Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

Functional characterization of the diatom cyclin-dependent kinase A2 as a mitotic regulator reveals plant-like properties in a non-green lineage

Background: Cyclin-dependent kinases (CDKs) are crucial regulators of cell cycle progression in eukaryotes. The diatom CDKA2 was originally assigned to the classical A-type CDKs, but its cell cycle phase-specific transcription at the G2-to-M phase transition is typical for plant-specific B-type CDKs. Results: Here, we report the functional characterization of CDKA2 from the diatom Phaeodactylum tricornutum. Through a yeast two-hybrid library screen, CDKA2 was found to interact with the G2/M-specific CDK scaffolding factor CKS1. Localization of CDKA2 was found to be nuclear in interphase cells, while in cells undergoing cytokinesis, the signal extended to the cell division plane. In addition, overexpression of CDKA2 induced an overall reduction in the cell growth rate. Expression analysis of cell cycle marker genes in the overexpression lines indicates that this growth reduction is primarily due to a prolongation of the mitotic phase. Conclusions: Our study indicates a role for CDKA2 during cell division in diatoms. The functional characterization of a CDK with clear CDKB properties in a non-green organism questions whether the current definition of B-type CDKs being plant-specific might need revision

Chytridiomycosis of marine diatoms : the role of stress physiology and resistance in parasite-host recognition and accumulation of defense molecules

Little is known about the role of chemotaxis in the location and attachment of chytrid zoospores to potential diatom hosts. Hypothesizing that environmental stress parameters affect parasite-host recognition, four chytrid-diatom tandem cultures (Chytridium sp./Navicula sp., Rhizophydium type I/Nitzschia sp., Rhizophydium type IIa/Rhizosolenia sp., Rhizophydium type IIb/Chaetoceros sp.) were used to test the chemotaxis of chytrid zoospores and the presence of potential defense molecules in a non-contact-co-culturing approach. As potential triggers in the chemotaxis experiments, standards of eight carbohydrates, six amino acids, five fatty acids, and three compounds known as compatible solutes were used in individual and mixed solutions, respectively. In all tested cases, the whole-cell extracts of the light-stressed (continuous light exposure combined with 6 h UV radiation) hosts attracted the highest numbers of zoospores (86%), followed by the combined carbohydrate standard solution (76%), while all other compounds acted as weak triggers only. The results of the phytochemical screening, using biomass and supernatant extracts of susceptible and resistant host-diatom cultures, indicated in most of the tested extracts the presence of polyunsaturated fatty acids, phenols, and aldehydes, whereas the bioactivity screenings showed that the zoospores of the chytrid parasites were only significantly affected by the ethanolic supernatant extract of the resistant hosts

Distribution of benthic diatom assemblages in the Westerschelde (Zeeland, The Netherlands)

The benthic diatom assemblages of the Westerschelde-estuary were studied by means of multivariate analysis. Two main groups and eight subgroups were distinguished. The relation with salinity and sediment composition was investigated. A clear relation between grain size and the distribution of the assemblages was found

Parent participation at school: a research study on the perspectives of children

The present article discusses the attitude of children towards parent participation at school. To this end, a quantitative study was conducted among 250 10-year-old children in Flanders. The analysis shows that children tend to rather like parent participation, and that this attitude is related to the extent to which parents participate. Children from 'deprived' schools tend to like parent participation better. This article argues that children should be approached as fully-fledged, active participants in their parents' participation process and that it is necessary to take account of the specific perspectives of children on this topic

Accurate long read mapping using enhanced suffix arrays

With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes. Recent developments in sequencing technology allow longer reads, but the mappers for short reads are not suited for reads of several hundreds of base pairs. We propose an algorithm for mapping longer reads, which is based on chaining maximal exact matches and uses heuristics and the Needleman-Wunsch algorithm to bridge the gaps. To compute maximal exact matches we use a specialized index structure, called enhanced suffix array. The proposed algorithm is very accurate and can handle large reads with mutations and long insertions and deletions

A paleolimnological reconstruction of mid and late holocene climate change in South Georgia

South Georgia is located at the barrier between Antarctica and the mid-latitudes which makes it a key location to determine the main drivers of past and present-day climate variability and to assess whether the climate in the South Atlantic was synchronous with Antarctica or South America. Here we performed a sedimentological, high resolution (ITRAX) geochemical, and fossil diatom and pigment analysis of a 5.41 m long, ca. 8000 cal yr BP, sediment core from Fan Lake, Annenkov Island, South Georgia (54°29’0’’S, 37°5’0’’W) in an attempt to separate the influence of Holocene palaeoclimatic variability from changes in catchment stability and glacier activity. While radiocarbon ages of events in the top 250 cm (c. 4 ka) of this core appear to be broadly in line with some other studies on South Georgia, the chronology of the lower half still poses several questions. The main lithological division in the profile is marked by the establishment of finely laminated sedimentation at c. 250 cm (4000 yrs BP) and is also picked out by the diatom and pigment analysis. This change is characterized by a reduction to low stable magnetic susceptibility values and a step-change increase in organic matter, and is most likely related to deglaciation of the lake catchment during the ‘Mid Holocene Hypsithermal’. Although the diatom composition is dominated by a single species (i.e., Cyclotella stelligera), relatively minor, but sometimes significant, fluctuations in other diatom species occur in the top 250 cm (mid-late Holocene). Interestingly, the most remarkable change in the diatom record occurs at c. 100 cm (1000 cal yr BP) and coincides with an increase in general lake productivity. We link these changes to increased catchment disturbance at c. 1000 cal yr BP, which is possibly associated with deglaciation following one of four relatively minor ‘post-cooling events’ during the late Holocene