Gene expression changes associated with cytotoxicity identified using cDNA arrays

In order to investigate gene expression changes associated with cytotoxicity, we used cDNA arrays to monitor the expression of over 5,000 genes in response to toxic stress in the HepG2 liver cell line. Cells were treated with cytotoxic doses of acetaminophen, caffeine or thioacetamide for nine time points ranging from 1 to 24 h. Samples of mRNA from each time point were used to prepare radiolabeled cDNA, which was hybridized to nylon-membrane-based cDNA arrays. High-stringency washes were applied to reduce cross-hybridization. Analysis of spot intensities revealed that each compound led to approximately 150-250 gene expression changes that were sustained over at least three adjacent time points. The affected genes could be classified into clusters based on their temporal patterns of differential expression. A common set of 44 genes showed similar expression changes in response to all three compounds. Of these changes, 90% could be confirmed by quantitative RT-PCR analysis. The results indicate that detailed array-based time-course studies, coupled with a sensitive and highly specific confirmation assay, provide a powerful means of identifying cytotoxicity-associated gene expression changes. Electronic Publication     

Use of Heteroduplex Mobility Analysis (HMA) for Differentiating Phytoplasma Isolates Causing Witches' Broom Disease on Populus nigra cv Italica and Stolbur or Big Bud Symptoms on Tomato

Heteroduplex mobility analysis (HMA) was performed to distinguish French and German isolates of phytoplasmas from Populus nigra cv Italica witches broom. The French isolate was similar to the phytoplasma responsible for the European aster yellows while the German isolate was different but closely related to it. When phytoplasmas inducing similar "stolbur" symptoms in tomato were compared to HMA, a high degree of genetic differences was observed among the reference stolbur C (StC) isolate, the European aster yellows and the other phytoplasmas inducing stolbur or big bud symptoms in tomato. Pseudo-stolbur B and D from Brazil were differentiated from the reference St C using this method.     

Computing the selection gradient and evolutionary response of an infinite-dimensional trait

 Following the results developed in a previous paper, an equation describing the evolutionary response to selection is extended from finite- to infinite-dimensional traits. The selection gradient and evolutionary response are then computed for a large class of infinite-dimensional traits of broad biological interest. In this framework, traits are modeled as Gaussian processes, and reproducing kernel Hilbert spaces constitute a primary tool. Received 12 September 1996     

Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer

Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.     

High day-to-day repeatability of lower extremity muscle activation patterns and joint biomechanics of dual-belt treadmill gait: A reliability study in healthy young adults

PurposeThe reliability of lower extremity muscle activation patterns has not been clearly studied in a dual-belt instrumented treadmill environment. The primary study objective was to quantify the day-to-day reliability of quadriceps, hamstrings, gastrocnemius and gluteus medius activation patterns in healthy young adult gait. Secondarily, the reliability of spatiotemporal, and knee/hip motion and moment-based gait outcomes was assessed.Scope: 20 young adults were recruited and tested on two separate days. Using standardized procedures, participants were prepared for surface electromyography and lower extremity motion capture. All individuals walked on a dual-belt instrumented treadmill while muscle activation, segment motions and ground reaction forces were recorded. Sagittal plane motion and net external sagittal and frontal plane moments were calculated. Discrete biomechanical and muscle activation measures were calculated, and non-negative matrix factorization extracted amplitude and temporal muscle activation features. Intraclass Correlation Coefficients, Standard Error of Measurement and Minimum Detectable Change were calculated.ConclusionsHigh to excellent Intraclass correlation coefficients were found between visits for most primary and secondary outcomes. The absolute and relative reliability, including Minimum Detectable Change values, provided in this study support the use of dual-belt instrumented treadmill walking as an acceptable medium to collect biomechanical and lower extremity EMG outcomes for future studies.     

Variation in mating system among birds: ecological basis revealed by hierarchical comparative analysis of mate desertion

Since most bird species are socially monogamous, variation among species in social mating systems is determined largely by variation in the frequency of mate desertion. Mate desertion is expected to occur when the benefits, in terms of additional reproductive opportunities, outweigh the costs, in terms of reduced reproductive success from the present brood. However, despite much research, the relative importance of costs and benefits in explaining mating system variation is not well understood. Here, we investigate this problem using a comparative method. We analyse changes in the frequency of mate desertion at different phylogenetic levels. Differences between orders and families in the frequency of desertion are negatively associated with changes in the potential costs of desertion, but are not associated with changes in the potential benefits of desertion. Conversely, differences among genera and species in the frequency of desertion are positively associated with increases in the potential benefits of desertion, but not with changes in the potential costs of desertion. Hence, we suggest that mate desertion in birds originates through a combination of evolutionary predisposition and ecological facilitation. In particular, ancient changes in life-history strategy determine the costs of desertion and predispose certain lineages to polygamy, while contemporary changes in the distribution of resources determine the benefits of desertion and thereby the likelihood that polygamy will be viable within these lineages. Thus, monogamy can arise via two very different evolutionary pathways. Groups such as albatrosses (Procellariidae) are constrained to social monogamy by the high cost to desertion, irrespective of the potential benefits. However, in groups such as the accentors (Prunellidae), which are predisposed to desertion, monogamy occurs only when the benefits of desertion are very limited. These conclusions emphasise the additional power which a hierarchical approach contributes to the modern comparative method.     

Cloning of the cellulase gene from Penicillium funiculosum and its expression in Escherichia coli

A gene of Penicillium funiculosum encoding an endoglucanase was cloned and expressed in Escherichia coli using the lacZ promoter of vector pUC 18. The gene product hydrolyzed carboxymethyl cellulose and showed strong cross reactivity with P. funiculosum anticellulases.     

Relationship between molecular and enological features of Patagonian wine yeasts: relevance in selection protocols

Summary In this paper, a study of the relationship between genetic patterns, obtained by the combination of mtDNA-RFLP and PCR-amplified inter-δ sequence DNA polymorphism analysis, and relevant enological phenotypic data (fermentative power, specific productivity, volatile and total acidity) was carried out on Argentinean Saccharomyces cerevisiae isolates from north Patagonia. The use of a powerful statistical tool, Generalized Procrustes analysis, allowed us to weigh the relationship for each isolate in particular, denoting a good enough degree of agreement between molecular and physiological data for most of the population analysed. The inclusion of a physiological feature, as the killer sensitivity biotype, within identification methods resulted in a higher degree of discrimination among isolates and in better correlation between both characterizations. The combined use of methods based on molecular polymorphisms and killer biotype could be applied so as not to miss any isolate with differential enological properties in selection protocols.