A. oryzae.

Conclusions

We mapped A. nidulans GO annotation to seven other Aspergilli. By depositing the newly mapped GO annotation online as well as integrating it into the web tool FetGOat, we provide new, valuable and easily accessible resources for omics data analysis and interpretation for the genus Aspergillus. Furthermore, we have given a general example of how a well annotated genome can help improving GO annotation of related species to subsequently facilitate the interpretation of omics data.

     

Sox2 Cooperates with Inflammation-Mediated Stat3 Activation in the Malignant Transformation of Foregut Basal Progenitor Cells

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Highlights? Sox2+ve basal stem/progenitor cells self-renew and differentiate in vitro and in vivo ? Conditional Sox2 overexpression promotes the expansion of basal progenitor cells ? Sox2 cooperates with an inflammatory microenvironment to induce squamous cancer ? Sox2 and Stat3 together transform mouse and human esophageal progenitor cells     

The influence of estimated body segment parameters on predicted joint kinetics during diplegic cerebral palsy gait

Inverse Dynamic calculations are routinely used in joint moment and power estimates during gait with anthropometric data often taken from published sources. Many biomechanical analyses have highlighted the need to obtain subject-specific anthropometric data (e.g. Mass, Centre of Mass, Moments of Inertia) yet the types of imaging techniques required to achieve this are not always available in the clinical setting. Differences in anthropometric sets have been shown to affect the reactive force and moment calculations in normal subjects but the effect on a paediatric diplegic cerebral palsy group has not been investigated. The aim of this study was to investigate the effect of using different anthropometric sets on predicted sagittal plane moments during normal and diplegic cerebral palsy gait. Three published anthropometric sets were applied to the reactive force and moment calculations of 14 Cerebral Palsy and 14 Control subjects. Statistically significant differences were found when comparing the different anthropometric sets but variability in the resulting sagittal plane moment calculations between sets was low (0.01–0.07 Nm/kg). In addition, the GDI-Kinetic, used as an outcome variable to assess whether differences were clinically meaningful, indicated no clinically meaningful difference between sets. The results suggest that the effects of using different anthropometric sets on the kinetic profiles of normal and diplegic cerebral palsy subjects are clinically insignificant.     

Multiplexed DNA sequencing-by-synthesis

We report a new DNA sequencing-by-synthesis method in which the sequences of DNA templates, hybridized to a surface-immobilized array of DNA primers, are determined by sensing the number of nucleotides by which the primers in each array spot are extended in sequential DNA polymerase-catalyzed nucleotide incorporation reactions, each with a single fluorescein-labeled deoxyribonucleoside triphosphate (dNTP) species. The fluorescein label is destroyed after each readout by a photostimulated reaction with diphenyliodonium chloride. A DNA polymerase with enhanced ability to incorporate, and to extend beyond, modified nucleotides is used. Self-quenching of adjacent fluorescein labels, which impedes readout of homopolymeric runs, is avoided by diluting the labeled dNTP with unlabeled reagent. Misincorporation effects have been quantified and are small; however, low-level contamination of dNTPs with other nucleotides mimics misincorporation and can produce significant false-positive signals. These impurities are removed by polymerase-catalyzed incorporation into complementary "cleaning duplexes." Here, we demonstrate the accurate sequence readout for a small array of known DNA templates, the ability to quantify homopolymeric runs, and a short sequencing example of sections of the wild-type and mutant BRCA1 gene. For a 20,000-spot array, readout rates in excess of 6000 bases per minute are projected.     

Social support for healthy behaviors: scale psychometrics and prediction of weight loss among women in a behavioral program

Social support could be a powerful weight-loss treatment moderator or mediator but is rarely assessed. We assessed the psychometric properties, initial levels, and predictive validity of a measure of perceived social support and sabotage from friends and family for healthy eating and physical activity (eight subscales). Overweight/obese women randomized to one of two 6-month, group-based behavioral weight-loss programs (N = 267; mean BMI 32.1 ± 3.5; 66.3% White) completed subscales at baseline, and weight loss was assessed at 6 months. Internal consistency, discriminant validity, and content validity were excellent for support subscales and adequate for sabotage subscales; qualitative responses revealed novel deliberate instances not reflected in current sabotage items. Most women (>75%) "never" or "rarely" experienced support from friends or family. Using nonparametric classification methods, we identified two subscales-support from friends for healthy eating and support from family for physical activity-that predicted three clinically meaningful subgroups who ranged in likelihood of losing ≥5% of initial weight at 6 months. Women who "never" experienced family support were least likely to lose weight (45.7% lost weight) whereas women who experienced both frequent friend and family support were more likely to lose weight (71.6% lost weight). Paradoxically, women who "never" experienced friend support were most likely to lose weight (80.0% lost weight), perhaps because the group-based programs provided support lacking from friendships. Psychometrics for support subscales were excellent; initial support was rare; and the differential roles of friend vs. family support could inform future targeted weight-loss interventions to subgroups at risk.