ALBERT

Description: Legionaminic acids (Leg) are bacterial analogs of neuraminic acid, with the same stereochemistry but different substituents at C5, C7 and C9. Hence they may be incorporated into useful analogs of sialoglycoconjugates, and we previously reported two sialyltransferases that could utilize cytidine monophosphate (CMP)-Leg5Ac7Ac for preparation of Leg glycoconjugates, which were resistant to sialidases [Watson DC, Leclerc S, Wakarchuk WW, Young NM. 2011. Enzymatic synthesis and properties of glycoconjugates with legionaminic acid as a replacement for neuraminic acid. Glycobiology . 21:99–108.]. These were the porcine ST3Gal1 and Pasteurella multocida sialyltransferases. We now report two additional sialyltransferases with superior Leg-transferase properties to the previous two. These are (i) a truncated form of a Photobacterium α2,6-sialyltransferase with an Ala-Met mutation in its active site, and (ii) an α2,3-sialyltransferase from Neisseria meningitidis MC58 with a higher transferase activity than the P. multocida enzyme, with either CMP-Neu5Ac or CMP-Leg5Ac7Ac as the donor. These enzymes will enable the production of useful Leg5Ac7Ac glycoconjugate derivatives with either α2,6 or α2,3 linkages and unique biological properties.

Description: The rare N-unsubstituted glucosamine ( $$\hbox{ GlcN }{{\hbox{ H }}_{3}}^{+}$$ ) residues in heparan sulfate (HS) have important biological and pathophysiological roles. Because of their low natural abundance, the use of chemically generated, structurally defined, N-unsubstituted heparin/HS oligosaccharides can greatly contribute to the investigation of their natural role in HS. However, the sequencing of mixtures of chemically generated oligosaccharides presents major challenges due to the difficulties in separating isomers and the available detection methods. In this study, we developed and validated a simple and sensitive method for the sequence analysis of N-unsubstituted heparin/HS oligosaccharides. This protocol involves pH 4 nitrous acid (HNO 2 ) degradation, size-exclusion HPLC and ion-pair reversed-phase liquid chromatography-ion trap/time-of-flight mass spectrometry (IPRP-LC-ITTOF MS). We unexpectedly found that absorbance at 232 nm (normally used for specific detection of C4–C5 unsaturated oligosaccharides) was, in most cases, still sufficiently sensitive to also simultaneously detect saturated oligosaccharides during HPLC, thus simplifying the positional analysis of $$\hbox{ GlcN }{{\hbox{ H }}_{3}}^{+}$$ residues. The IPRP-LC-ITTOF MS system can supply further structural information leading to full sequence determination of the original oligosaccharide. This new methodology has been used to separate and sequence a variety of chemically generated, N-unsubstituted dp6 species containing between 1 and 3 $$\hbox{ GlcN }{{\hbox{ H }}_{3}}^{+}$$ residues per oligosaccharide in different positional combinations. This strategy offers possibilities for the sequencing of natural N-unsubstituted oligosaccharides from HS and should also be applicable, with minor modification, for sequencing at N-sulfated residues using alternative pH 1.5 HNO 2 scission.

Description: A major aspect of carbohydrate-dependent galectin functionality is their cross-linking capacity. Using a cell surface as biorelevant platform for galectin binding and a panel of 40 glycans as sensor part of a fluorescent polyacrylamide neoglycopolymer for profiling galectin reactivity, properties of related proteins can be comparatively analyzed. The group of the chicken galectins (CGs) is an especially suited system toward this end due to its relatively small size, compared with mammalian galectins. The experiments reveal particularly strong reactivity toward N -acetyllactosamine repeats for all tested CGs and shared reactivity of CG-1A and CG-2 to histo-blood group ABH determinants. In cross-species comparison, CG-1B's properties closely resembled those of human galectin-1, as was the case for the galectin-2 (but not galectin-3) ortholog pair. Although binding-site architectures are rather similar, reactivity patterns can well differ.

Description: Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly understood. Here, we have carried out a study of the evolution of alternatively spliced exons after gene duplication to better understand the interaction between the two processes. We created a manually curated set of 97 human genes with mutually exclusively spliced homologous exons and analyzed the evolution of these exons across five distantly related vertebrates (lamprey, spotted gar, zebrafish, fugu, and coelacanth). Most of these exons had an ancient origin (more than 400 Ma). We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication. We observed 11 events in which gene duplication was accompanied by splice isoform separation, that is, each paralog specifically conserved just one distinct ancestral homologous exon. At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes. That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene.

Description: There is widespread interest today in understanding enhancers, which are regulatory elements typically harboring several transcription factor binding sites and mediating the combinatorial effect of transcription factors on gene expression. The evolution of enhancers poses interesting unanswered questions, for example, the evolutionary time taken for a typical enhancer to emerge or the factors shaping its evolution. Existing approaches to cis -regulatory evolution have often ignored the combinatorial nature and varied biochemical mechanisms of gene regulation encoded in enhancers. We report on our investigation of enhancer evolution through the use of PEBCRES, a framework for evolutionary simulation of enhancers that employs a mechanistic and well-supported sequence-to-expression model to assign fitness to the evolving enhancer genotype. We estimated the time necessary to evolve, from genomic background, enhancers capable of driving complex gene expression patterns similar to those involved in early development in Drosophila. We found the time-to-evolve to range between 0.5 and 10 Myr, and to vary greatly with the target expression pattern, complexity of the real enhancer known to encode that pattern, and the strength of input from specific transcription factors. To our knowledge, this is the first estimate of waiting times for realistic enhancers to evolve. The in silico evolved enhancers had, with a few interesting exceptions, site compositions similar to those seen in real enhancers for the same patterns. Our simulations also revealed that certain features of an enhancer might evolve not due to their biological function but as aids to the evolutionary process itself.

