Biggest challenges in bioinformatics

The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the ‘Biggest Challenges in Bioinformatics’ in a ‘World Café’ style event.     

Analysis of DNA Sequencing Reaction Products Made with 7-Halo-7-deaza-2′-deoxyguanosine-5′-triphosphate

Abstract

7-Chloro- and 7- Iodo-7-Deaza-2′-Deoxyguanosine-5′-Triphosphates were employed as substrates replacing dGTP, dITP, or 7-Deaza-2′-Deoxyguanosine-5′-Triphosphate in sequencing reactions with Thermo Sequenase^TM. Analysis of the reaction products by denaturing gel electrophoresis indicates DNA containing these halogenated analogs can form strong secondary structures.     

Uniform Band Intensities in Fluorescent Dye Terminator Sequencing

Abstract

The use of Cyanine dye (Cy^TM 5 and Cy5.5) labeled dideoxy terminators with Thermo Sequenase^TM DNA polymerase in DNA sequencing provides uniform band intensity, improved sequence read-length, and accuracy. It also greatly improves the ability to detect single base heterozygotes with dye-terminator sequencing method.     

The Histone Variant His2Av is Required for Adult Stem Cell Maintenance in the Drosophila Testis

Many tissues are sustained by adult stem cells, which replace lost cells by differentiation and maintain their own population through self-renewal. The mechanisms through which adult stem cells maintain their identity are thus important for tissue homeostasis and repair throughout life. Here, we show that a histone variant, His2Av, is required cell autonomously for maintenance of germline and cyst stem cells in the Drosophila testis. The ATP-dependent chromatin-remodeling factor Domino is also required in this tissue for adult stem cell maintenance possibly by regulating the incorporation of His2Av into chromatin. Interestingly, although expression of His2Av was ubiquitous, its function was dispensable for germline and cyst cell differentiation, suggesting a specific role for this non-canonical histone in maintaining the stem cell state in these lineages.     

Seasonal variation in grey crowned crane (Balearica regulorum) abundance in the Ngorongoro Crater,Tanzania

There are few quantitative estimates of numbers of Africa's endangered grey crowned cranes (Balearica regulorum), yet conservation of this species will depend on such estimates. We used line-transect distance sampling on multiple 2-km segments of an existing road network to estimate the abundance of grey crowned cranes in a portion of the Ngorongoro Crater, Tanzania, during the wet (April) and dry (August) seasons of 2016. We analysed data from 106 transects on which we observed 174 groups of 1–61 cranes (median and mode = 2). Abundance and density estimates on the areas surveyed were best modelled without group size as a covariate and indicated that mean crane densities were significantly lower in the wet season (2.4/km²) than in the dry season (20.2 cranes/km²). Even based on survey areas of different size, minimum estimated numbers of cranes in the Crater (wet season: 108–133; dry season: 362–401) likely reflect the concentration of cranes in the nonbreeding (dry) season in the perennial wetlands of the Crater and reinforce the notion of the Crater being a key seasonal habitat for crane populations in northern Tanzania, as previously suggested in the literature.     

Influence of sea turtle nesting on hunting behavior and movements of jaguars in the dry forest of northwest Costa Rica

Jaguars (Panthera onca) are opportunistic predators that prey on large profitable prey items, such as sea turtles at nesting beaches. Here, we use jaguar and sea turtle track-count surveys, combined with satellite telemetry of one jaguar, to evaluate whether jaguar hunting behavior and movements are influenced by seasonal sea turtle nesting in the Sector Santa Rosa of Área de Conservación Guanacaste in northwest Costa Rica. We used generalized linear models to evaluate the effect of moon phase and sea surface temperature on olive ridley (Lepidochelis olivacea) and green turtle (Chelonia mydas) nesting abundance, as well as the combination of these predictors on the frequency of jaguar predation activity (proximity to nesting beaches) and movements. For home-range size and location analyses, we calculated kernel density estimates for each season at three different temporal scales. Sea turtle nesting season influenced jaguar activity patterns, as well as sea turtle abundance was related to jaguar locations and predation events, but jaguar home-range size (88.8 km² overall) did not differ between nesting seasons or among temporal scales. Environmental conditions influenced sea turtle nesting and, as a consequence, also influenced jaguar movements and foraging activity. Our study defined the home range of a female jaguar in the tropical dry forest and its relationship to seasonally abundant turtles. Additional information related to the effect of tourism on jaguar–sea turtle interactions would improve conservation of these species at unique nesting beaches in the area.     

Secondary galling: a novel feeding strategy among ‘non‐pollinating’ fig wasps from Ficus curtipes

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