Deletion polymorphism of the angiotensin I-converting enzyme gene in elderly patients with coronary heart disease

Controversy exists as to whether the deletion/deletion (DD) genotype of angiotensin l-converting enzyme (ACE) gene polymorphism is associated with coronary heart disease (CHD). There are only a few studies dealing with this issue in the elderly, also with controversial results. The aim of this study was the assessment of correlation between genetic markers and the risk of CHD in the elderly. The results indicated DD genotype importance for CHD in the elderly as proven by discriminant analysis (chi2 = 25.77; df = 16; p = 0.0620). However, the use of univariate method demonstrated no correlation between DD genotype of ACE gene polymorphism and coronary artery disease. D allele of ACE gene was associated with higher activities of ACE plasma. A weak, but increased risk of MI is associated with high frequency of DD genotype in the elderly. Strong correlation between ACE polymorphism and ACE plasma activities was demonstrated.     

Cardiac matrix metalloproteinase-2 expression independently induces marked ventricular remodeling and systolic dysfunction

Although enhanced cardiac matrix metalloproteinase (MMP)-2 synthesis has been associated with ventricular remodeling and failure, whether MMP-2 expression is a direct mediator of this process is unknown. We generated transgenic mice expressing active MMP-2 driven by the alpha-myosin heavy chain promoter. At 4 mo MMP-2 transgenic hearts demonstrated expression of the MMP-2 transgene, myocyte hypertrophy, breakdown of Z-band registration, lysis of myofilaments, disruption of sarcomere and mitochondrial architecture, and cardiac fibroblast proliferation. Hearts from 8-mo-old transgenic mice displayed extensive myocyte disorganization and dropout with replacement fibrosis and perivascular fibrosis. Older transgenic mice also exhibited a massive increase in cardiac MMP-2 expression, representing recruitment of endogenous MMP-2 synthesis, with associated expression of MMP-9 and membrane type 1 MMP. Increases in diastolic [control (C) 33 +/- 3 vs. MMP 51 +/- 12 microl; P = 0.003] and systolic (C 7 +/- 2 vs. MMP 28 +/- 14 microl; P = 0.003) left ventricular (LV) volumes and relatively preserved stroke volume (C 26 +/- 4 vs. MMP 23 +/- 3 microl; P = 0.16) resulted in markedly decreased LV ejection fraction (C 78 +/- 7% vs. MMP 48 +/- 16%; P = 0.0006). Markedly impaired systolic function in the MMP transgenic mice was demonstrated in the reduced preload-adjusted maximal power (C 240 +/- 84 vs. MMP 78 +/- 49 mW/microl(2); P = 0.0003) and decreased end-systolic pressure-volume relation (C 7.5 +/- 1.5 vs. MMP 4.7 +/- 2.0; P = 0.016). Expression of active MMP-2 is sufficient to induce severe ventricular remodeling and systolic dysfunction in the absence of superimposed injury.     

Macro-invertebrates in a dynamic river environment: analysis of time series from artificial substrates,using a ‘white box’ neural network modelling method

New statistical modelling methods, such as neural networks (NNs), allow us to take a step further in the understanding of complex relations in aquatic ecosystems. In this paper the results from the analysis of macro-invertebrate communities in a complex riverine environment are presented. We attempted to explain observed changes in species composition and abundance with neural network modelling methods and compared the results to linear regression. The NN method used is an improved form of the RF5 algorithm, developed to effectively discover numeric laws from data. RF5 uses Product Unit Networks (PUNs), which are in effect multivariate non-discrete power functions. The data set consisted of a 10-year time series of monthly samples of macro-invertebrates on artificial substrates in the rivers Rhine and Meuse in the Netherlands. During this period the invertebrate community has largely changed coinciding with the␣invasion of Ponto-Caspian crustaceans. We used physical–chemical data and data on the abundance of the invasive taxa Corophium curvispinum and Dikerogammarus villosis to explain the observed changes in the resident invertebrate community. The analyses showed temperature, abundance of invasive taxa and peak discharges as important factors. Comparison of the results from NN modelling to linear regression revealed that the factors temperature and abundance of Dikerogammarus villosis explained equally well in both cases. Only the neural network was able to use information on peak discharge and timing of the peak in the previous winter to improve model performances. Neural networks are known to yield excellent modelling results, a drawback however is their lack of transparency or their ‘black box’ character. The use of relatively easy interpretable (white box) PUNs allows us to investigate the extracted relations in more detail and can enhance our understanding of ecosystem functioning. Our results show that peak discharges might be an important factor structuring invertebrate communities in rivers and hint on the existence of interacting effects from invasive species and discharge peaks. They finally show the value of biological data sets that are collected over a long period and in a highly standardised way.     

