Calcium content and distribution as a function of growth and transformation in the mouse 3T3 cell

Total Ca content and that fraction of Ca sensitive to removal by the chelator ethylene glycol-bis(β-aminoethyl ether)N,N,N',N'-tetraacetate (EGTA) have been investigated in the mouse 3T3 cell as a function of growth stage, transformation with SV40 virus, and serum levels of the media. Cells were allowed to grow through several doublings in media containing (45)Ca. The cellular content of (45)Ca was used to access total cell Ca. That fraction of (45)Ca removed by EGTA was presumed to represent primarily surface-localized Ca. The data are expressed on a per cell volume basis to compensate for size differences as a function of growth stage and transformation. During exponential growth phase, the 3T3 cell contains 525pmol Ca/μl cell volume. Of this, approx. 457 pmol/μl is not removable by EGTA and, presumably, is cytoplasmically located. This value is in close agreement with previous studies on the HeLa cell (470 pmol Ca/μl cell water after the removal of the surface Ca). The low level of EGTA- removable Ca present in the 3T3 cell during early exponential growth (68 pmol Ca/μl cell volume) increases progressively with increasing cell density, and upon quiescence it is sevenfold greater. In contrast, SV40- transformed 3T3 cells growing exponentially possess total levels of Ca which are approximately two-thirds the levels of the normal 3T3 cell. However, their EGTA-sensitive Ca is not significantly different from that of exponentially growing, normal 3T3 cells. As the transformed cells continue to grow at high density, their total ca and their sensitivity to EGTA do not change, in contrast to the normal 3T3 cell. Thus, an increase in Ca associated with the cell surface appears to be correlated with growth inhibition. This has been investigated further by regulating growth of the normal and transformed cell with alterations in the serum level of the media. In 4 percent calf serum the normal cell is stopped from continued proliferation. Growth stoppage under these conditions is characterized by a nearly fourfold increase in EGTA-removable Ca, similar to the increase observed upon quiescence in depleted 10 percent serum. Similar treatment of the transformed cell does not reduce its growth rate, nor does it significantly alter Ca distribution. However, at 0.5 percent medium serum levels, the SV40 3T3 growth rate is substantially reduced and, under these conditions, EGTA-removable Ca increases twofold.     

The Mio-Pliocene European primate fossil record: dynamics and habitat tracking

We present here a study of European Neogene primate occurrences in the context of changing humidity. We studied the differences of primate localities versus non-primate localities by using the mammal communities and the ecomorphological data of the taxa present in the communities. The distribution of primates is influenced by humidity changes during the whole Neogene, and the results suggest that the primates track the changes in humidity through time. The exception to this is the Superfamily Cercopithecoidea which shows a wider range of choices in habitats. All primate localities seem to differ from non-primate localities in that the mammal community structure is more closed habitat oriented, while in non-primate localities the community structure changes towards open-habitat oriented in the late Neogene. The differences in primate and non-primate localities are stronger during the times of deep environmental change, when primates are found in their preferred habitats and non-primate localities have faunas better able to adapt to changing conditions.     

Recombinant adeno-associated virus type 2-mediated gene delivery into the <Emphasis Type="Italic">Rpe65</Emphasis><Superscript>-/-</Superscript> knockout mouse eye results in limited rescue

Background  

Leber's congenital amaurosis (LCA) is a severe form of retinal dystrophy. Mutations in the RPE65 gene, which is abundantly expressed in retinal pigment epithelial (RPE) cells, account for approximately 10–15% of LCA cases. In this study we used the high turnover, and rapid breeding and maturation time of the Rpe65 ^-/- knockout mice to assess the efficacy of using rAAV-mediated gene therapy to replace the disrupted RPE65 gene. The potential for rAAV-mediated gene treatment of LCA was then analyzed by determining the pattern of RPE65 expression, the physiological and histological effects that it produced, and any improvement in visual function.     

