An evolutionary approach reveals a high protein-coding capacity of the human genome

We developed a new evolutionary method for identifying exons from genomic sequences and found 19000 potential coding exons that are absent from all existing annotations of the human genome. Of these, 13700 satisfied very stringent criteria and can with confidence be considered as novel exons. Evidently, a large number of new human genes can be identified using evolutionary approaches.     

Respiratory electron transport system (ETS) activity as an estimator of the thermal tolerance of two Daphnia hybrids

The influence of temperature on the activity of the respiratoryelectron transport system (ETS) was measured in one clone ofDaphnia hyalina x galeata and one of Daphnia cucullata x galeata,isolated from Lake Bled (Slovenia). The ETS activity of ovigerousfemales acclimated to 7, 20 and 25°C, was measured at 5,10, 15, 20, 25 and 30°C. Population growth experiments showedthat D. cucullata x galeata grew better at high rather thanlow temperatures. Daphnia hyalina x galeata, however, grew moresuccessfully at low temperatures than did D. cucullata x galeata.The highest Q₁₀ of ETS activity of D. cucullata x galeata atthe lowest temperature range of 5–15°C indicated theabsence of enzymes that could function sufficiently well atlow temperatures. The ETS activity of the warm-acclimated hybridD. hyalina x galeata reached a maximum at an incubation temperatureof 20°C, while D. cucullata x galeata had maximal ETS activityat 25°C. Thus D. cucullata x galeata has a more efficientenzyme system than D. hyalina x galeata at the higher temperature.The higher Arrhenius activation energy (E_a) for D. cucullatax galeata than for D. hyalina x galeata indicates that enzymesfrom D. cucullata x galeata are more temperature sensitive thanthose from D. hyalina x galeata. In conclusion, the ETS of D.cucullata x galeata is adapted to a higher temperature and tonarrower temperature fluctuations than that of D. hyalina xgaleata.     

Abundance and Distribution of Sympatric Gibbons in a Threatened Sumatran Rain Forest

Agile gibbons (Hylobates agilis) and siamangs (Symphalangus syndactylus) are sympatric small apes inhabiting threatened forests of Sumatra, Indonesia. We censused both species in the 3,568-km² Bukit Barisan Selatan National Park, at the southern limit of their ranges, over a 7-mo period in 2001. First, we monitored daily calling rates from known populations to develop probabilities of calling during a specified number of days and used the probability of calling at 1 time during 3 days to convert calling rates to abundance. Next, we used 3-day calibrated call count censuses (n=31) stratified by distance from forest edge and across a range of elevations to estimate species-specific group densities. We used group size from the known populations as well as data collected ad libitum during the census to convert group density to individual density. Agile gibbon group density averaged 0.67 km^–2 (SE = 0.082) and group size averaged 2.6 (SE = 0.73) for a population estimate of 4,479 (SE = 1,331) individuals. Siamang group density averaged 2.23 km^–2 (SE = 0.245), and group size averaged 3.9 (SE = 1.09) for a population estimate of 22,390 (SE = 8,138). Agile gibbon and siamang densities are negatively correlated, with agile gibbons more abundant in mid-elevation forests and siamangs most abundant in lowland and submontane forests. The small group sizes of agile gibbons indicate potential survival problems in infant and juvenile size classes. Although neither species is presently threatened by direct human disturbance, continued deforestation will jeopardize the long-term viability of both species in Bukit Barsian Selatan National Park and on Sumatra.     

Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays

MOTIVATION: A crucial step in microarray data analysis is the selection of subsets of interesting genes from the initial set of genes. In many cases, especially when comparing a specific condition to a reference, the genes of interest are those which are differentially expressed. Two common methods for gene selection are: (a) selection by fold difference (at least n fold variation) and (b) selection by altered ratio (at least n standard deviations away from the mean ratio). RESULTS: The novel method proposed here is based on ANOVA and uses replicate spots to estimate an empirical distribution of the noise. The measured intensity range is divided in a number of intervals. A noise distribution is constructed for each such interval. Bootstrapping is used to map the desired confidence levels from the noise distribution corresponding to a given interval to the measured log ratios in that interval. If the method is applied on individual arrays having replicate spots, the method can calculate an overall width of the noise distribution which can be used as an indicator of the array quality. We compared this method with the fold change and unusual ratio method. We also discuss the relationship with an ANOVA model proposed by Churchill et al. In silico experiments were performed while controlling the degree of regulation as well as the amount of noise. Such experiments show the performance of the classical methods can be very unsatisfactory. We also compared the results of the 2-fold method with the results of the noise sampling method using pre and post immortalization cell lines derived from the MDAH041 fibroblasts hybridized on Affymetrix GeneChip arrays. The 2-fold method reported 198 genes as upregulated and 493 genes as downregulated. The noise sampling method reported 98 gene upregulated and 240 genes downregulated at the 99.99% confidence level. The methods agreed on 221 genes downregulated and 66 genes upregulated. Fourteen genes from the subset of genes reported by both methods were all confirmed by Q-RT-PCR. Alternative assays on various subsets of genes on which the two methods disagreed suggested that the noise sampling method is likely to provide fewer false positives.     

Activation of pig and cattle oocytes by butyrolactone I: morphological and biochemical study

In this study a specific inhibitor of cyclin-dependent kinases (cdks), butyrolactone I (BL I), was used for activation of pig and cattle metaphase II (MII) oocytes. BL I at a concentration of 100 microM was able to induce activation of both pig and cattle MII oocytes in a manner dependent on exposure time; however, precise timing of BL I exposure was required for the best activation results. The optimum activation rates were obtained when cattle MII oocytes were treated for 5 h with BL I and subsequently for 3-11 h in control medium, and pig MII oocytes for 8 h in BL I and then for 8-16 h in control medium; the percentage of activated oocytes after such treatment varied between 55% and 74% and between 53% and 81% for cattle and pig oocytes, respectively. Shorter exposures to BL I led to re-entry of the oocytes to the metaphase state in 35-50% of oocytes, the remaining oocytes forming a pronuclear stage; longer exposure to BL I led to increased numbers of oocytes being abnormal or degenerated. The behaviour of histone H1 kinase and mitogen activated protein (MAP) kinase, also measured during the experiment, reflected the morphological changes in the oocytes: both were inactivated after BL I treatment, though the inactivation of histone H1 kinase occurred 2 h ahead of that of MAP kinase. However, in the oocytes treated for a shorter time with BL I, with the reoccurrence of condensed chromatin in proportion of the oocytes cultured in control medium after BL I treatment, both kinases became reactivated. Taken together, these results suggest the possibility of using BL I for activation and cloning experiments in both species.