Description: Despite significant progress in the structural and functional characterization of the human genome, understanding of the mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. Here, I report that transposable element-derived sequences, most notably LTR7/HERV-H, LTR5_Hs, and L1HS, harbor 99.8% of the candidate human-specific regulatory loci (HSRL) with putative transcription factor-binding sites in the genome of human embryonic stem cells (hESC). A total of 4,094 candidate HSRL display selective and site-specific binding of critical regulators (NANOG [Nanog homeobox], POU5F1 [POU class 5 homeobox 1], CCCTC-binding factor [CTCF], Lamin B1), and are preferentially located within the matrix of transcriptionally active DNA segments that are hypermethylated in hESC. hESC-specific NANOG-binding sites are enriched near the protein-coding genes regulating brain size, pluripotency long noncoding RNAs, hESC enhancers, and 5-hydroxymethylcytosine-harboring regions immediately adjacent to binding sites. Sequences of only 4.3% of hESC-specific NANOG-binding sites are present in Neanderthals’ genome, suggesting that a majority of these regulatory elements emerged in Modern Humans. Comparisons of estimated creation rates of novel TF-binding sites revealed that there was 49.7-fold acceleration of creation rates of NANOG-binding sites in genomes of Chimpanzees compared with the mouse genomes and further 5.7-fold acceleration in genomes of Modern Humans compared with the Chimpanzees genomes. Preliminary estimates suggest that emergence of one novel NANOG-binding site detectable in hESC required 466 years of evolution. Pathway analysis of coding genes that have hESC-specific NANOG-binding sites within gene bodies or near gene boundaries revealed their association with physiological development and functions of nervous and cardiovascular systems, embryonic development, behavior, as well as development of a diverse spectrum of pathological conditions such as cancer, diseases of cardiovascular and reproductive systems, metabolic diseases, multiple neurological and psychological disorders. A proximity placement model is proposed explaining how a 33–47% excess of NANOG, CTCF, and POU5F1 proteins immobilized on a DNA scaffold may play a functional role at distal regulatory elements.

Description: Organisms can adapt to local environmental conditions as a plastic response or become adapted through natural selection on genetic variation. The ability to adapt to increased water temperatures will be of paramount importance for many fish species as the climate continues to warm and water resources become limited. Because increased water temperatures will reduce the dissolved oxygen available for fish, we hypothesized that adaptation to low oxygen environments would involve improved respiration through oxidative phosphorylation (OXPHOS). To test this hypothesis, we subjected individuals from two ecologically divergent populations of inland (redband) rainbow trout ( Oncorhynchus mykiss gairdneri ) with historically different temperature regimes (desert and montane) and their F1 progeny to diel cycles of temperature stress and then examined gene expression data for 80 nuclear- and mitochondrial-encoded OXPHOS subunits that participate in respiration. Of the 80 transcripts, 7 showed ≥ 2-fold difference in expression levels in gill tissue from desert fish under heat stress whereas the montane fish had none and the F1 only had one differentially expressed gene. A structural analysis of the proteins encoded by those genes suggests that the response could coordinate the formation of supercomplexes and oligomers. Supercomplexes may increase the efficiency of respiration because complexes I, III, and IV are brought into close proximity and oligomerization of complex V alters the macrostructure of mitochondria to improve respiration. Significant differences in gene expression patterns in response to heat stress in a common environment indicate that the response was not due to plasticity but had a genetic basis.

Description: Successful implementation of Ecosystem-Based Fisheries Management (EBFM) requires appropriate action as informed by reference points in an ecosystem context. Thresholds in the response of ecological indicators to system drivers have been suggested as reference points for EBFM, though the management performance of these indicators and possible values for their reference points have not been widely evaluated. We used Management Strategy Evaluation to test the performance of control rules that used ecological indicators to adjust the advice from single-species stock assessments, using the Georges Bank finfish fishery as a case study. We compare the performance of control rules that used ecological indicators to that of single-species F MSY control rules when the system dynamics were governed by the same multispecies population model. Control rules that used indicator-based reference points were able to perform better against catch and biodiversity objectives than when harvests were based on single-species advice alone. Indicators and values for reference points associated with good performance varied depending on the management objective. We quantified tradeoffs between total catch, biodiversity, and interannual variability in catch, noting that it was possible in some instances to achieve higher than average biodiversity while maintaining high catches using indicator-based control rules. While improved performance was noted using ecological indicators, outcomes were variable, and the gains in performance obtained may be similar to alternative methods of implementing precaution in single-species fishery control rules.

Description: Climate change and fishing can have major impacts on the distribution of natural marine resources. Climate change alters the distribution of suitable habitat, forcing organisms to shift their range or attempt to survive under suboptimal conditions. Fishing reduces the abundance of marine populations and truncates their age structure leading to range contractions or shifts. Along the east coast of the United States, there have been major changes in fish populations due to the impacts of fishing and subsequent regulations, as well as changes in the climate. Black sea bass, scup, summer flounder, and winter flounder are important commercial and recreational species, which utilize inshore and offshore waters on the northeast shelf. We examined the distributions of the four species with the Northeast Fisheries Science Center trawl surveys to determine if the along-shelf centres of biomass had changed over time and if the changes were attributed to changes in temperature or fishing pressure through changes in abundance and length structure. Black sea bass, scup, and summer flounder exhibited significant poleward shifts in distributions in at least one season while the Southern New England/Mid-Atlantic Bight stock of winter flounder did not shift. Generalized additive modelling indicated that the changes in the centres of biomass for black sea bass and scup in spring were related to climate, while the change in the distribution of summer flounder was largely attributed to a decrease in fishing pressure and an expansion of the length–age structure. While the changes in ocean temperatures will have major impacts on the distribution of marine taxa, the effects of fishing can be of equivalent magnitude and on a more immediate time scale. It is important for management to take all factors into consideration when developing regulations for natural marine resources.