THE IMPACT OF REGIONAL CLIMATE ON THE EVOLUTION OF MAMMALS: A CASE STUDY USING FOSSIL HORSES

One of the classic examples of faunal turnover in the fossil record is the Miocene transition from faunas dominated by anchitheriine horses with low-crowned molar teeth to faunas with hipparionine horses characterized by high-crowned teeth. The spread of hipparionine horses is associated with increased seasonality and the expansion of open habitats. It is generally accepted that anchitheriine horses did not display an evolutionary increase in tooth crown height prior to their extinction. Nevertheless, to test whether anchitheriines showed any changes interpretable as adaptation to local conditions, we analyzed molar teeth from multiple populations of Anchitherium in three dimensions. Our results show differences in tooth morphology that suggest incipient hypsodonty in Spain, the first region experiencing increasingly arid conditions in the early Miocene of Europe. Furthermore, analyses of tooth wear show that Spanish specimens cluster with present ungulates that eat foliage together with grasses and shrubs, whereas German specimens cluster with present-day ungulates that eat mostly foliage. Taken together, even a taxon such as Anchitherium , with a long and successful history of forest adaptation, did respond to regional environmental changes in an adaptive manner.     

Importance of factors determining the effective lifetime of a mass, long-lasting, insecticidal net distribution: a sensitivity analysis

Background

Long-lasting insecticidal nets (LLINs) reduce malaria transmission by protecting individuals from infectious bites, and by reducing mosquito survival. In recent years, millions of LLINs have been distributed across sub-Saharan Africa (SSA). Over time, LLINs decay physically and chemically and are destroyed, making repeated interventions necessary to prevent a resurgence of malaria. Because its effects on transmission are important (more so than the effects of individual protection), estimates of the lifetime of mass distribution rounds should be based on the effective length of epidemiological protection.

Methods

Simulation models, parameterised using available field data, were used to analyse how the distribution's effective lifetime depends on the transmission setting and on LLIN characteristics. Factors considered were the pre-intervention transmission level, initial coverage, net attrition, and both physical and chemical decay. An ensemble of 14 stochastic individual-based model variants for malaria in humans was used, combined with a deterministic model for malaria in mosquitoes.

Results

The effective lifetime was most sensitive to the pre-intervention transmission level, with a lifetime of almost 10 years at an entomological inoculation rate of two infectious bites per adult per annum (ibpapa), but of little more than 2 years at 256 ibpapa. The LLIN attrition rate and the insecticide decay rate were the next most important parameters. The lifetime was surprisingly insensitive to physical decay parameters, but this could change as physical integrity gains importance with the emergence and spread of pyrethroid resistance.

Conclusions

The strong dependency of the effective lifetime on the pre-intervention transmission level indicated that the required distribution frequency may vary more with the local entomological situation than with LLIN quality or the characteristics of the distribution system. This highlights the need for malaria monitoring both before and during intervention programmes, particularly since there are likely to be strong variations between years and over short distances. The majority of SSA's population falls into exposure categories where the lifetime is relatively long, but because exposure estimates are highly uncertain, it is necessary to consider subsequent interventions before the end of the expected effective lifetime based on an imprecise transmission measure.     

Biomine: predicting links between biological entities using network models of heterogeneous databases

ABSTRACT: BACKGROUND: Biological databases contain large amounts of data concerning the functions and associationsof genes and proteins. Integration of data from several such databases into a single repositorycan aid the discovery of previously unknown connections spanning multiple types ofrelationships and databases. RESULTS: Biomine is a system that integrates cross-references from several biological databases into agraph model with multiple types of edges, such as protein interactions, gene-diseaseassociations and gene ontology annotations. Edges are weighted based on their type,reliability, and informativeness. We present Biomine and evaluate its performance in linkprediction, where the goal is to predict pairs of nodes that will be connected in the future,based on current data. In particular, we formulate protein interaction prediction and diseasegene prioritization tasks as instances of link prediction. The predictions are based on aproximity measure computed on the integrated graph. We consider and experiment withseveral such measures, and perform a parameter optimization procedure where different edgetypes are weighted to optimize link prediction accuracy. We also propose a novel method fordisease-gene prioritization, defined as finding a subset of candidate genes that cluster togetherin the graph. We experimentally evaluate Biomine by predicting future annotations in thesource databases and prioritizing lists of putative disease genes. CONCLUSIONS: The experimental results show that Biomine has strong potential for predicting links when aset of selected candidate links is available. The predictions obtained using the entire Biominedataset are shown to clearly outperform ones obtained using any single source of data alone,when different types of links are suitably weighted. In the gene prioritization task, anestablished reference set of disease-associated genes is useful, but the results show that underfavorable conditions, Biomine can also perform well when no such information is available.The Biomine system is a proof of concept. Its current version contains 1.1 million entities and8.1 million relations between them, with focus on human genetics. Some of its functionalitiesare available in a public query interface at http://biomine.cs.helsinki.fi, allowing searching forand visualizing connections between given biological entities.     

