GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads.     

A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality

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A Simple Regression-Based Method to Map Quantitative Trait Loci Underlying Function-Valued Phenotypes

Most statistical methods for quantitative trait loci (QTL) mapping focus on a single phenotype. However, multiple phenotypes are commonly measured, and recent technological advances have greatly simplified the automated acquisition of numerous phenotypes, including function-valued phenotypes, such as growth measured over time. While methods exist for QTL mapping with function-valued phenotypes, they are generally computationally intensive and focus on single-QTL models. We propose two simple, fast methods that maintain high power and precision and are amenable to extensions with multiple-QTL models using a penalized likelihood approach. After identifying multiple QTL by these approaches, we can view the function-valued QTL effects to provide a deeper understanding of the underlying processes. Our methods have been implemented as a package for R, funqtl.     

Quilt Plots: A Simple Tool for the Visualisation of Large Epidemiological Data

Background

Graphical representation of data is one of the most easily comprehended forms of explanation. The current study describes a simple visualization tool which may allow greater understanding of medical and epidemiological data.

Method

We propose a simple tool for visualization of data, known as a “quilt plot”, that provides an alternative to presenting large volumes of data as frequency tables. Data from the Australian Needle and Syringe Program survey are used to illustrate “quilt plots”.

Conclusion

Visualization of large volumes of data using “quilt plots” enhances interpretation of medical and epidemiological data. Such intuitive presentations are particularly useful for the rapid assessment of problems in the data which cannot be readily identified by manual review. We recommend that, where possible, “quilt plots” be used along with traditional quantitative assessments of the data as an explanatory data analysis tool.     

A Global Multiregional Proteomic Map of the Human Cerebral Cortex

The Brodmann area(BA)-based map is one of the most widely used cortical maps for studies of human brain functions and in clinical practice; however, the molecular architecture of BAs remains unknown. The present study provided a global multiregional proteomic map of the human cerebral cortex by analyzing 29 BAs. These 29 BAs were grouped into 6 clusters based on similarities in proteomic patterns: the motor and sensory cluster, vision cluster, auditory and Broca’s area cluster, Wernicke’s area c...     

Excitation-Emission Map as a Tool in Studies of Photosynthetic Pigment-Protein Complexes

Excitation-emission maps were constructed by measuring emission spectra from tobacco thylakoids and from thylakoids and intact cells of the cyanobacterium Synechocystis 6803. The measurement of such maps is greatly facilitated by the current diode-array detector technology. We show that excitation-emission maps are valuable tools for studies of the structure and energy transfer pathways in photosynthetic systems. This revised version was published online in August 2006 with corrections to the Cover Date.     

Enhancement of Grazing Gastropod Populations as a Coral Reef Restoration Tool: Predation Effects and Related Applied Implications

We aimed to evaluate the efficacy of the gastropod grazer Trochus niloticus in controlling epilithic algae and enhancing coral recruitment on artificial substrata on coral reefs where the biomass of herbivorous fishes was low due to heavy fishing pressure. Hatchery‐reared, subadult trochus were stocked onto pallet balls (small artificial reefs composed of concrete and limestone aggregate) at a density of approximately four individuals per square meter (external surface area). This density was re‐established with releases of new trochus each month for 6 months. At the end of the experiment, there were no significant differences in algal biomass, cover and community composition, or the density of coral recruits on substrata with and without trochus. High monthly attrition of stocked trochus on the pallet balls, apparently due mainly to predation by octopus, did not allow the evaluation of the efficiency of the trochus enhancement, at the desired density, as a restoration tool. However, at the lower trochus densities (circa 1 m^?2), which occurred as a result of predation in this study, no apparent enhancement of algal grazing or coral recruitment were observed. The surprisingly high predation of stocked trochus in a heavily fished and gleaned reef site stresses the importance of understanding all the factors affecting the survival of stocked animals. To help mitigate predation of trochus, artificial habitat with refuge spaces that allow the grazers to escape predation could be provided and individuals of a larger size could be released.     