Description: Many snow crab fisheries have fluctuated widely over time in a quasi-cyclic way due to highly variable recruitment. The causes of this variability are still debated. Bottom-up processes related to climate variability may strongly affect growth and survival during early life, whereas top-down predator effects may be a major source of juvenile mortality. Moreover, intrinsic density-dependent processes, which have received much less attention, are hypothetically responsible for the cycles in recruitment. This study explored how climate, larval production, intercohort cannibalism and groundfish predation may have affected recruitment of early juvenile snow crab in the northwest Gulf of St Lawrence (eastern Canada) over a period of 23 years. Abundance of early juvenile snow crabs (2.5–22.9 mm in carapace width), representing the first 3 years of benthic life, came from an annual trawl survey and was used to determine cohort strength. Analyses revealed a cyclic pattern in abundance of 0 + crabs that may arise from cohort resonant effects. This pattern consisted of three recruitment pulses but was reduced to two pulses by age 2 + , while the interannual variability of cohort strength was dampened. This reconfiguration of the earliest recruitment pattern was dictated primarily by bottom water temperature and cannibalism, which progressively overruled the pre-settlement factors of larval production and surface water temperature that best explained abundance of 0 + crabs. The results strongly suggest that bottom-up and density-dependent processes prevail over top-down control in setting the long-term trends and higher-frequency oscillations of snow crab early recruitment patterns.

Description: Fisheries biology encompasses a tremendous diversity of research questions, methods, and models. Many sub-fields use observational or experimental data to make inference about biological characteristics that are not directly observed (called "latent states"), such as heritability of phenotypic traits, habitat suitability, and population densities to name a few. Latent states will generally cause model residuals to be correlated, violating the assumption of statistical independence made in many statistical modelling approaches. In this exposition, we argue that mixed-effect modelling (i) is an important and generic solution to non-independence caused by latent states; (ii) provides a unifying framework for disparate statistical methods such as time-series, spatial, and individual-based models; and (iii) is increasingly practical to implement and customize for problem-specific models. We proceed by summarizing the distinctions between fixed and random effects, reviewing a generic approach for parameter estimation, and distinguishing general categories of non-linear mixed-effect models. We then provide four worked examples, including state-space, spatial, individual-level variability, and quantitative genetics applications (with working code for each), while providing comparison with conventional fixed-effect implementations. We conclude by summarizing directions for future research in this important framework for modelling and statistical analysis in fisheries biology.

Description: While the impact of environmental forcing on recruitment variability in marine populations remains largely elusive, studies spanning large spatial areas and many stocks are able to identify patterns common to different regions and species. In this study, we investigate the effects of the environment on the residuals of a Ricker stock–recruitment (SR) model, used as a proxy of prerecruits' survival, of 18 assessed stocks in the Baltic and North Seas. A probabilistic principal components (PCs) analysis permits the identification of groups of stocks with shared variability in the prerecruits' survival, most notably a group of pelagics in the Baltic Sea and a group composed of gadoids and herring in the North Sea. The first two PCs generally grouped the stocks according to their localizations: the North Sea, the Kattegat–Western Baltic, and the Baltic Sea. This suggests the importance of the local environmental variability on the recruitment strength. Hence, the prerecruits' survival variability is studied according to geographically disaggregated and potentially impacting abiotic or biotic variables. Time series (1990–2009) of nine environmental variables consistent with the spawning locations and season for each stock were extracted from a physical–biogeochemical model to evaluate their ability to explain the survival of prerecruits. Environmental variables explained 〉70% of the survival variability for eight stocks. The variables water current, salinity, temperature, and biomass of other fish stocks are regularly significant in the models. This study shows the importance of the local environment on the dynamics of SR. The results provide evidence of the necessity of including environmental variables in stock assessment for a realistic and efficient management of fisheries.

Description: Ecosystem-based fisheries management seeks to consider trade-offs among management objectives for interacting species, such as those that arise through predator–prey linkages. In particular, fisheries-targeting forage fish (small and abundant pelagic fish) might have a detrimental effect on fisheries-targeting predators that consume them. However, complexities in ecological interactions might dampen, negate, or even reverse this trade-off, because small pelagic fish can be important predators on egg stages of piscivorous fish. Further, the strength of this trade-off might depend on the extent to which piscivorous fish targeted by fisheries regulate forage species productivity. Here, we developed a novel delay-differential bioeconomic model of predator–prey and fishing dynamics to quantify how much egg predation or weak top-town control affects the strength of trade-off between forage and piscivore fisheries, and to measure how ecological interactions dictate policies that maximize steady-state profits. We parameterized the model based on ecological and economic data from the North Sea Atlantic cod ( Gadus morhua ) and Atlantic herring ( Clupea harengus ). The optimal policy was very sensitive to the ecological interactions (either egg predation or weak top-down control of forage by predators) at relatively low forage prices but was less sensitive at high forage fish prices. However, the optimal equilibrium harvest rates on forage and piscivores were not substantially different from what might be derived through analyses that did not consider species interactions. Applying the optimal multispecies policy would produce substantial losses (〉25%) in profits in the piscivore fishery, and the extent of loss was sensitive to ecological scenarios. While our equilibrium analysis is informative, a dynamic analysis under similar ecological scenarios is necessary to reveal the full economic and ecological benefits of applying ecosystem-based fishery management policies to predator–prey fishery systems.

