SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies.

BACKGROUND: SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It takes a guide gene tree as input and generates a gene sequence with its transcripts for each node of the tree, from the root to the leaves. However, the sets of transcripts simulated at different nodes of the guide gene tree lack evolutionary connections. Consequently, SimSpliceEvol is not suitable for evaluating methods for transcript phylogeny inference or gene phylogeny inference that rely on transcript conservation. RESULTS: Here, we introduce SimSpliceEvol2, which, compared to the first version, incorporates an explicit model of transcript evolution for simulating alternative transcripts along the branches of a guide gene tree, as well as the transcript phylogenies inferred. We offer a comprehensive software with a graphical user interface and an updated version of the web server, ensuring easy and user-friendly access to the tool. CONCLUSION: SimSpliceEvol2 generates synthetic datasets that are useful for evaluating methods and tools for spliced RNA sequence analysis, such as spliced alignment methods, methods for identifying conserved transcripts, and transcript phylogeny reconstruction methods. The web server is accessible at https://simspliceevol.cobius.usherbrooke.ca , where you can also download the standalone software. Comprehensive documentation for the software is available at the same address. For developers interested in the source code, which requires the installation of all prerequisites to run, it is provided at  https://github.com/UdeS-CoBIUS/SimSpliceEvol .

Orthology and Paralogy Relationships at Transcript Level.

Eukaryotic genes undergo a mechanism called alternative processing, resulting in transcriptome diversity by allowing the production of multiple distinct transcripts from a gene. More than half of human genes are affected, and the resulting transcripts are highly conserved among orthologous genes of distinct species. In this work, we present the definition of orthology and paralogy between transcripts of homologous genes, together with an algorithm to compute clusters of conserved orthologous and paralogous transcripts. Gene-level homology relationships are utilized to define various types of homology relationships between transcripts originating from the same ancestral transcript. A Reciprocal Best Hits approach is employed to infer clusters of isoorthologous and recent paralogous transcripts. We applied this method to transcripts from simulated gene families as well as real gene families from the Ensembl-Compara database. The results are consistent with those from previous studies that compared orthologous gene transcripts. Furthermore, our findings provide evidence that searching for conserved transcripts between homologous genes, beyond the scope of orthologous genes, is likely to yield valuable information.

From pairwise to multiple spliced alignment.

Motivation: Alternative splicing is a ubiquitous process in eukaryotes that allows distinct transcripts to be produced from the same gene. Yet, the study of transcript evolution within a gene family is still in its infancy. One prerequisite for this study is the availability of methods to compare sets of transcripts while accounting for their splicing structure. In this context, we generalize the concept of pairwise spliced alignments (PSpAs) to multiple spliced alignments (MSpAs). MSpAs have several important purposes in addition to empowering the study of the evolution of transcripts. For instance, it is a key to improving the prediction of gene models, which is important to solve the growing problem of genome annotation. Despite its essentialness, a formal definition of the concept and methods to compute MSpAs are still lacking. Results: We introduce the MSpA problem and the SplicedFamAlignMulti (SFAM) method, to compute the MSpA of a gene family. Like most multiple sequence alignment (MSA) methods that are generally greedy heuristic methods assembling pairwise alignments, SFAM combines all PSpAs of coding DNA sequences and gene sequences of a gene family into an MSpA. It produces a single structure that represents the superstructure and models of the gene family. Using real vertebrate and simulated gene family data, we illustrate the utility of SFAM for computing accurate gene family superstructures, MSAs, inferring splicing orthologous groups and improving gene-model annotations. Availability and implementation: The supporting data and implementation of SFAM are freely available at https://github.com/UdeS-CoBIUS/SpliceFamAlignMulti. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

A systematic review on MEG and its use in the presurgical evaluation of localization-related epilepsy.

