MetaTM - a consensus method for transmembrane protein topology prediction

Background  

Transmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their topology (i. e. which parts of the amino acid sequence are buried in the membrane and which are located on either side of the membrane), but only a few topologies are known. Consequently, various computational TM topology predictors have been developed, but their accuracies are far from perfect. The prediction quality can be improved by applying a consensus approach, which combines results of several predictors to yield a more reliable result.     

Cloning and characterization of 29 tetranucleotide and two dinucleotide polymorphic microsatellite loci from the endangered marbled murrelet (Brachyramphus marmoratus)

We developed 31 novel, polymorphic microsatellite loci in the marbled murrelet (Brachyramphus marmoratus), a critically endangered seabird. Variability was tested on 15 individuals from the Santa Cruz, California population, with each locus characterized by two to 12 alleles. Observed levels of heterozygosity ranged from 0.13 to 0.93. These loci provide a valuable means of assessing the population structure and demographic parameters of this species, which may be critical to its conservation across a fragmented habitat.     

Alkaloid profile of leaves and seeds of Lupinus hintonii C. P. Smith

L. hintonii C. P. Smith grows in the Central Highland forests of Mexico at altitudes between 2800 m to 3200 m above see level. Members of the genus Lupinus produce quinolizidine alkaloids as main chemical defensive compounds against herbivores. Surprisingly alkaloid profiles are rather constant within this species, while substantial variation was found when compared to morphologically closely related other taxa. As part of a phytochemical project on Mexican wild lupins, we report on the alkaloid profiles of seeds and leaves of L. hintonii. 19 alkaloids could be identified by capillary GLC-MS. Six major alkaloids occurred in leaves and seeds: 13-hydroxylupanine (28% and 45% respectively), tetrahydrorhombifoline (31% and 23% respectively), angustifoline (2% and 4% respectively), lupanine (7% and 5% respectively), 13alpha-tigloyloxylupanine (19% and 5% respectively) and 4alpha-angeloyl-3beta-hydroxylupanine (9% and 2%). This chemical pattern resembles that of the North American lupin L. floribundus.     

Development of 22 new microsatellite loci for fishers (Martes pennanti) with variability results from across their range

We developed 22 new microsatellite loci for the fisher (Martes pennanti), a North American mesocarnivore. The loci were developed with samples from the southern Sierra Nevada Mountains in California, and were screened with samples from this population and four other populations. We observed a range of six to 21 polymorphic loci per population, with the Sierra Nevada population exhibiting markedly lower levels of variation compared to the other four.