Description: Leptocephali, the larvae of eels, grow to large sizes and are widely distributed in tropical and subtropical oceans. Their role in oceanic food webs is poorly known because they are rarely reported as food items in fish stomach content studies. Data from 13 years of research on the trophic dynamics of Pacific Ocean predatory fish indicate that among 8746 fish of 76 species/taxa (33 families) that had been feeding, only 16 fish of 6 species had remains of 34 leptocephali in their stomachs. Only 0.013% of the 256 308 total prey items were leptocephalus larvae, and 0.03% of the total prey items were juvenile or adult eels (mostly snipe eels: Nemichthyidae). There were 10 fish of 2 species of lancetfish ( Alepisaurus spp., n = 152), 2 rainbow runners ( Elagatis bipinnulata , n = 222), and 2 yellowfin tuna ( Thunnus albacares , n = 3103) that had leptocephali in their stomach contents, but all except one T. albacares (contained 15 leptocephali) had each eaten ≤3 leptocephali. A swallower, Pseudoscopelus sp., and a frigate tuna, Auxis thazard , had eaten single leptocephali. Twenty-eight bigeye tuna, Thunnus obesus , had eaten 76 juvenile/adult nemichthyid or serrivomerid eels. A literature survey found that only 15 out of 75 examined publications listed leptocephali in the stomach contents of a total of 6 species out of ~ 42 300 predatory fish of 40 species. The transparency of leptocephali and their apparent mimicry of gelatinous zooplankton could contribute to lower rates of predation. Their soft bodies likely digest rapidly, so although this study and existing literature indicate that leptocephali sometimes contribute to predatory fish diets, particularly for fish that do not exclude gelatinous prey types, and fish with low digestion rates in their stomachs such as lancetfish, their levels of contribution to fish diets and the impacts of predators on eel recruitment remain uncertain.

Description: Effective individual transferable quotas (ITQ) systems rebuild stocks and allow transfer of quotas to more efficient operators. This process requires functional markets for both quota sales and temporary quota leases. These markets are expected to respond to changes in economic rent from the fishery, which is influenced by stock abundance and the international rock lobster price. This research used multistate Markov modelling and Granger causality test to examine changes in the permanent and temporary quota trade in the Tasmanian rock lobster fishery quota market, during periods of both increasing and decreasing stock abundance. The permanent quota trade market was more active during the period of stock growth, while the quota lease market was active in both periods of stock growth and decline. In contrast to theoretical trends in ITQ fisheries, trades in both markets were not linked to the technical efficiency (i.e. catching capability) of operators, but were more driven by the quota owners' financial capacity (i.e. number of owned quotas). Prolonged and unexpected stock decline affected the quota market so that it deviated from the theoretical pattern of ITQ fisheries. Operators previously active in the market reduced their activity, while smaller operators and firms that previously had not traded became more active, so the fleet expanded with smaller operators entering.

Description: Jellyfish disruption of fisheries has been described in some coastal systems, but few thorough investigations have been conducted. To ascertain the economic impact and trend of jellyfish blooms in the Northern California Current (NCC), we mailed surveys to resident commercial shrimpers, salmon trollers, rockfish (blue, black), and groundfish fishers ( n = 872). We asked fishers to estimate the damages caused by jellyfish—including costs of relocating to avoid blooms, lost fishing time, time lost to bycatch sorting, fish depreciation, and gear damage. Of the total respondents ( n = 111), 67% reported that jellyfish reduce their seasonal revenue, but the degree of impact ranged considerably by fishery and location. Highest jellyfish nuisance corresponded to regions with the most salmon trolling effort. Using the mean revenue losses provided by respondents, we estimate that the combined economic impact of jellyfish on Oregon's salmon and pink shrimp fishers was over $650 000 in peak jellyfish season (June–September) in 2012. Fishers reported that jellyfish biomass varies annually, but most respondents (51%) reported observing no appreciable change in jellyfish populations in the last 5 years. Since economic impact analyses have been conducted primarily in areas with anomalous, high-density blooms, data from the NCC, which is not known to be experiencing increases in jellyfish abundance, provides baseline information on the socio-economic impact of jellyfish blooms in this region. In addition, the finding that jellyfish impact hook and line fisheries—not solely net fisheries—has implications for many other regions where fishers employ this gear type.

Description: Odontocete depredation on longlines involves socioeconomic and conservation issues with significant losses for fisheries and potential impacts on wild populations of depredating species. As technical solutions to this conflict are limited and difficult to implement, this study aimed to identify fishing practices that could reduce odontocete depredation, with a focus on killer whales (Orcinus orca) interacting with Patagonian toothfish (Dissostichus eleginoides) longliners off the Crozet islands. Data collected by fishery observers from 6013 longline sets between 2003 and 2013 allowed us to statistically detect the significant influence of five operational variables using GLMMs. The probability of interactions between vessels and killer whales was decreased by (i) the number of vessels operating simultaneously in the area: the limited number of depredating killer whales may induce a dilution effect with increased fleet size, and (ii) depth of longline sets: vessels operating in shallow waters may be more accessible to whales that are initially distributed on peri-insular shelves. The cpue was negatively influenced by (iii) length of longlines: longer sets may provide killer whales access to a greater proportion of hooked fish per set, and positively influenced by (iv) hauling speed: increased speed may shorten the time during which toothfish are accessible to whales during hauling. The time it takes for killer whales to reach vessels was positively correlated to (v) the distance travelled between longline sets with an estimated threshold of 100 km beyond which whales seem to temporarily lose track of vessels. These findings provide insightful guidelines about what fishing strategy to adopt given these variables to reduce killer whale depredation here and in similar situations elsewhere. To a greater extent, this study is illustrative of how collaborative work with fishermen in a fully controlled fishery framework may lead to the definition of cost-limited and easy-to-implement mitigation solutions when facing such human-wildlife conflict.