BACKGROUND: Magnetoencephalography (MEG), also referred to as magnetic source imaging (MSI) when combined with structural imaging, provides a new, noninvasive tool for epilepsy localization. In contrast to EEG, the magnetic fields generated by electrical discharges are minimally affected by intervening tissue layers. The purpose of this study was to determine the effectiveness of MEG/MSI in the presurgical evaluation of localization-related epilepsies by means of a systematic review. METHODS: We searched MEDLINE, the Cochrane library, and EMBASE between 1987 and 2006 for English articles. References of reviews and book chapters were searched. In addition, we contacted experts in MEG and epilepsy. Studies including a minimum of four patients with at least 6 months follow-up after surgery were reviewed. In each study, surgical outcome (seizure freedom) was correlated with the concordance of MEG source localization and resection area. RESULTS: The literature search generated 192 articles. Twenty-eight papers satisfied the inclusion criteria. Eleven of the 28 articles were excluded due to an inability to determine the concordance between the MEG epileptic focus and the resected area based on the published data. Analysis of the 17 remaining studies allowed us to obtain sensitivity (range: 0.20-1.0) values for all articles, and specificity (0.06-1.00) values, positive likelihood ratios (0.67-2.0) and negative likelihood ratios (0.40-2.13) for some articles. CONCLUSIONS: There is insufficient evidence in the current literature to support the relationship between the use of MEG in surgical planning and seizure-free outcome after epilepsy surgery. Additional studies are needed.

Hyperinsulinemia in colon, stomach and breast cancer patients.

The objective of this study was to collect more information on the intricate relationship between the presence of a tumor, insulin status and blood lipids. We selected non-obese subjects suffering from colon, stomach and breast cancer and determined the concentration of fasting insulin, glucose, cholesterol, and triglycerides in blood before (BS) and after surgery (AS). Controls were healthy non-obese subjects. Insulin was also measured in tumors and non-cancerous tissues from the same organ. BS insulin and glucose (with the exception of glucose in colon patients) were significantly higher than the controls and fell to almost normal levels at AS. Serum cholesterol and triglycerides levels were reduced in stomach patients, BS and AS and cholesterol in colon patients BS. Tumors had 1.9-3.0 times as much insulin, or insulin-like substances, as control tissues. These results are consistent with our previous studies showing hyperinsulinemia in the presence of a tumor.

Subcutaneous, omentum and tumor fatty acid composition, and serum insulin status in patients with benign or cancerous ovarian or endometrial tumors. Do tumors preferentially utilize polyunsaturated fatty acids?

The relationships between the fatty acid composition of cancerous endometrium and ovary, and peripheral adipose tissues were studied in Israeli Jewish women, and are presented together since no differences were shown between them. The results suggest a mobilization of linoleic acid from subcutaneous and omental depots and its incorporation into tumors accompanied by a high degree of desaturation. High blood insulin concentrations characterized patients with stage I and II disease, and low concentrations characterized patients with advanced degrees of malignancy.

Suppression of tumor growth and metastasis by dietary fish oil combined with vitamins E and C and cisplatin.

