The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be problematic. One challenge is the comparison of temporal expression data obtained from different growth conditions where the patterns of expression may be shifted in time. We propose the use of wavelet analysis to transform the data obtained under different growth conditions to permit comparison of expression patterns from experiments that have time shifts or delays. We demonstrate this approach using detailed temporal data for a single bacterial gene obtained under 72 different growth conditions. This general strategy can be applied in the analysis of data sets of thousands of genes under different conditions.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]     

Validity of Antibodies in Lymphocyte Supernatant in Diagnosing Tuberculosis in Severely Malnourished Children Presenting with Pneumonia

BackgroundThe diagnosis of tuberculosis (TB) in young children can be challenging, especially in severely malnourished children. There is a critical need for improved diagnostics for children. Thus, we sought to evaluate the performance of a technique that measures antibodies in lymphocyte supernatant (ALS) for the diagnosis of TB in severely malnourished children presenting with suspected pneumonia.MethodsChildren less than 5 years with severe acute malnutrition and radiological features of pneumonia admitted to the Dhaka Hospital of International Centre for Diarrhoeal Disease Research, Bangladesh, were enrolled consecutively following informed written consent. In addition to clinical and radiological assessment, samples taken for TB diagnosis included gastric lavage fluid and induced sputum for microbiological confirmation. ALS was measured from venous blood, and results were evaluated in children classified as “confirmed”, “non-confirmed TB” or “not TB”.ResultsAmong 224 children who had ALS analysis, 12 (5.4%) children had microbiologically “confirmed TB”, a further 41 (18%) had clinically diagnosed “non-confirmed TB” and the remaining 168 (75%) were considered not to have TB. ALS was positive in 89 (40%) and negative in 85 (39%) of children, with a large number (47 or 21%) reported as “borderline”. These proportions were similar between the three diagnostic groups. The sensitivity and specificity of ALS when comparing “Confirmed TB” to “Not TB” was only 67% (95% CI: 31–91%) and 51% (95% CI: 42–60%), respectively.

Conclusions and Significance

Our data suggest that ALS is not sufficiently accurate to improve the diagnosis of TB in children with severe malnutrition.     

The Role of the Immune Response in the Pathogenesis of Thyroid Eye Disease: A Reassessment

Background

Although thyroid eye disease is a common complication of Graves’ disease, the pathogenesis of the orbital disease is poorly understood. Most authorities implicate the immune response as an important causal factor. We sought to clarify pathogenesis by using gene expression microarray.

Methods

An international consortium of ocular pathologists and orbital surgeons contributed formalin fixed orbital biopsies. RNA was extracted from orbital tissue from 20 healthy controls, 25 patients with thyroid eye disease (TED), 25 patients with nonspecific orbital inflammation (NSOI), 7 patients with sarcoidosis and 6 patients with granulomatosis with polyangiitis (GPA). Tissue was divided into a discovery set and a validation set. Gene expression was quantified using Affymetrix U133 Plus 2.0 microarrays which include 54,000 probe sets.

Results

Principal component analysis showed that gene expression from tissue from patients with TED more closely resembled gene expression from healthy control tissue in comparison to gene expression characteristic of sarcoidosis, NSOI, or granulomatosis with polyangiitis. Unsupervised cluster dendrograms further indicated the similarity between TED and healthy controls. Heat maps based on gene expression for cytokines, chemokines, or their receptors showed that these inflammatory markers were associated with NSOI, sarcoidosis, or GPA much more frequently than with TED.

Conclusion

This is the first study to compare gene expression in TED to gene expression associated with other causes of exophthalmos. The juxtaposition shows that inflammatory markers are far less characteristic of TED relative to other orbital inflammatory diseases.     

Specificity, promiscuity and localization of ARF protein interactions with NCS-1 and phosphatidylinositol-4 kinase-III beta