Description: In Alaskan waters, depredation on sablefish longline gear by sperm whales increases harvesting cost, negatively biases stock assessments, and presents a risk of entanglement for whales. The Southeast Alaska Sperm Whale Avoidance Project (SEASWAP), a collaborative effort involving industry, scientists, and managers, since 2003 has undertaken research to evaluate depredation with a goal of recommending measures to reduce interactions. Prior to 2003, little was known about sperm whale distribution and behaviour in the Gulf of Alaska (GOA). Although fishers were reporting increasing interactions, the level of depredation varied with no apparent predictor of occurrence across vessels. Between 2003 and 2007, fishers were provided with fishery logbooks and recorded information on whale behaviour, whale presence and absence, during the set, soak, and haul for 319 sets in the GOA. Data were evaluated for a vessel, area, and seasonal (month) effect in the presence and absence of sperm whales. Using catch per unit effort ( cpue ) as a metric, in kg/100 hooks, results indicated that depredation depended on both the vessel and the area. More whales associated with vessels from April to August. Sperm whales were also likely to be present when cpue was high, revealing that whales and fishers both knew the most productive fishing areas, but confounding the use of cpue as a metric for depredation. Using a Bayesian mark-recapture analysis and the sightings histories of photo-identified whales, an estimated $$\hat{N}=135$$ (95% CI 124, 153) sperm whales were associating with vessels in 2014. A spatial model was fitted to 319 longline sets and quantified a 3% loss in cpue , comparable to other global studies on sperm whale depredation. Through all phases of SEASWAP, our understanding of depredation has gained significantly. This successful collaboration should be considered as a model to create partnerships and build collaborations between researchers and fisherpeople encountering marine mammal interactions with fishing gear.

Description: This paper provides a synthesis of results obtained as part of a long-term collaborative study involving biologists, fishers, and resource managers—centring on the occurrence of killer whales in the Crozet Archipelago before and after the implementation of a demersal longline fishery for Patagonian toothfish. Depredation behaviour was reported as soon as the fishery was initiated, with dramatic effects on both the demographic trajectories of the killer whales and on the amount of fish lost by the fishers. Killer whales interacting with the fishery exhibited very high mortality rates when illegal fishing took place, while killer whales not interacting were unaffected. However, after illegal fishing ended, killer whales interacting with the fishery exhibited both higher fecundity and survival rates compared with killer whales not interacting. Since whales typically removed fish entirely from the hooks, an adapted methodology that did not rely on determining the number of damaged fish was developed to estimate depredation rates. In the Crozet EEZ over a 10-year period, 33.9% of the total amount of Patagonian toothfish caught, representing a total of 28 million , was estimated to be lost due to the combined effects of killer whale and sperm whale depredation. In an effort to reduce depredation losses, modifications to fishing methods, such as changing the fishing season, changing fishing areas when exposed to depredation and changing longline length and hauling speed were successfully tested. Acoustic deterrent devices were ineffective in deterring killer whales from depredating longlines. Alternative fishing gears, such as fish pots, were also tested. However, while providing encouraging results regarding the suppression of depredation and seabird bycatch, fish pots were not efficient enough to sustain an economically viable fishery. In conclusion, we discuss how the findings of this comprehensive study can be used elsewhere in fisheries confronted with depredation.

Description: The heart is a muscle with high energy demands. Hence, most patients with mitochondrial disease produced by defects in the oxidative phosphorylation (OXPHOS) system are susceptible to cardiac involvement. The presentation of mitochondrial cardiomyopathy includes hypertrophic, dilated and left ventricular noncompaction, but the molecular mechanisms involved in cardiac impairment are unknown. One of the most frequent OXPHOS defects in humans frequently associated with cardiomyopathy is cytochrome c oxidase (COX) deficiency caused by mutations in COX assembly factors such as Sco1 and Sco2. To investigate the molecular mechanisms that underlie the cardiomyopathy associated with Sco deficiency, we have heart specifically interfered scox expression, the single Drosophila Sco orthologue. Cardiac-specific knockdown of scox reduces fly lifespan, and it severely compromises heart function and structure, producing dilated cardiomyopathy. Cardiomyocytes with low levels of scox have a significant reduction in COX activity and they undergo a metabolic switch from OXPHOS to glycolysis, mimicking the clinical features found in patients harbouring Sco mutations. The major cardiac defects observed are produced by a significant increase in apoptosis, which is dp53-dependent. Genetic and molecular evidence strongly suggest that dp53 is directly involved in the development of the cardiomyopathy induced by scox deficiency. Remarkably, apoptosis is enhanced in the muscle and liver of Sco2 knock-out mice, clearly suggesting that cell death is a key feature of the COX deficiencies produced by mutations in Sco genes in humans.

Description: Understanding the regulatory landscape of the human genome is a central question in complex trait genetics. Most single-nucleotide polymorphisms (SNPs) associated with cancer risk lie in non-protein-coding regions, implicating regulatory DNA elements as functional targets of susceptibility variants. Here, we describe genome-wide annotation of regions of open chromatin and histone modification in fallopian tube and ovarian surface epithelial cells (FTSECs, OSECs), the debated cellular origins of high-grade serous ovarian cancers (HGSOCs) and in endometriosis epithelial cells (EECs), the likely precursor of clear cell ovarian carcinomas (CCOCs). The regulatory architecture of these cell types was compared with normal human mammary epithelial cells and LNCaP prostate cancer cells. We observed similar positional patterns of global enhancer signatures across the three different ovarian cancer precursor cell types, and evidence of tissue-specific regulatory signatures compared to non-gynecological cell types. We found significant enrichment for risk-associated SNPs intersecting regulatory biofeatures at 17 known HGSOC susceptibility loci in FTSECs ( P = 3.8 x 10 –30 ), OSECs ( P = 2.4 x 10 –23 ) and HMECs ( P = 6.7 x 10 –15 ) but not for EECs ( P = 0.45) or LNCaP cells ( P = 0.88). Hierarchical clustering of risk SNPs conditioned on the six different cell types indicates FTSECs and OSECs are highly related (96% of samples using multi-scale bootstrapping) suggesting both cell types may be precursors of HGSOC. These data represent the first description of regulatory catalogues of normal precursor cells for different ovarian cancer subtypes, and provide unique insights into the tissue specific regulatory variation with respect to the likely functional targets of germline genetic susceptibility variants for ovarian cancer.