PURPOSE: The anticancer activity of omega-3 polyunsaturated fatty acids (omega-3 PUFA) has been shown in a large number of studies. This study was undertaken to analyze the combined effect of omega-3 PUFA and antioxidative vitamins on the level of spontaneous metastatic dissemination. The supportive effect of this dietary combination on chemotherapy with cisplatin (CP) was determined in parallel. METHODS: C57BL/6J mice bearing the Lewis lung carcinoma 3LL were fed ad libitum one of three isocaloric diets containing 5% soybean oil supplemented with 40 mg/kg alpha-tocopherol acetate (SO diet), or 4% fish oil plus 1% corn oil, and basal amounts of vitamin E (FO diet) or FO diet supplemented with vitamins E and C (FO+E+C diet). These diets were tested in combination with the conventional cytotoxic agent CP in a series of regimens. Tumor growth, feed consumption, body weight, lung metastasis and lung histology were followed. RESULTS: Both the FO dietary groups showed significantly lower tumor development than the SO group in all examined parameters, indicating that omega-3 PUFA have anticancer activity. However, the FO diet, in comparison with the FO+E+C diet induced a significantly slower rate of tumor growth, and lower metastatic load, as reflected in lung weight. The decrease in the anticancer activity of FO by the addition of vitamins E and C suggests that in situ oxidation of omega-3 PUFA underlies their anticancer action. It is thus proposed that oxidized omega-3 PUFA accumulates in the membranes and the cytosol of tumor cells, reducing their vitality and eventually leading to their death. No signs of anorexia or cachexia were observed in either FO group, in contrast to the SO group. CP treatment with the SO diet had no apparent therapeutic effect, while with the FO diets it reduced the metastatic load. The best regimen of this combined treatment was FO diet followed by CP treatment with FO diet supplemented with vitamins E and C after resection of the primary growth. This regimen could be translated to a combined therapy for human cancer. CONCLUSIONS: Diets enriched with omega-3 PUFA may have beneficial anticancer effects in particular when containing only basal amounts of antioxidants such as vitamin E or C. Furthermore, the addition of drugs which promote oxidation of omega-3 PUFA, such as ferrous salts (e.g. as prescribed for the treatment of anemia), may further increase these effects. However, the supportive effect of omega-3 PUFA in chemotherapy (e.g. with CP) increases when vitamins E and C are also included.

Insulin-cancer relationships: possible dietary implication.

Insulin is a major anabolic hormone in mammals and its involvement in malignancies is well documented. An attempt is made to classify experimental and human cancers into four groups, according to the way the tumors are affected by, or interact with, insulin. Such an approach provides a better understanding of the dietary effects on tumorigenesis. Since human cancers are of the insulin-producing/secreting or insulin-dependent types, it is suggested that screening of individuals for blood insulin level and reducing the insulin status by dietary means may lead to a decreased risk of cancer. Anti-insulin drugs may be useful as supplements to therapeutic treatment.

Inhibition of adrenocortical function by intravenous administration of sodium pentobarbital in cocks.

The response of awake and anesthesized cocks with sodium pentobarbital to stressful stimuli has been examined. The stressful stimuli was immersion in cold water. In the awake cocks plasma corticosterone concentration was increased about 4 fold; they started shivering shortly after immersion and recovered after cessation of the treatment. In the anesthesized ones there was no increase in plasma corticosterone concentration, they did not shiver and died shortly after immersion.

Effects of stress on the corticosterone content of the blood plasma and adrenal gland of intact and bursectomized Gallus domesticus.

The response of intact and bursectomized chicks to stressful stimuli has been examined. The stressors imposed were: a. fast-acting ACTH adminstration; b. immersion in cold water; c. starvation. In Bursa-intact chicks the results were as follows: 1. Plasma corticosterone was increased by all stimuli. 2. Adrenal corticosterone was decreased by ACTH treatment while it was increased by immersion in cold water and by starvation. 3. Plasma glucose was increased by ACTH administration and cold water immersion and decreased by starvation of the birds. 4. Adrenal ascorbic acid concentration was not influenced by all stimuli. 5. Adrenal weights were found to be increased by ACTH and starvation treatments only. 6. Bursa weights were increased by ACTH administration. 7. A very low concentration of corticosterone was found in the Bursa of Fabricius. Bursectomized chicks differed from the intact ones in the following: 1. Plasma and adrenal corticosterone concentrations were not increased by starvation. 2. Plasma glucose increased moderately with ACTH administration. 3. Adrenal ascorbic acid was depleted by all stimuli but was not related to the corticosterone level in the adrenals and blood plasma.

[The effect of omega-3 fatty acids on risk factors for cardiovascular diseases].