Effects of willow nutrition and morphology on calving success of moose

Across much of North America, populations of moose (Alces alces) are declining because of disease, predation, climate change, and anthropogenic-driven habitat loss. Contrary to this trend, populations of moose in Colorado, USA, have continued to grow. Studying successful (i.e., persistent or growing) populations of moose can facilitate continued conservation by identifying habitat features critical to persistence of moose. We hypothesized that moose using habitat with higher quality willow (Salix spp.) would have a higher probability of having a calf-at-heel (i.e., calving success). We evaluated moose calving success using repeated ground observations of collared individuals with calves in an occupancy model framework to account for detection probability. We then evaluated the impact of willow habitat quality and nutrition on moose calving success by studying 2 spatially segregated populations of moose in Colorado. Last, we evaluated correlations between willow characteristics (browse intensity, height, cover, leaf length, and species) and willow nutrition (dry matter digestibility [DMD]) to assess the utility of using those characteristics to assess willow nutrition. We found willow height and cover had a high probability of being positively associated with higher individual-level calving success. Willow DMD, browse intensity, and leaf length were not predictive of individual moose calving success; however, the site with higher mean DMD consistently had higher mean estimates of calving success for the same year. Our results suggest surveying DMD is likely not a useful metric for assessing differences in calving success of individual moose but may be of use at population levels. Further, the assessment of willow morphology and density may be used to identify areas that support higher levels of moose calving success.     

Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis

Background

Insertion sequences (ISs) are approximately 1 kbp long “jumping” genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I (“cut-and-paste”) Mobile Genetic Elements. ISs are proposed to be involved in the reductive evolution of symbiotic prokaryotes. Our previous sequencing of the genome of the cyanobacterium ‘Nostoc azollae’ 0708, living in a tight perpetual symbiotic association with a plant (the water fern Azolla), revealed the presence of an eroding genome, with a high number of insertion sequences (ISs) together with an unprecedented large proportion of pseudogenes. To investigate the role of ISs in the reductive evolution of ‘Nostoc azollae’ 0708, and potentially in the formation of pseudogenes, a bioinformatic investigation of the IS identities and positions in 47 cyanobacterial genomes was conducted. To widen the scope, the IS contents were analysed qualitatively and quantitatively in 20 other genomes representing both free-living and symbiotic bacteria.

Results

Insertion Sequences were not randomly distributed in the bacterial genomes and were found to transpose short distances from their original location (“local hopping”) and pseudogenes were enriched in the vicinity of IS elements. In general, symbiotic organisms showed higher densities of IS elements and pseudogenes than non-symbiotic bacteria. A total of 1108 distinct repeated sequences over 500 bp were identified in the 67 genomes investigated. In the genome of ‘Nostoc azollae’ 0708, IS elements were apparent at 970 locations (14.3%), with 428 being full-length. Morphologically complex cyanobacteria with large genomes showed higher frequencies of IS elements, irrespective of life style.

Conclusions

The apparent co-location of IS elements and pseudogenes found in prokaryotic genomes implies earlier IS transpositions into genes. As transpositions tend to be local rather than genome wide this likely explains the proximity between IS elements and pseudogenes. These findings suggest that ISs facilitate the reductive evolution in for instance in the symbiotic cyanobacterium ‘Nostoc azollae’ 0708 and in other obligate prokaryotic symbionts.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1386-7) contains supplementary material, which is available to authorized users.     