Description: The gene mapt codes for the microtubule-associated protein Tau. The R406W amino acid substitution in Tau is associated with frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17) characterized by Tau-positive filamentous inclusions. These filamentous Tau inclusions are present in a group of neurodegenerative diseases known as tauopathies, including Alzheimer's disease (AD). To gain more insights into the pathomechanism of tauopathies, we performed an RNAi-based large-scale screen in Drosophila melanogaster to identify genetic modifiers of Tau[R406W]-induced toxicity. A collection of RNAi lines, putatively silencing more than 7000 genes, was screened for the ability to modify Tau[R406W]-induced toxicity in vivo . This collection covered more than 50% of all protein coding fly genes and more than 90% of all fly genes known to have a human ortholog. Hereby, we identified 62 genes that, when silenced by RNAi, modified Tau-induced toxicity specifically. Among these 62 modifiers were three subunits of the Dynein/Dynactin complex. Analysis on segmental nerves of fly larvae showed that pan neural Tau[R406W] expression and concomitant silencing of Dynein/Dynactin complex members synergistically caused strong pathological changes within the axonal compartment, but only minor changes at synapses. At the larval stage, these alterations did not cause locomotion deficits, but became evident in adult flies. Our data suggest that Tau-induced detrimental effects most likely originate from axonal rather than synaptic dysfunction and that impaired retrograde transport intensifies detrimental effects of Tau in axons. In conclusion, our findings contribute to the elucidation of disease mechanisms in tauopathies like FTDP-17 or AD.

Description: Retinitis pigmentosa (RP), the most common form of inherited retinal degeneration, is clinically and genetically heterogeneous and can appear as syndromic or non-syndromic. Mucopolysaccharidosis type IIIC (MPS IIIC) is a lethal disorder, caused by mutations in the heparan-alpha-glucosaminide N-acetyltransferase ( HGSNAT ) gene and characterized by progressive neurological deterioration, with retinal degeneration as a prominent feature. We identified HGSNAT mutations in six patients with non-syndromic RP. Whole exome sequencing (WES) in an Ashkenazi Jewish Israeli RP patient revealed a novel homozygous HGSNAT variant, c.370A〉T, which leads to partial skipping of exon 3. Screening of 66 Ashkenazi RP index cases revealed an additional family with two siblings homozygous for c.370A〉T. WES in three Dutch siblings with RP revealed a complex HGSNAT variant, c.[398G〉C; 1843G〉A] on one allele, and c.1843G〉A on the other allele. HGSNAT activity levels in blood leukocytes of patients were reduced compared with healthy controls, but usually higher than those in MPS IIIC patients. All patients were diagnosed with non-syndromic RP and did not exhibit neurological deterioration, or any phenotypic features consistent with MPS IIIC. Furthermore, four of the patients were over 60 years old, exceeding by far the life expectancy of MPS IIIC patients. HGSNAT is highly expressed in the mouse retina, and we hypothesize that the retina requires higher HGSNAT activity to maintain proper function, compared with other tissues associated with MPS IIIC, such as the brain. This report broadens the spectrum of phenotypes associated with HGSNAT mutations and highlights the critical function of HGSNAT in the human retina.

Description: Increased age, BMI and HbA1c levels are risk factors for several non-communicable diseases. However, the impact of these factors on the genome-wide DNA methylation pattern in human adipose tissue remains unknown. We analyzed the DNA methylation of ~480 000 sites in human adipose tissue from 96 males and 94 females and related methylation to age, BMI and HbA1c. We also compared epigenetic signatures in adipose tissue and blood. Age was significantly associated with both altered DNA methylation and expression of 1050 genes (e.g. FHL2 , NOX4 and PLG ). Interestingly, many reported epigenetic biomarkers of aging in blood, including ELOVL2 , FHL2 , KLF14 and GLRA1 , also showed significant correlations between adipose tissue DNA methylation and age in our study. The most significant association between age and adipose tissue DNA methylation was found upstream of ELOVL2 . We identified 2825 genes (e.g. FTO , ITIH5 , CCL18 , MTCH2 , IRS1 and SPP1 ) where both DNA methylation and expression correlated with BMI. Methylation at previously reported HIF3A sites correlated significantly with BMI in females only. HbA1c (range 28–46 mmol/mol) correlated significantly with the methylation of 711 sites, annotated to, for example, RAB37 , TICAM1 and HLA-DPB1 . Pathway analyses demonstrated that methylation levels associated with age and BMI are overrepresented among genes involved in cancer, type 2 diabetes and cardiovascular disease. Our results highlight the impact of age, BMI and HbA1c on epigenetic variation of candidate genes for obesity, type 2 diabetes and cancer in human adipose tissue. Importantly, we demonstrate that epigenetic biomarkers in blood can mirror age-related epigenetic signatures in target tissues for metabolic diseases such as adipose tissue.

Description: Interstitial lung disease, nephrotic syndrome and junctional epidermolysis bullosa is an autosomal recessive multiorgan disorder caused by mutations in the gene for the integrin α3 subunit ( ITGA3 ). The full spectrum of manifestations and genotype–phenotype correlations is still poorly characterized. Here, we uncovered the disease-causing role and the molecular mechanisms underlying a homozygous ITGA3 mutation leading to the single amino acid substitution, p.R463W. The patient suffered from respiratory distress and episodes of cyanosis with onset in the first week of life and had a nephrotic syndrome. Although there was no clinical evidence for cutaneous fragility, the analysis of a skin sample and of skin epithelial cells enabled the direct assessment of the authentic mutant protein. We show that the mutation altered the conformation of the extracellular β-propeller domain of the integrin α3 subunit preventing correct processing of N-linked oligosaccharides, heterodimerization with β1 integrin and maturation through cleavage into heavy and light chains in the Golgi. Confocal microscopy demonstrated that the mutant protein accumulated intracellularly, but it was not present in focal adhesions or on the cell membrane as shown by flow cytometry. These findings highlight that single amino acid changes in the integrin α3 subunit may crucially alter the structure and complex processing of this integrin, completely preventing its functionality. The present report also underscores that ITGA3 mutations may account for atypical cases solely with early onset respiratory and renal involvement.