First detection, isolation and molecular characterization of infectious salmon anaemia virus associated with clinical disease in farmed Atlantic salmon (Salmo salar) in Chile

Background  

Several forms of progressive retinal atrophy (PRA) segregate in more than 100 breeds of dog with each PRA segregating in one or a few breeds. This breed specificity may be accounted for by founder effects and genetic drift, which have reduced the genetic heterogeneity of each breed, thereby facilitating the identification of causal mutations. We report here a new form of PRA segregating in the Border Collie breed. The clinical signs, including the loss of night vision and a progressive loss of day vision, resulting in complete blindness, occur at the age of three to four years and may be detected earlier through systematic ocular fundus examination and electroretinography (ERG).     

Clusterings should not be compared by visual inspection: response to Gagné & Proulx

In Heikinheimo et al . ( Journal of Biogeography , 2007, 34 , 1053–1064) we used clustering to analyse European land mammal fauna. Gagné & Proulx criticized our choice of the Euclidean distance measure in the analysis, and advocated the use of the Hellinger distance measure, claiming that this leads to very different clustering results. The criticism fails to take into account the probabilistic nature of the methods used and the fact that in this case the similarity measures correlate strongly. Gagné & Proulx used subjective inspection as the criterion of similarity between clusterings. We show that this is insufficient and misleading. Namely, owing to the local minimum problem, two clustering runs rarely give identical results. In the case of our study, the measured similarity (using the kappa statistic) between the Euclidean- and Hellinger-based clusterings is roughly equal to the similarity between two clusterings that both use the Hellinger distance but different random initialization points.     

Biogeography of European land mammals shows environmentally distinct and spatially coherent clusters

Aim  To produce a spatial clustering of Europe on the basis of species occurrence data for the land mammal fauna.
Location  Europe defined by the following boundaries: 11°W, 32°E, 71°N, 35°N.
Methods  Presence/absence records of mammal species collected by the Societas Europaea Mammalogica with a resolution of 50 × 50 km were used in the analysis. After pre-processing, the data provide information on 124 species in 2183 grid cells. The data were clustered using the k -means and probabilistic expectation maximization (EM) clustering algorithms. The resulting geographical pattern of clusters was compared against climate variables and against an environmental stratification of Europe based on climate, geomorphology and soil characteristics (EnS).
Results  The mammalian presence/absence data divide naturally into clusters, which are highly connected spatially and most strongly determined by the small mammals with the highest grid cell incidence. The clusters reflect major physiographic and environmental features and differ significantly in the values of basic climate variables. The geographical pattern is a fair match for the EnS stratification and is robust between non-overlapping subsets of the data, such as trophic groups.
Main conclusions  The pattern of clusters is regarded as reflecting the spatial expression of biologically distinct, metacommunity-like entities influenced by deterministic forces ultimately related to the physical environment. Small mammals give the most spatially coherent clusters of any subgroup, while large mammals show stronger relationships to climate variables. The spatial pattern is mainly due to small mammals with high grid cell incidence and is robust to noise from other subsets. The results support the use of spatially resolved environmental reconstructions based on fossil mammal data, especially when based on species with the highest incidence.