UNLABELLED: Cardiovascular disease (CVD) is associated with dyslipidemia and frequently with insulin resistance, both of which are in general no alleviated by antilipidemic drugs. Our objective was to examine whether a dietary supplement containing omega-3 fatty acids (n-3 FA) can reduce the levels of serum lipids, fasting insulin and glucose in documented CVD patients treated by statins or bezafibrates. In a double-blind placebo-controlled trial of parallel design, 52 patients, age 69.2 years +/- 3.6 treated by antilipidemic drugs, were randomly assigned to receive daily 7 gr of a dietary concentrated supplement containing 67% n-3 FA (185 mg EPA and 465 mg/g DHA) in a form of spread (Yamega Ltd, Israel) or olive oil spread (placebo) and recommended to reduce the consumption of omega-6 fatty acids for 12 weeks. The average values +/- SD before and after dietary supplementations were compared. RESULTS: 44 patients (23 in the n-3 FA group) completed the study. In the n-3FA group we observed a significant decrease (p < 0.05) of total cholesterol (12.2%). LDL-cholesterol (16.8%), triglycerides (36.1%), insulin in hyperinsulinemic subjects (> 20 microunits/ml) (34.9%), and no significant changes in HDL-cholesterol and glucose. No hyperglycemia was detected. In the olive oil group we observed a significant decrease (p < 0.05) in the LDL-cholesterol values of 15.5% and no significant changes in the other parameters. No side effects were reported during the study in any of the participants. Our findings demonstrate that the incorporation of the dietary supplement containing EPA and DHA omega-3 fatty acids reduces significantly the above risk factors for CVD.

Insulin-tumour interrelationships in thymoma bearing mice. Effects of dietary glucose and fructose.

Control (C) or Thymoma (T) implanted male C57BL/6J mice received a basal diet containing 16.5% glucose (G) or fructose (F). Compared to the C-G group, the C-F mice consumed more food and less water, and gained more weight. The blood glucose, insulin and triglyceride levels were higher in the C-F than in the C-G mice. Thymoma implantation into the right flank caused a transient decrease in body weight followed by a steady increase due to tumour growth. Tumours were detected earlier and tumour size was greater in the T-F group than in the T-G mice. Tumour chemical composition was similar in both groups. Blood analysis showed that the T mice had lower glucose and higher insulin and triglyceride levels than the C group. Carcasses from the T groups contained more water and ash and less fat than their C counterparts, but the type of sugar did not affect the body composition of the C or T groups. The results suggest that dietary fructose may enhance the growth of tumour via its hyperinsulinaemic action.

Diet and disease--the Israeli paradox: possible dangers of a high omega-6 polyunsaturated fatty acid diet.

Israel has one of the highest dietary polyunsaturated/saturated fat ratios in the world; the consumption of omega-6 polyunsaturated fatty acids (PUFA) is about 8% higher than in the USA, and 10-12% higher than in most European countries. In fact, Israeli Jews may be regarded as a population-based dietary experiment of the effect of a high omega-6 PUFA diet, a diet that until recently was widely recommended. Despite such national habits, there is paradoxically a high prevalence of cardiovascular diseases, hypertension, non-insulin-dependent diabetes mellitus and obesity-all diseases that are associated with hyperinsulinemia (HI) and insulin resistance (IR), and grouped together as the insulin resistance syndrome or syndrome X. There is also an increased cancer incidence and mortality rate, especially in women, compared with western countries. Studies suggest that high omega-6 linoleic acid consumption might aggravate HI and IR, in addition to being a substrate for lipid peroxidation and free radical formation. Thus, rather than being beneficial, high omega-6 PUFA diets may have some long-term side effects, within the cluster of hyperinsulinemia, atherosclerosis and tumorigenesis.

Insulin-tumour interrelationship in EL4 lymphoma or thymoma-bearing mice. I. Alloxan-diabetic or non-diabetic mice.

A study has been carried out in which a comparison was made between EL4 lymphoma (assumed to be an insulin-producing secreting tumour) and thymoma (an insulin-dependent tumour). Tumour development and incidence, 3H-thymidine incorporation and insulin content in tumours, the host's food intake, blood insulin, glucose and cholesterol were determined in non-diabetic and alloxan-diabetic mice. Whereas no significant differences were observed between the diabetic and non-diabetic EL4 tumour-bearing mice, the diabetic, thymoma tumour-bearing mice showed reduced tumour growth and lower tumour incidence as compared with their non-diabetic counterparts. Insulin administration to diabetic tumour bearing mice, enhanced 3H-thymidine incorporation in the thymoma tumour cells only, and the insulin content of the EL4 tumours was found to be higher than that of the thymoma tumours. Rapid diabetes remission was observed in the diabetic, EL4 tumour-bearing mice as compared with the thymoma tumour-bearing mice.