Description: Gestational age (GA) and birth weight have been implicated in the determination of long-term health. It has been hypothesized that changes in DNA methylation may mediate these long-term effects. We obtained DNA methylation profiles from cord blood and peripheral blood at ages 7 and 17 in the same children from the Avon Longitudinal Study of Parents and Children. Repeated-measures data were used to investigate changes in birth-related methylation during childhood and adolescence. Ten developmental phenotypes (e.g. height) were analysed to identify possible mediation of health effects by DNA methylation. In cord blood, methylation at 224 CpG sites was found to be associated with GA and 23 CpG sites with birth weight. Methylation changed in the majority of these sites over time, but neither birth characteristic was strongly associated with methylation at age 7 or 17 (using a conservative correction for multiple testing of P 〈 1.03 x 10 –7 ), suggesting resolution of differential methylation by early childhood. Associations were observed between birth weight-associated CpG sites and phenotypic characteristics in childhood. One strong association involved birth weight, methylation of a CpG site proximal to the NFIX locus and bone mineral density at age 17. Analysis of serial methylation from birth to adolescence provided evidence for a lack of persistence of methylation differences beyond early childhood. Sites associated with birth weight were linked to developmental genes and have methylation levels which are associated with developmental phenotypes. Replication and interrogation of causal relationships are needed to substantiate whether methylation differences at birth influence the association between birth weight and development.

Description: Glycosaminoglycans (GAG) play a ubiquitous role in tissues and cells. In eukaryotic cells, heparan sulfate (HS) is initially degraded by an endo-β-glucuronidase called heparanase-1 (HPSE). HS oligosaccharides generated by the action of HPSE intensify the activity of signaling molecules, activating inflammatory response, tumor metastasis, and angiogenesis. The aim of the present study was to understand if sulfated GAG could modulate HPSE, since the mechanisms that regulate HPSE have not been completely defined. CHO-K1 cells were treated with 4-methylumbelliferone (4-MU) and sodium chlorate, to promote total inhibition of GAG synthesis, and reduce the sulfation pattern, respectively. The GAG profile of the wild CHO-K1 cells and CHO-745, deficient in xylosyltransferase, was determined after [ 35 S]-sulfate labeling. HPSE expression was determined via real-time quantitative polymerase chain reaction. Total ablation of GAG with 4-MU in CHO-K1 inhibited HPSE expression, while the lack of sulfation had no effect. Interestingly, 4-MU had no effect in CHO-745 cells for these assays. In addition, a different enzyme location was observed in CHO-K1 wild-type cells, which presents HPSE mainly in the extracellular matrix, in comparison with the CHO-745 mutant cells, which is found in the cytoplasm. In view of our results, we can conclude that GAG are essential modulators of HPSE expression and location. Therefore, GAG profile could impact cell behavior mediated by the regulation of HPSE.

Description: Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder affecting carriers of the fragile X-premutation, who have an expanded CGG repeat in the 5'-UTR of the FMR1 gene. FXTAS is characterized by progressive development of intention tremor, ataxia, parkinsonism and neuropsychological problems. The disease is thought to be caused by a toxic RNA gain-of-function mechanism, and the major hallmark of the disease is ubiquitin-positive intranuclear inclusions in neurons and astrocytes. We have developed a new transgenic mouse model in which we can induce expression of an expanded repeat in the brain upon doxycycline (dox) exposure (i.e. Tet-On mice). This Tet-On model makes use of the PrP-rtTA driver and allows us to study disease progression and possibilities of reversibility. In these mice, 8 weeks of dox exposure was sufficient to induce the formation of ubiquitin-positive intranuclear inclusions, which also stain positive for the RAN translation product FMRpolyG. Formation of these inclusions is reversible after stopping expression of the expanded CGG RNA at an early developmental stage. Furthermore, we observed a deficit in the compensatory eye movements of mice with inclusions, a functional phenotype that could be reduced by stopping expression of the expanded CGG RNA early in the disease development. Taken together, this study shows, for the first time, the potential of disease reversibility and suggests that early intervention might be beneficial for FXTAS patients.

Description: Mutations affecting specific splicing regulatory elements offer suitable models to better understand their interplay and to devise therapeutic strategies. Here we characterize a meaningful splicing model in which numerous Hemophilia B-causing mutations, either missense or at the donor splice site (5'ss) of coagulation F9 exon 2, promote aberrant splicing by inducing the usage of a strong exonic cryptic 5'ss. Splicing assays with natural and artificial F9 variants indicated that the cryptic 5'ss is regulated, among a network of regulatory elements, by an exonic splicing silencer (ESS). This finding and the comparative analysis of the F9 sequence across species showing that the cryptic 5'ss is always paralleled by the conserved ESS support a compensatory mechanism aimed at minimizing unproductive splicing. To recover splicing we tested antisense oligoribonucleotides masking the cryptic 5'ss, which were effective on exonic changes but promoted exon 2 skipping in the presence of mutations at the authentic 5'ss. On the other hand, we observed a very poor correction effect by small nuclear RNA U1 (U1snRNA) variants with increased or perfect complementarity to the defective 5'ss, a strategy previously exploited to rescue splicing. Noticeably, the combination of the mutant-specific U1snRNAs with antisense oligonucleotides produced appreciable amounts of correctly spliced transcripts (from 0 to 20–40%) from several mutants of the exon 2 5'ss. Based on the evidence of an altered interplay among ESS, cryptic and the authentic 5'ss as a disease-causing mechanism, we provide novel experimental insights into the combinatorial correction activity of antisense molecules and compensatory U1snRNAs.

