Integrating functional genomics data using maximum likelihood based simultaneous component analysis

Background  

In contemporary biology, complex biological processes are increasingly studied by collecting and analyzing measurements of the same entities that are collected with different analytical platforms. Such data comprise a number of data blocks that are coupled via a common mode. The goal of collecting this type of data is to discover biological mechanisms that underlie the behavior of the variables in the different data blocks. The simultaneous component analysis (SCA) family of data analysis methods is suited for this task. However, a SCA may be hampered by the data blocks being subjected to different amounts of measurement error, or noise. To unveil the true mechanisms underlying the data, it could be fruitful to take noise heterogeneity into consideration in the data analysis. Maximum likelihood based SCA (MxLSCA-P) was developed for this purpose. In a previous simulation study it outperformed normal SCA-P. This previous study, however, did not mimic in many respects typical functional genomics data sets, such as, data blocks coupled via the experimental mode, more variables than experimental units, and medium to high correlations between variables. Here, we present a new simulation study in which the usefulness of MxLSCA-P compared to ordinary SCA-P is evaluated within a typical functional genomics setting. Subsequently, the performance of the two methods is evaluated by analysis of a real life Escherichia coli metabolomics data set.     

Further evidence of the African antiquity of hyaenodontid (‘Creodonta’, Mammalia) evolution

We report here the new ‘creodont’ Lahimia selloumi gen. et sp. nov. from the late Palaeocene of the Ouled Abdoun Basin (Morocco) as the oldest known Hyaenodontidae with Tinerhodon from the Ouarzazate Basin (Morocco). By contrast to Tinerhodon, Lahimia is unexpectedly derived. Most of its specializations, such as the shortening of the anterior dentition (e.g. loss of P₁) and the talonid reduction and simplification, are strikingly shared with Boualitomus from the Ypresian of the Ouled Abdoun Basin, and are distinctive from other hyaenodontids, including ‘proviverrines’. They are interpreted as synapomorphies evidencing a precociously specialized early African hyaenodontid lineage. Although Lahimia and Boualitomus remain known only by the lower dentition, their relationships with Koholia are suggested by comparison of their molar occlusal pattern. Lahimia and Boualitomus are referred to the Koholiinae, which is representative of an old African endemic lineage, as initially recognized. This remarkable lineage is characterized by synapomorphies of Lahimia and Boualitomus, and also by a shared original prevallum/postvallid shearing. The discovery of Lahimia provides direct evidence for the antiquity of the African evolution of the Hyaenodontidae. This is in agreement with an African origin of the Hyaenodontidae, and with the probable diphyletism of the ‘Creodonta’. Lahimia and the Koholiinae, as well as the diversity of the first Laurasian hyaenodontid lineages, emphasize our poor knowledge of the striking early African hyaenodontid radiation.     

INCITE: A randomised trial comparing constraint induced movement therapy and bimanual training in children with congenital hemiplegia

Background  

Congenital hemiplegia is the most common form of cerebral palsy (CP) accounting for 1 in 1300 live births. These children have limitations in capacity to use the impaired upper limb and bimanual coordination deficits which impact on daily activities and participation in home, school and community life. There are currently two diverse intensive therapy approaches. Traditional therapy has adopted a bimanual approach (BIM training) and recently, constraint induced movement therapy (CIMT) has emerged as a promising unimanual approach. Uncertainty remains about the efficacy of these interventions and characteristics of best responders. This study aims to compare the efficacy of CIMT to BIM training to improve outcomes across the ICF for school children with congenital hemiplegia.     