Prochlorococcus, a Marine Photosynthetic Prokaryote of Global Significance

The minute photosynthetic prokaryote Prochlorococcus, which was discovered about 10 years ago, has proven exceptional from several standpoints. Its tiny size (0.5 to 0.7 μm in diameter) makes it the smallest known photosynthetic organism. Its ubiquity within the 40°S to 40°N latitudinal band of oceans and its occurrence at high density from the surface down to depths of 200 m make it presumably the most abundant photosynthetic organism on Earth. Prochlorococcus typically divides once a day in the subsurface layer of oligotrophic areas, where it dominates the photosynthetic biomass. It also possesses a remarkable pigment complement which includes divinyl derivatives of chlorophyll a (Chl a) and Chl b, the so-called Chl a₂ and Chl b₂, and, in some strains, small amounts of a new type of phycoerythrin. Phylogenetically, Prochlorococcus has also proven fascinating. Recent studies suggest that it evolved from an ancestral cyanobacterium by reducing its cell and genome sizes and by recruiting a protein originally synthesized under conditions of iron depletion to build a reduced antenna system as a replacement for large phycobilisomes. Environmental constraints clearly played a predominant role in Prochlorococcus evolution. Its tiny size is an advantage for its adaptation to nutrient-deprived environments. Furthermore, genetically distinct ecotypes, with different antenna systems and ecophysiological characteristics, are present at depth and in surface waters. This vertical species variation has allowed Prochlorococcus to adapt to the natural light gradient occurring in the upper layer of oceans. The present review critically assesses the basic knowledge acquired about Prochlorococcus both in the ocean and in the laboratory.     

Horizontal and Vertical Distribution of Marine Virioplankton: A Basin Scale Investigation Based on a Global Cruise

Despite the fact that marine viruses have been increasingly studied in the last decade, there is little information on viral abundance and distribution on a global scale. In this study, we report on a global-scale survey covering the Pacific, Atlantic, and Indian Oceans on viral distribution using flow cytometry. Viruses were stained with the SYBR Green I, which targets only dsDNA viruses. The average viral abundance was 1.10±0.73×10⁷ ml⁻¹ in global surface oceans and decreased from the areas with high chlorophyll concentration (on average, 1.47±0.78×10⁷ ml⁻¹) to the oligotrophic subtropical gyres (on average, 6.34±2.18×10⁶ ml⁻¹). On a large-spatial-scale, viruses displayed significant relationships with both heterotrophic and autotrophic picoplankton abundance, suggesting that viral distribution is dependent on their host cell abundance. Our study provided a basin scale pattern of marine viral distributions and their relationship with major host cells, indicating that viruses play a significant role in the global marine ecosystem.     

Global Patterns in Ecological Indicators of Marine Food Webs: A Modelling Approach

Background

Ecological attributes estimated from food web models have the potential to be indicators of good environmental status given their capabilities to describe redundancy, food web changes, and sensitivity to fishing. They can be used as a baseline to show how they might be modified in the future with human impacts such as climate change, acidification, eutrophication, or overfishing.

Methodology

In this study ecological network analysis indicators of 105 marine food web models were tested for variation with traits such as ecosystem type, latitude, ocean basin, depth, size, time period, and exploitation state, whilst also considering structural properties of the models such as number of linkages, number of living functional groups or total number of functional groups as covariate factors.

Principal findings

Eight indicators were robust to model construction: relative ascendency; relative overhead; redundancy; total systems throughput (TST); primary production/TST; consumption/TST; export/TST; and total biomass of the community. Large-scale differences were seen in the ecosystems of the Atlantic and Pacific Oceans, with the Western Atlantic being more complex with an increased ability to mitigate impacts, while the Eastern Atlantic showed lower internal complexity. In addition, the Eastern Pacific was less organised than the Eastern Atlantic although both of these systems had increased primary production as eastern boundary current systems. Differences by ecosystem type highlighted coral reefs as having the largest energy flow and total biomass per unit of surface, while lagoons, estuaries, and bays had lower transfer efficiencies and higher recycling. These differences prevailed over time, although some traits changed with fishing intensity. Keystone groups were mainly higher trophic level species with mostly top-down effects, while structural/dominant groups were mainly lower trophic level groups (benthic primary producers such as seagrass and macroalgae, and invertebrates). Keystone groups were prevalent in estuarine or small/shallow systems, and in systems with reduced fishing pressure. Changes to the abundance of key functional groups might have significant implications for the functioning of ecosystems and should be avoided through management.

Conclusion/significance

Our results provide additional understanding of patterns of structural and functional indicators in different ecosystems. Ecosystem traits such as type, size, depth, and location need to be accounted for when setting reference levels as these affect absolute values of ecological indicators. Therefore, establishing absolute reference values for ecosystem indicators may not be suitable to the ecosystem-based, precautionary approach. Reference levels for ecosystem indicators should be developed for individual ecosystems or ecosystems with the same typologies (similar location, ecosystem type, etc.) and not benchmarked against all other ecosystems.     

C-Banding as a Simple Tool to Discriminate Between Micronuclei Induced by Clastogens and Aneugens

If mouse bone marrow preparations are treated with a classical C-banding procedure, it may be possible to distinguish between micronuclei with or without centromeres. This allows discrimination between micronuclei originating from chromosome breakage and those originating from chromosome loss. Thus, using C-banding, the micronucleus test can be used not only for the detection of clastogens but also aneugens. In this way, more exhaustive methods such as immunological staining using antikinetochore antibodies may not be necessary.     

Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs

Uncovering conserved 3D protein–ligand binding patterns on the basis of functional groups (FGs) shared by a variety of small molecules can greatly expand our knowledge of protein–ligand interactions. Despite that conserved binding patterns for a few commonly used FGs have been reported in the literature, large-scale identification and evaluation of FG-based 3D binding motifs are still lacking. Here, we propose a computational method, Automatic FG-based Three-dimensional Motif Extractor (AFTME), for automatic mapping of 3D motifs to different FGs of a specific ligand. Applying our method to 233 naturally-occurring ligands, we define 481 FG-binding motifs that are highly conserved across different ligand-binding pockets. Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs. Combinations of FG-binding motifs facilitate the binding of proteins to a wide spectrum of ligands with various binding affinities. Finally, we show that our FG–motif map can be used to nominate FGs that potentially bind to specific drug targets, thus providing useful insights and guidance for rational design of small-molecule drugs.     

Global Patterns of Pre-Dispersal Propagule Predation in Mangrove Forests1

Mangroves in disparate families produce viviparous seedlings (propagules) that are attacked by many crab and insect predators both before and after dispersal. While post-dispersal predation is viewed as an important factor in structuring many mangrove communities, pre-dispersal predation rates and agents have been characterized for few species. Ten species of mangrove and 3299 propagules were surveyed for pre-dispersal propagule predation at 42 sites around the world. Pre-dispersal predation rates were variable among sites and species, ranging from 0 to 93 percent within sands, with a global total predation rate of 23.3 percent (across all propagules examined) and a mean level of 28.3 percent across sites. Grapsid crabs, Coleoptera and Lepidoptera were the primary predators identified. Forests near human population centers and stands occurring at high intertidal sites exhibited higher levels of propagule predation than those in unpopulated or low-intertidal sites. Predation rates on a species were weakly, negatively correlated with conspecific seedling density at a site. To explore temporal variation in, and ramifications of pre-dispersal predation for propagule growth and abscission dynamics, Rhizophora mangle propagules were monitored over two years at three sites in Belize, Central America. Predation did not significantly reduce hypocotylar growth of germinated propagules on the parent tree, but nearly doubled the abscission rate of premature propagules. Pre-dispersal propagule predation is a ubiquitous feature of mangrove forests world-wide, and must be accounted for in estimates of reproductive output, stand health, and propagule availability for forestry and restoration efforts.     

BRED: A Simple and Powerful Tool for Constructing Mutant and Recombinant Bacteriophage Genomes

Advances in DNA sequencing technology have facilitated the determination of hundreds of complete genome sequences both for bacteria and their bacteriophages. Some of these bacteria have well-developed and facile genetic systems for constructing mutants to determine gene function, and recombineering is a particularly effective tool. However, generally applicable methods for constructing defined mutants of bacteriophages are poorly developed, in part because of the inability to use selectable markers such as drug resistance genes during viral lytic growth. Here we describe a method for simple and effective directed mutagenesis of bacteriophage genomes using Bacteriophage Recombineering of Electroporated DNA (BRED), in which a highly efficient recombineering system is utilized directly on electroporated phage DNA; no selection is required and mutants can be readily detected by PCR. We describe the use of BRED to construct unmarked gene deletions, in-frame internal deletions, base substitutions, precise gene replacements, and the addition of gene tags.     

Transkingdom Genetic Transfer from Escherichia coli to Saccharomyces cerevisiae as a Simple Gene Introduction Tool

Transkingdom conjugation (TKC) permits transfer of DNA from bacteria to eukaryotic cells using a bacterial conjugal transfer system. However, it is not clear whether the process of DNA acceptance in a recipient eukaryote is homologous to the process of conjugation between bacteria. TKC transfer requires mobilizable shuttle vectors that are capable of conjugal transfer and replication in the donor and recipient strains. Here, we developed TKC vectors derived from plasmids belonging to the IncP and IncQ groups. We also investigated forms of transfer of these vectors from Escherichia coli into Saccharomyces cerevisiae to develop TKC as a simple gene introduction method. Both types of vectors were transferred precisely, conserving the origin of transfer (oriT) sequences, but IncP-based vectors appeared to be more efficient than an IncQ-based vector. Interestingly, unlike in agrobacterial T-DNA (transfer DNA) transfer, the efficiency of TKC transfer was similar between a wild-type yeast strain and DNA repair mutants defective in homologous recombination (rad51Δ and rad52Δ) or nonhomologous end joining (rad50Δ, yku70Δ, and lig4Δ). Lastly, a shuttle vector with two repeats of IncP-type oriT (oriT^P) sequences flanking a marker gene was constructed. TKC transfer of this vector resulted in precise excision of both the oriT^P loci as well as the marker gene, albeit at a low frequency of 17% of all transconjugants. This feature would be attractive in biotechnological applications of TKC. Taken together, these results strongly suggest that in contrast to agrobacterial T-DNA transfer, the circularization of vector single-stranded DNA occurs either before or after transfer but requires a factor(s) from the donor. TKC is a simple method of gene transfer with possible applications in yeast genetics and biotechnology.     

