Infantile neuronal ceroid-lipofuscinosis is not an allelic form of Batten disease: exclusion of chromosome 16 region with linkage analyses

Infantile neuronal ceroid-lipofuscinosis (CLN1) is the form of neuronal ceroid-lipofuscinoses (NCL) with the earliest onset of symptoms. The locus of the most common form of these disorders, juvenile NCL (CLN3), has been mapped to chromosome 16. We report here linkage data of the same region in Finnish CLN1 families. Our results indicate that CLN1 is not allelic with CLN3 but represents a different locus, which is not located within about 70 cM in chromosome 16.     

Water chemistry of Lake Ladoga and Russian-Finnish intercalibration of analyses

As part of the Russian-Finnish research studies on Lake Ladoga, joint expeditions were organized in 1992 and 1993. Water samples were collected for intercalibration of chemical analysis methods and to monitor the chemical quality of the lake water.In August of 1992 water samples were taken from northern Lake Ladoga for intercalibration of Russian and Finnish analysis methods. In August 1993 water samples were collected from 23 sampling stations in all parts of the lake; some of these were also used for intercalibration purposes.The oxygen, colour and COD_Mn results were at the same level in the intercalibration. In 1993, the P_tot results obtained were acceptable. In N_tot, Fe and Mn analysis there seemed to be systematic and random errors between some results.The Secchi depth ranged from 1.5 m to 3.3 m. The average concentrations for the total phosphorus ranged from 15 µg 1^–1 to 29 µg 1^–1. The total nitrogen values were from 620 µg 1^–1 to 690 µg 1^–1. The N:P ratio varied from 24 to 40. The concentration of phosphorus indicated mesotrophic or even eutrophic conditions in the lake. Phosphorus seemed to be the limiting nutrient to bacteria and algae.     

Effect of growth temperature on lipid fatty acids of four fungi (Aspergillus niger,Neurospora crassa,Penicillium chrysogenum,andTrichoderma reesei)

The effect of growth temperature on the lipid fatty acid composition was studied over a temperature range from 35 to 10° C with 5° C intervals in four exponentially growing fungi: Aspergillus niger, Neurospora crassa, Penicillium chrysogenum, and Trichoderma reesei. Fatty acid unsaturation increased in A. niger, P. chrysogenum, and T. reesei when the temperature was lowered to 20–15, 20, and 26–20° C, respectively. In A. niger and T. reesei, this was due to the increase in linolenic acid content. In P. chrysogenum, the linolenic acid content increased concomitantly with a more pronounced decrease in the less-unsaturated fatty acid, oleic acid, and in palmitic and linoleic acids; consequently, the fatty acid content decreased as the temperature was lowered to 20° C. In T. reesei, when the growth temperature was reduced below 26–20° C, fatty acid unsaturation decreased since the mycelial linolenic acid content decreased. In A. niger and P. chrysogenum, the mycelial fatty acid content increased greatly at temperatures below 20–15° C. In contrast, in N. crassa, fatty acid unsaturation was nearly temperature-independent, although palmitic and linoleic acid contents clearly decreased when the temperature was lowered between 26 and 20° C; concomitantly, the growth rate decreased. Therefore, large differences in the effects of growth temperature on mycelial fatty acids were observed among various fungal species. However, the similarities found may indicate common regulatory mechanisms causing the responses. Received: 1 March 1995 / Accepted: 8 May 1995     

Thallium inhibition of ouabain-sensitive sodium transport and of the (Na+K)-ATPase in human erythrocytes

The influence of Tl⁺ on Na⁺ transport and on the ATPase activity in human erythrocytes was studied. 0.1–1.0 mM Tl⁺ added to a K⁺-free medium inhibited the ouabain-sensitive self-exchange of Na⁺ and activated both the ouabain-sensitive ²²Na outward transport and the transport related ATPase. 5–10 mM external Tl⁺ caused inhibition of the ouabain-sensitive ²²Na efflux as well as the (Na⁺ + Tl⁺)-ATPase. Competition between the internal Na⁺ and rapidly penetrating thallous ions at the inner Na⁺-specific binding sites of the erythrocyte membrane could account for the inhibitory effect of Tl⁺. An increase of the internal Na⁺ concentration in erythrocytes or in ghosts protected the system against the inhibitory effect of high concentration of Tl⁺. A protective effect of Na⁺ was also demonstrated on the (Na⁺ + Tl⁺)-ATPase of fragmented erythrocyte membranes studied at various Na⁺ and Tl⁺ concentrations.     