Chronic mTOR inhibition in mice with rapamycin alters T,B, myeloid,and innate lymphoid cells and gut flora and prolongs life of immune‐deficient mice

The mammalian (mechanistic) target of rapamycin (mTOR) regulates critical immune processes that remain incompletely defined. Interest in mTOR inhibitor drugs is heightened by recent demonstrations that the mTOR inhibitor rapamycin extends lifespan and healthspan in mice. Rapamycin or related analogues (rapalogues) also mitigate age‐related debilities including increasing antigen‐specific immunity, improving vaccine responses in elderly humans, and treating cancers and autoimmunity, suggesting important new clinical applications. Nonetheless, immune toxicity concerns for long‐term mTOR inhibition, particularly immunosuppression, persist. Although mTOR is pivotal to fundamental, important immune pathways, little is reported on immune effects of mTOR inhibition in lifespan or healthspan extension, or with chronic mTOR inhibitor use. We comprehensively analyzed immune effects of rapamycin as used in lifespan extension studies. Gene expression profiling found many and novel changes in genes affecting differentiation, function, homeostasis, exhaustion, cell death, and inflammation in distinct T‐ and B‐lymphocyte and myeloid cell subpopulations. Immune functions relevant to aging and inflammation, and to cancer and infections, and innate lymphoid cell effects were validated in vitro and in vivo. Rapamycin markedly prolonged lifespan and healthspan in cancer‐ and infection‐prone mice supporting disease mitigation as a mechanism for mTOR suppression‐mediated longevity extension. It modestly altered gut metagenomes, and some metagenomic effects were linked to immune outcomes. Our data show novel mTOR inhibitor immune effects meriting further studies in relation to longevity and healthspan extension.     

A general model for ontogenetic growth under food restriction

Food restriction (FR) retards animals' growth. Understanding the underlying mechanisms of this phenomenon is important to conceptual problems in life-history theory, as well as to applied problems in animal husbandry and biomedicine. Despite a considerable amount of empirical data published since the 1930s, there is no relevant general theoretical framework that predicts how animals vary their energy budgets and life-history traits under FR. In this paper, we develop such a general quantitative model based on fundamental principles of metabolic energy allocation during ontogeny. This model predicts growth curves under varying conditions of FR, such as the compensatory growth, different age at which FR begins, its degree and its duration. Our model gives a quantitative explanation for the counterintuitive phenomenon that under FR, lower body temperature and lower metabolism lead to faster growth and larger adult size. This model also predicts that the animals experiencing FR reach the same fraction of their adult mass at the same age as their ad libitum counterparts. All predictions are well supported by empirical data from mammals and birds of varying body size, under different conditions of FR.     

Reproducibility of protein identification of selected cell types in Barrett's esophagus analyzed by combining laser-capture microdissection and mass spectrometry

Barrett's esophagus (BE) is associated with increased risk of esophageal adenocarcinoma (EAC) and characterized by replacement of normal esophageal squamous epithelium by columnar epithelium. These alterations are also reflected in changes in the protein-expression profiles of the cell types involved. To separately investigate the proteomes of selected cell-types we combined laser-capture microdissection (LCM) and liquid chromatography-mass spectrometry (LC-MS). Aims were to determine the sensitivity, specificity, and technical reproducibility of the sampling method, and the biological variability within and between biopsies and patients. Frozen biopsies were cryo-sectioned, samples of around 2000 epithelial or stroma cells microdissected, digested and measured by Orbitrap LC-MS. Proteins were then identified by MS/MS database search and quantified by label-free analysis. An average of 366 protein-groups were identified per sample, and more protein-groups were found in epithelial samples than in stromal samples (442 vs 301, p < 0.0001). Altogether, 1254 distinct protein-groups were found, 289 and 88 of them significantly more often in epithelial and stroma samples, respectively. We assessed five different types of reproducibilities (run-to-run, intrabiopsy, biopsy-to-biopsy, experiment-to-experiment, and patient-to-patient) for protein identification and protein quantification. Reproducibility of protein identification ranged from 78 to 57%, and standard deviation of protein quantification was on patient-to-patient level four times higher than for run-to-run. We conclude that sampling around 2000 cells requires groups of 32 samples to detect significant, over 10-fold differences in protein abundances and thus creates a successful compromise between throughput and quality of results. We therefore believe that this method is suitable for investigating protein-expression profiles during carcinogenesis.