Insulin-tumour interrelationships in EL4-lymphoma or thymoma-bearing mice. II. Effects of dietary omega-3 and omega-6 polyunsaturated fatty acids.

Male C57BL/65 mice received a basal diet supplemented with 4% soya-bean oil, linseed oil or fish oil, in which the major polyunsaturated fatty acids were linoleic acid, alpha-linolenic acid and long chain omega-3 fatty acids, respectively. Groups of animals were injected into the right flank with EL4-lymphoma cells, others with thymoma cells. Tumour implantation caused a gradual decrease in food consumption with both types of tumour, while body weight increased, especially in the EL4-bearing animals receiving the soya-bean diet. The weight gain was due to body water accumulation and was accompanied by decreases in body fat and minor changes in carcass protein and ash contents. The dietary treatments did not produce significant differences in tumour incidence and mortality, but tumour size was decreased by diets supplying omega-3 fatty acids: in the EL4 mice tumour weight was markedly depressed by linseed oil, compared to soya-bean oil, whereas thymoma tumour weight was lowest in mice receiving fish oil and highest in the soya-bean oil group. Both types of tumour caused pronounced hypoglycaemia and hyperinsulinaemia in the hosts, and the effect was modulated by the diets in the EL4 but not in the thymoma animals: the plasma glucose level was especially low in the linseed oil group and relatively highest in the soya-bean oil treatment. The degree of hyperinsulinaemia depended on the diet only in the thymoma-bearing mice, with linseed and fish oils producing higher insulin levels than soya-bean oil. A slight hyperinsulinaemia was also observed in linseed and fish oil-fed control mice. Serum triglycerides were elevated in tumour-bearing animals, without consistent differences between dietary treatments. Although no clear pattern emerged concerning total cholesterol and LDL levels, HDL values were strongly affected by the type of oil: in the control animals linseed oil caused an increase in HDL-cholesterol compared to the other two oils. The thymoma-bearing mice responded to the linseed and fish oil diets with greatly elevated HDL-cholesterol levels. The results point to important differences in the responses of the two implanted tumours and hosts not only to the omega-6 and omega-3 fatty acids, but also to the type of dietary omega-3 fatty acids, namely alpha-linolenic acid and long chain fish oil polyunsaturated fatty acids.

Insulin and glucose status, tissue and plasma lipids in patients with tumours of the ovary or endometrium: possible dietary implications.

The relationship between tumour growth, insulin status, blood lipids and adipose linoleic acid (LA, reflecting long-term LA intake) was studied in 19 Jewish women suffering from early and advanced stages (ES and AS) of ovarian and endometrial tumours. Blood insulin in patients with ES tumours was four times higher than the control value in cancer-free subjects, but fell to normal levels at AS and after ES surgery (PES). Tumours and abdominal adipose tissue (AAT) had 4-6 and 1.4-1.7 times as much insulin as non-cancerous control organs. Serum total cholesterol (CHOL) and LDL-cholesterol were high at ES, dropped below normal at AS, but normalised at PES, while HDL-cholesterol increased after ES surgery. Linoleic acid in subcutaneous adipose tissue (SAT) was high in controls (26.4 + 1.5% of total fatty acids), but lower in cancer patients (20.5 + 3.7%, P < 0.05), while palmitic acid showed the opposite change. The results suggest mobilisation of glucose, cholesterol and linoleic acid for the supply of energy and structural lipids to rapidly multiplying tumour cells and possibly for prostaglandin synthesis. They also raise the question of whether the high linoleic acid intake by the Jewish population in Israel predisposes individuals to tumour development.