The Impact of Predation by Marine Mammals on Patagonian Toothfish Longline Fisheries

Predatory interaction of marine mammals with longline fisheries is observed globally, leading to partial or complete loss of the catch and in some parts of the world to considerable financial loss. Depredation can also create additional unrecorded fishing mortality of a stock and has the potential to introduce bias to stock assessments. Here we aim to characterise depredation in the Patagonian toothfish (Dissostichus eleginoides) fishery around South Georgia focusing on the spatio-temporal component of these interactions. Antarctic fur seals (Arctocephalus gazella), sperm whales (Physeter macrocephalus), and orcas (Orcinus orca) frequently feed on fish hooked on longlines around South Georgia. A third of longlines encounter sperm whales, but loss of catch due to sperm whales is insignificant when compared to that due to orcas, which interact with only 5% of longlines but can take more than half of the catch in some cases. Orca depredation around South Georgia is spatially limited and focused in areas of putative migration routes, and the impact is compounded as a result of the fishery also concentrating in those areas at those times. Understanding the seasonal behaviour of orcas and the spatial and temporal distribution of “depredation hot spots” can reduce marine mammal interactions, will improve assessment and management of the stock and contribute to increased operational efficiency of the fishery. Such information is valuable in the effort to resolve the human-mammal conflict for resources.     

MRSA in Africa: Filling the Global Map of Antimicrobial Resistance

We sought to assess the prevalence of methicillin-resistance among Staphylococcus aureus isolates in Africa. We included articles published in 2005 or later reporting for the prevalence of MRSA among S. aureus clinical isolates. Thirty-two studies were included. In Tunisia, the prevalence of MRSA increased from 16% to 41% between 2002–2007, while in Libya it was 31% in 2007. In South Africa, the prevalence decreased from 36% in 2006 to 24% during 2007–2011. In Botswana, the prevalence varied from 23–44% between 2000–2007. In Algeria and Egypt, the prevalence was 45% and 52% between 2003–2005, respectively. In Nigeria, the prevalence was greater in the northern than the southern part. In Ethiopia and the Ivory Coast, the prevalence was 55% and 39%, respectively. The prevalence of MRSA was lower than 50% in most of the African countries, although it appears to have risen since 2000 in many African countries, except for South Africa.     

The Future of the Oceans Past: Towards a Global Marine Historical Research Initiative

Historical research is playing an increasingly important role in marine sciences. Historical data are also used in policy making and marine resource management, and have helped to address the issue of shifting baselines for numerous species and ecosystems. Although many important research questions still remain unanswered, tremendous developments in conceptual and methodological approaches are expected to contribute to a comprehensive understanding of the global history of human interactions with life in the seas. Based on our experiences and knowledge from the “History of Marine Animal Populations” project, this paper identifies the emerging research topics for future historical marine research. It elaborates on concepts and tools which are expected to play a major role in answering these questions, and identifies geographical regions which deserve future attention from marine environmental historians and historical ecologists.     

Toward a High-ResolutionPlasmodium falciparumLinkage Map: Polymorphic Markers from Hundreds of Simple Sequence Repeats

A total of 507 simple sequence repeats (SSRs or “microsatellites”) were identified fromPlasmodium falciparumsequences in GenBank and from inserts in a genomic DNA library. Oligonucleotide primers from sequences that flank 224 of these SSRs were synthesized and used in PCR assays to test for simple sequence length polymorphisms (SSLPs). Of the 224 SSRs, 188 showed SSLPs among 12 differentP. falciparumlines; 116 of these SSLPs were assigned to chromosome linkage groups by physical mapping and by comparing their inheritance patterns against those of restriction fragment length polymorphism markers in a genetic cross (HB3×Dd2). The predominant SSLPs inP. falciparumwere found to contain [TA]_n, [T]_n, and [TAA]_n, a feature that is reminiscent of plant genomes and is consistent with the proposed algal-like origin of malaria parasites. Since such SSLPs are abundant and readily isolated, they are a powerful resource for genetic analysis ofP. falciparum.