Characterization of phosphorus fractions in the sediments of a tropical intertidal mangrove ecosystem

Solid phases of phosphorus fractions in the surface and core sediments were studied to understand the biogeochemical cycling and bioavailability of phosphorus in the Pichavaram intertidal mangrove sediments of India. Total P in surface and core sediments ranged between 451–552 and 459–736 μg g⁻¹ respectively and Fe bound P was the dominant fraction. Low levels of Fe bound P in the mangrove zone than the two estuarine zones may be because of high salinity inhibition of phosphate adsorption onto the Fe-oxides/hydroxides. Post-depositional reorganization of P was observed in surface sediments, converting organic P and Fe bound P into the authigenic P. High levels of organic P in the mangrove zone is primarily due to intensive cycling and degradation of organic matter and adsorption of phosphate on the organic molecules. The burial rates and regeneration efficiency of P in the intertidal mangrove ecosystem ranged from 5.41 to 7.27 μmol P cm⁻² year⁻¹ and 0.122 to 0.233 μmol P cm⁻² year⁻¹, respectively. High burial efficiency (≈99%) of P proves the earlier observation of limiting nature of P for the biological productivity. Further, bioavailable P (exchangeable P + Fe bound P + organic P) constituted a considerable proportion of sedimentary P pool of which an average accounted for 55 and 50% in surface and core sediments respectively. The results indicate that significant amount of P is locked in sediments in the form of authigenic P and detrital P which makes P as a limiting nutrient for the biological productivity.     

Development and prospective validation of a model for predicting weaning in chronic ventilator dependent patients

Background

HTLV-I infection has been linked to lung pathology and HTLV-II has been associated with an increased incidence of pneumonia and acute bronchitis. However it is unknown whether HTLV-I or -II infection alters pulmonary function.

Methods

We performed pulmonary function testing on HTLV-I, HTLV-II and HTLV seronegative subjects from the HTLV outcomes study (HOST), including vital capacity (VC), forced expiratory volume in one second (FEV₁), and diffusing lung capacity for carbon monoxide (DLCO) corrected for hemoglobin and lung volume. Multivariable analysis adjusted for differences in age, gender, race/ethnicity, height and smoking history.

Results

Mean (standard deviation) pulmonary function values among the 257 subjects were as follows: FVC = 3.74 (0.89) L, FEV₁ = 2.93 (0.67) L, DLCO_corr = 23.82 (5.89) ml/min/mmHg, alveolar ventilation (VA) = 5.25 (1.20) L and DLCO_corr/VA = 4.54 (0.87) ml/min/mmHg/L. There were no differences in FVC, FEV1 and DLCO_corr/VA by HTLV status. For DLCO_corr, HTLV-I and HTLV-II subjects had slightly lower values than seronegatives, but neither difference was statistically significant after adjustment for confounding.

Conclusions

There was no difference in measured pulmonary function and diffusing capacity in generally healthy HTLV-I and HTLV-II subjects compared to seronegatives. These results suggest that previously described HTLV-associated abnormalities in bronchoalveolar cells and fluid may not affect pulmonary function.     

Spatial distribution of vectors of Ross River virus and Barmah Forest virus on Russell Island, Moreton Bay, Queensland

Abstract We used a network of 20 carbon dioxide- and octenol-supplemented light traps to sample adult mosquitoes throughout Russell Island in southern Moreton Bay, south-east Queensland. Between February and April 2001, an estimated 1365 564 adult female mosquitoes were collected. In contrast to an average catch of 9754 female mosquitoes per trap night on Russell Island, reference traps set on Macleay Island and on the mainland returned average catches of 3172 and 222, respectively. On Russell Island, Ochlerotatus vigilax (Skuse), Coquillettidia linealis (Skuse), Culex annulirostris Skuse and Verrallina funerea (Theobald), known or suspected vectors of Ross River (RR) and/or Barmah Forest (BF) viruses, comprised 89.6% of the 25 taxa collected. When the spatial distributions of the above species were mapped and analysed using local spatial statistics, all were found to be present in highest numbers towards the southern end of the island during most of the 7 weeks. This indicated the presence of more suitable adult harbourage sites and/or suboptimal larval control efficacy. As immature stages and the breeding habitat of Cq. linealis are as yet undescribed, this species in particular presents a considerable impediment to proposed development scenarios. The method presented here of mapping the numbers of mosquitoes throughout a local government area allows specific areas that have high vector numbers to be defined.     