ADP-ribosylation factor (ARF) proteins are involved in multiple intracellular vesicular transport pathways. Most studies have focused on the functions of ARF1 or ARF6 and little is known about the remaining ARF isoforms. Although the mammalian ARF proteins share a high degree of sequence identity, recent evidence has indicated that they may control distinct trafficking steps within cells. A unanswered issue is the degree of specificity of ARF family members for different interacting proteins. To investigate potential functional differences between the human ARF proteins, we have examined the localization of all human ARF isoforms and their interactions with two ARF1 binding proteins, neuronal calcium sensor-1 (NCS-1) and phosphatidylinositol-4 kinase-IIIbeta (PI4Kbeta). Use of a fluorescent protein fragment complementation method showed direct interactions between ARFs 1, 3, 5 and 6 with NCS-1 but at different intracellular locations in live HeLa cells. Photobleaching experiments indicated that complementation did not detect dynamic changes in protein interactions over short-time scales. A more specific interaction between ARFs 1/3 and PI4Kbeta was observed. Consistent with these latter findings ARF1 but not ARF5 or 6 enhanced the stimulatory effect of PI4Kbeta on regulated exocytosis, suggesting a specific role for class-I ARFs in the regulation of PI4Kbeta.     

The α-Globin Gene Family of an Australian Marsupial, Macropus eugenii: The Long Evolutionary History of the θ-Globin Gene and Its Functional Status in Mammals

Comparative evolutionary analyses of gene families among divergent lineages can provide information on the order and timing of major gene duplication events and evolution of gene function. Here we investigate the evolutionary history of the α-globin gene family in mammals by isolating and characterizing α-like globin genes from an Australian marsupial, the tammar wallaby, Macropus eugenii. Sequence and phylogenetic analyses indicate that the tammar α-globin family consists of at least four genes including a single adult-expressed gene (α), two embryonic/neonatally expressed genes (ζ and ζ′), and θ-globin, each orthologous to the respective α-, ζ-, and θ-globin genes of eutherian mammals. The results suggest that the θ-globin lineage arose by duplication of an ancestral adult α-globin gene and had already evolved an unusual promoter region, atypical of all known α-globin gene promoters, prior to the divergence of the marsupial and eutherian lineages. Evolutionary analyses, using a maximum likelihood approach, indicate that θ-globin, has evolved under strong selective constraints in both marsupials and the lineage leading to human θ-globin, suggesting a long-term functional status. Overall, our results indicate that at least a four-gene cluster consisting of three α-like and one β-like globin genes linked in the order 5′–ζ–α–θ–ω–3′ existed in the common ancestor of marsupials and eutherians. However, results are inconclusive as to whether the two tammar ζ-globin genes arose by duplication prior to the radiation of the marsupial and eutherian lineages, with maintenance of exon sequences by gene conversion, or more recently within marsupials.Reviewing Editor: Dr. John Oakeshott     

Models meet data: Challenges and opportunities in implementing land management in Earth system models

As the applications of Earth system models (ESMs) move from general climate projections toward questions of mitigation and adaptation, the inclusion of land management practices in these models becomes crucial. We carried out a survey among modeling groups to show an evolution from models able only to deal with land‐cover change to more sophisticated approaches that allow also for the partial integration of land management changes. For the longer term a comprehensive land management representation can be anticipated for all major models. To guide the prioritization of implementation, we evaluate ten land management practices—forestry harvest, tree species selection, grazing and mowing harvest, crop harvest, crop species selection, irrigation, wetland drainage, fertilization, tillage, and fire—for (1) their importance on the Earth system, (2) the possibility of implementing them in state‐of‐the‐art ESMs, and (3) availability of required input data. Matching these criteria, we identify “low‐hanging fruits” for the inclusion in ESMs, such as basic implementations of crop and forestry harvest and fertilization. We also identify research requirements for specific communities to address the remaining land management practices. Data availability severely hampers modeling the most extensive land management practice, grazing and mowing harvest, and is a limiting factor for a comprehensive implementation of most other practices. Inadequate process understanding hampers even a basic assessment of crop species selection and tillage effects. The need for multiple advanced model structures will be the challenge for a comprehensive implementation of most practices but considerable synergy can be gained using the same structures for different practices. A continuous and closer collaboration of the modeling, Earth observation, and land system science communities is thus required to achieve the inclusion of land management in ESMs.     