Male Distribution and Mate Searching in the Yellow Dung Fly Scathophaga stercoraria: Comparison between Paired and Unpaired Males

Movements by individual males were examined in the yellow dung fly, Scathophaga stercoraria. Males were observed from their arrival until they found a female (paired males) or departed (unpaired males). The focal variables were the male mating status, body size and the number of males and females at the site. Paired males, independent of size, spent more time in the best mate-searching area (pat and the first up-wind zone) than unpaired males. Paired males in all size classes moved around and attacked other males more often than unpaired males. Among paired males, males that caught a single female and those that took over a female from another male were very similar in their mate-searching behaviour. The total time spent searching at the pat was positively related to its resource value as indicated by the number of pairs. Time spent in the best mate-searching area was negatively related with male numbers. The causes of differences in movements and aggression between paired and unpaired males are discussed. The male distribution around cow pats can be understood only if the differences in movement patterns by paired and unpaired males are taken into account.     

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

Background

The global effect of copy number and epigenetic alterations on miRNA expression in cancer is poorly understood. In the present study, we integrate genome-wide DNA methylation, copy number and miRNA expression and identify genetic mechanisms underlying miRNA dysregulation in breast cancer.

Results

We identify 70 miRNAs whose expression was associated with alterations in copy number or methylation, or both. Among these, five miRNA families are represented. Interestingly, the members of these families are encoded on different chromosomes and are complementarily altered by gain or hypomethylation across the patients. In an independent breast cancer cohort of 123 patients, 41 of the 70 miRNAs were confirmed with respect to aberration pattern and association to expression. In vitro functional experiments were performed in breast cancer cell lines with miRNA mimics to evaluate the phenotype of the replicated miRNAs. let-7e-3p, which in tumors is found associated with hypermethylation, is shown to induce apoptosis and reduce cell viability, and low let-7e-3p expression is associated with poorer prognosis. The overexpression of three other miRNAs associated with copy number gain, miR-21-3p, miR-148b-3p and miR-151a-5p, increases proliferation of breast cancer cell lines. In addition, miR-151a-5p enhances the levels of phosphorylated AKT protein.

Conclusions

Our data provide novel evidence of the mechanisms behind miRNA dysregulation in breast cancer. The study contributes to the understanding of how methylation and copy number alterations influence miRNA expression, emphasizing miRNA functionality through redundant encoding, and suggests novel miRNAs important in breast cancer.     

Leukemia Prediction Using Sparse Logistic Regression

We describe a supervised prediction method for diagnosis of acute myeloid leukemia (AML) from patient samples based on flow cytometry measurements. We use a data driven approach with machine learning methods to train a computational model that takes in flow cytometry measurements from a single patient and gives a confidence score of the patient being AML-positive. Our solution is based on an regularized logistic regression model that aggregates AML test statistics calculated from individual test tubes with different cell populations and fluorescent markers. The model construction is entirely data driven and no prior biological knowledge is used. The described solution scored a 100% classification accuracy in the DREAM6/FlowCAP2 Molecular Classification of Acute Myeloid Leukaemia Challenge against a golden standard consisting of 20 AML-positive and 160 healthy patients. Here we perform a more extensive validation of the prediction model performance and further improve and simplify our original method showing that statistically equal results can be obtained by using simple average marker intensities as features in the logistic regression model. In addition to the logistic regression based model, we also present other classification models and compare their performance quantitatively. The key benefit in our prediction method compared to other solutions with similar performance is that our model only uses a small fraction of the flow cytometry measurements making our solution highly economical.