Isospora dawadimiensis n. sp. (Protozoa: Eimeriidae) from the Jerboa (Jaculus jaculus) in Saudi Arabia

Isospora dawadimiensis n. sp. is described from the jerboa, Jaculus jaculus, from Dawadimi, Saudi Arabia. Sporulated oocysts of I. dawadimiensis n. sp. were ovoidal or nearly subspherical 22–26.5 times 20.5–22 μm (24.4 times 21.4 μm). Oocyst wall had one layer. Micropyle, oocyst residuum, and polar granule were absent. Sporocysts were ellipsoid 12–16.5 times 9–10.5 μm (14.6 times 9.9 μm). Sporocyst residuum was present. The sporocysts lack a Stieda body. Sporozoites 8–11 times 2–3 μm (10 times 2.6 μm) were sausage-shaped, slightly curved, and tapered at one end.     

Purification of galectin-3 from ovine placenta: developmentally regulated expression and immunological relevance

Galectins, beta-galactoside-binding lectins, are extensively distributed in the animal kingdom and share some basic molecular properties. Galectin-3, a member of this family, is generally associated with differentiation, morphogenesis, and metastasis. In this study, galectin-3 was isolated from ovine placental cotyledons round the middle of the gestation period by lactose extraction followed by affinity chromatography on lactosyl-agarose, and separated from galectin-1 by size exclusion chromatography on a Superose 12 column. Under native conditions this lectin behaved as a monomer with an apparent molecular weight of approximately 29,000 and an isoelectric point of 9.0. The partial amino acid sequence of the peptides obtained by tryptic digestion of this protein followed by HPLC separation showed striking homology with other members of the galectin-3 subfamily. Furthermore, ovine placental galectin-3 exhibited specific mitogenic activity toward rat spleen mononuclear cells. Besides, this protein strongly reacted with a rabbit antiserum raised against a chicken galectin. Results obtained by Western blot analysis showed that its expression was greatly decreased in term placenta with respect to the middle of the gestation period, suggesting a regulated expression throughout development.      

Continuous ethanol production byZymomonas mobilis andSaccharomyces cerevisiae in biofilm reactors

Continuous ethanol fermentations were performed in duplicate for 60 days withZymomonas mobilis ATCC 331821 orSaccharomyces cerevisiae ATCC 24859 in packed-bed reactors with polypropylene or plastic composite-supports. The plastic composite-supports used contained polypropylene (75%) with ground soybean-hulls (20%) and zein (5%) forZ. mobilis, or with ground soybean-hulls (20%) and soybean flour (5%) forS. cerevisiae. Maximum ethanol productivities of 536 gL^–1 h^–1 (39% yield) and 499 gL^–1 h^–1 (37% yield) were obtained withZ. mobilis on polypropylene and plastic composite-supports of soybean hull-zein, respectively. ForZ. mobilis, and optimal yield of 50% was observed at a 1.92h^–1 dilution rate for soybean hull-zein plastic composite-supports with a productivity of 96gL^–1h^–1, whereas with polypropylene-supports the yield was 32% and the productivity was 60gL^–1h^–1. With aS. cerevisiae fermentation, the ethanol production was less, with a maximum productivity of 76gL^–1h^–1 on the plastic composite-support at a 2.88h^–1 dilution rate with a 45% yield. Polypropylene-support bioreactors were discontinued due to reactor plugging by the cell mass accumulation. Support shape (3-mm chips) was responsible for bioreactor plugging due to extensive biofilm development on the plastic composite-supports. With suspensionculture continuous fermentations in continuously-stirred benchtop fermentors, maximum productivities of 5gL^–1h^–1 were obtained with a yield of 24 and 26% withS. cerevisiae andZ. mobilis, respectively. Cell washout in suspensionculture continuous fermentations was observed at a 1.0h^–1 dilution rate. Therefore, for continuous ethanol fermentations, biofilm reactors out-performed suspension-culture reactors, with 15 to 100-fold higher productivities (gL^–1h^–1) and with higher percentage yields forS. cerevisiae andZ. mobilis, respectively. Further research is needed with these novel supports to evaluate different support shapes and medium compositions that will permit medium flow, stimulate biofilm formation, reduce fermentation costs, and produce maximum yields and productivities.This is Journal Paper No. J-16357 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Project No. 3253