Temporal dynamics of acute isovolume bronchoconstriction in the rat

Bates, Jason H. T., Thomas F. Schuessler, Carrie Dolman, andDavid H. Eidelman. Temporal dynamics of acute isovolume bronchoconstriction in the rat. J. Appl.Physiol. 82(1): 55-62, 1997.The time course oflung impedance changes after intravenous injection of bronchial agonisthave produced significant insights into the mechanisms ofbronchoconstriction in the dog (J. H. T. Bates, A.-M. Lauzon, G. S. Dechman, G. N. Maksym, and T. F. Shuessler. J. Appl.Physiol. 76: 616-626, 1994). We studied the timecourse of acute induced bronchoconstriction in five anesthetizedparalyzed open-chest rats injected intravenously with a bolus ofmethacholine. For the 16 s immediately after injection, we held thelung volume constant while applying small-amplitude flow oscillationsat 1.48, 5.45, and 19.69 Hz simultaneously, which provided us withcontinuous estimates of lung resistance(RL) and elastance(EL) at eachfrequency. This procedure was repeated at initial lung inflationpressures of 0.2, 0.4, and 0.6 kPa. BothRL andEL increased progressively aftermethacholine administration; however, the rate of change ofEL increased dramatically asfrequency was increased, whereas RL remained relativelyindependent of frequency. We interpret these findings in terms of athree-compartment model of the rat lung, featuring two parallelalveolar compartments feeding into a central airway compartment. Modelsimulations support the notions that both central airway shunting andregional ventilation inhomogeneity developed to a significant degree inour constricted rats. We also found that the rates of increase in bothRL andEL were greatly enhanced as theinitial lung inflation pressure was reduced, in accord with the notionthat parenchymal tethering is an important mechanism limiting theextent to which airways can narrow when their smooth muscle isstimulated to contract.

     

Recreational Use of the Countryside: No Evidence that High Nature Value Enhances a Key Ecosystem Service

In Western Europe, recreational amenity is presented as an important cultural ecosystem service that, along with other values, helps justify policies to conserve biodiversity. However, whether recreational use by the public is enhanced at protected areas designated for nature conservation is unknown. This is the first study to model outdoor recreation at a national scale, examining habitat preferences with statutory designation (Site of Special Scientific Interest) as an indicator of nature conservation importance. Models were based on a massive, three year national household survey providing spatially-referenced recreational visits to the natural environment. Site characteristics including land cover were compared between these observed visit sites (n = 31,502) and randomly chosen control sites (n = 63,000). Recreationists preferred areas of coast, freshwater, broadleaved woodland and higher densities of footpaths and avoided arable, coniferous woodland and lowland heath. Although conservation designation offers similar or greater public access than undesignated areas of the same habitat, statutory designation decreased the probability of visitation to coastal and freshwater sites and gave no effect for broadleaved woodland. Thus general recreational use by the public did not represent an important ecosystem service of protected high-nature-value areas, so that intrinsic and existence values remain as the primary justifications for conservation of high nature value areas. Management of ‘green infrastructure’ sites of lower conservation value that offer desirable habitats and enhanced provision of footpaths, could mitigate recreational impacts on nearby valuable conservation areas.     

How dry are anhydrous enzymes? Measurement of residual and buried 18O-labeled water molecules using mass spectrometry

There is continual debate over the central role of water in protein folding, structure, stability, and dynamics. Catalytic activity has been demonstrated in organic media with, apparently “anhydrous” enzymes. Hence there is considerable discussion over whether there are a few residual water molecules or if the enzymes are demonstrating activity in the complete absence of water. Here we present measurements designed to test this hypothesis based on the detection of ¹⁸O-labeled water by mass spectrometry. This extremely sensitive technique avoids many of the potential errors associated with published methods for measuring water content such as gravimetry or Karl Fischer titrations. We have also explored the mass spectrometric detection of ²H-enriched water and found that lyophilization of deuteron-labeled protein can lead to extensive loss of the isotopic label during the drying process. “Anhydrous” protein was produced by extended drying, over P₂O₅, of lyophilized powders hydrated through the vapor phase with ¹⁸O-labeled water. Redissolution in standard water released the remaining protein-bound ¹⁸O-labeled water molecules, and the isotopic enrichment of the water was used to calculate the number of bound molecules per mole of protein. In the cases of lysozyme and subtilisin Carlsberg, 4 ± 2 and 15 ± 2 waters per mole were found, respectively. Comparisons with crystal structures showed these values correspond closely to the expected number of buried water molecules in these proteins. This is consistent with the idea that water physically entrapped within the rigid protein structure is retained but all the other more accessible surface-bound hydration molecules can be removed by the drying process. Such anhydrous subtilisin Carlsberg preparations have been found to be weakly catalytic and therefore it appears that additional water molecules on the surface of the enzyme are not essential for this level of enzyme activity. © 1997 John Wiley & Sons, Inc.