Description: Facioscapulohumeral muscular dystrophy (FSHD) is caused by the aberrant expression of the DUX4 transcription factor in skeletal muscle. The DUX4 retrogene is encoded in the D4Z4 macrosatellite repeat array, and smaller array size or a mutation in the SMCHD1 gene results in inefficient epigenetic repression of DUX4 in skeletal muscle, causing FSHD1 and FSHD2, respectively. Previously we showed that the entire D4Z4 repeat is bi-directionally transcribed with the generation of small si- or miRNA-like fragments and suggested that these might suppress DUX4 expression through the endogenous RNAi pathway. Here we show that exogenous siRNA targeting the region upstream of the DUX4 transcription start site suppressed DUX4 mRNA expression and increased both H3K9 methylation and AGO2 recruitment. In contrast, similarly targeted MOE-gapmer antisense oligonucleotides that degrade RNA but do not engage the RNAi pathway did not repress DUX4 expression. In addition, knockdown of DICER or AGO2 using either siRNA or MOE-gapmer chemistries resulted in the induction of DUX4 expression in control muscle cells that normally do not express DUX4 , indicating that the endogenous RNAi pathway is necessary to maintain repression of DUX4 in control muscle cells. Together these data demonstrate a role of the endogenous RNAi pathway in repeat-mediated epigenetic repression of the D4Z4 macrosatellite repeat, and show that enhancing the activity of this pathway by supplying exogenous siRNA oligonucleotides represents a potential therapeutic approach to silencing DUX4 in FSHD.

Description: Overgrowth syndromes comprise a group of heterogeneous disorders characterised by excessive growth parameters, often in association with intellectual disability. To identify new causes of human overgrowth, we have been undertaking trio-based exome sequencing studies in overgrowth patients and their unaffected parents. Prioritisation of functionally relevant genes with multiple unique de novo mutations revealed four mutations in protein phosphatase 2A (PP2A) regulatory subunit B family genes protein phosphatase 2, regulatory Subunit B’, beta (PPP2R5B) ; protein phosphatase 2, regulatory Subunit B’, gamma (PPP2R5C) ; and protein phosphatase 2, regulatory Subunit B’, delta (PPP2R5D). This observation in 3 related genes in 111 individuals with a similar phenotype is greatly in excess of the expected number, as determined from gene-specific de novo mutation rates ( P = 1.43 x 10 –10 ). Analysis of exome-sequencing data from a follow-up series of overgrowth probands identified a further pathogenic mutation, bringing the total number of affected individuals to 5. Heterozygotes shared similar phenotypic features including increased height, increased head circumference and intellectual disability. The mutations clustered within a region of nine amino acid residues in the aligned protein sequences ( P = 1.6 x 10 –5 ). We mapped the mutations onto the crystal structure of the PP2A holoenzyme complex to predict their molecular and functional consequences. These studies suggest that the mutations may affect substrate binding, thus perturbing the ability of PP2A to dephosphorylate particular protein substrates. PP2A is a major negative regulator of v-akt murine thymoma viral oncogene homolog 1 (AKT). Thus, our data further expand the list of genes encoding components of the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/AKT signalling cascade that are disrupted in human overgrowth conditions.

Description: Miles–Carpenter syndrome (MCS) was described in 1991 as an XLID syndrome with fingertip arches and contractures and mapped to proximal Xq. Patients had microcephaly, short stature, mild spasticity, thoracic scoliosis, hyperextendable MCP joints, rocker-bottom feet, hyperextended elbows and knees. A mutation, p.L66H, in ZC4H2 , was identified in a XLID re-sequencing project. Additional screening of linked families and next generation sequencing of XLID families identified three ZC4H2 mutations: p.R18K, p.R213W and p.V75in15aa. The families shared some relevant clinical features. In silico modeling of the mutant proteins indicated all alterations would destabilize the protein. Knockout mutations in zc4h2 were created in zebrafish and homozygous mutant larvae exhibited abnormal swimming, increased twitching, defective eye movement and pectoral fin contractures. Because several of the behavioral defects were consistent with hyperactivity, we examined the underlying neuronal defects and found that sensory neurons and motoneurons appeared normal. However, we observed a striking reduction in GABAergic interneurons. Analysis of cell-type-specific markers showed a specific loss of V2 interneurons in the brain and spinal cord, likely arising from mis-specification of neural progenitors. Injected human wt ZC4H2 rescued the mutant phenotype. Mutant zebrafish injected with human p.L66H or p.R213W mRNA failed to be rescued, while the p.R18K mRNA was able to rescue the interneuron defect. Our findings clearly support ZC4H2 as a novel XLID gene with a required function in interneuron development. Loss of function of ZC4H2 thus likely results in altered connectivity of many brain and spinal circuits.

Description: Alterations in oxidative metabolism are considered to be one of the major contributors to Huntington's disease (HD) pathogenesis. However, existing data about oxidative metabolism in HD are contradictory. Here, we investigated the effect of mutant huntingtin (mHtt) on oxidative metabolism in YAC128 mice. Both mHtt and wild-type huntingtin (Htt) were associated with mitochondria and the amount of bound Htt was four-times higher than the amount of bound mHtt. Percoll gradient-purified brain synaptic and non-synaptic mitochondria as well as unpurified brain, liver and heart mitochondria, isolated from 2- and 10-month-old YAC128 mice and age-matched WT littermates had similar respiratory rates. There was no difference in mitochondrial membrane potential or ADP and ATP levels. Expression of selected nuclear-encoded mitochondrial proteins in 2- and 10-month-old YAC128 and WT mice was similar. Cultured striatal and cortical neurons from YAC128 and WT mice had similar respiratory and glycolytic activities as measured with Seahorse XF24 analyzer in medium containing 10 m m glucose and 15 m m pyruvate. In the medium with 2.5 m m glucose, YAC128 striatal neurons had similar respiration, but slightly lower glycolytic activity. Striatal neurons had lower maximal respiration compared with cortical neurons. In vivo experiments with YAC128 and WT mice showed similar O 2 consumption, CO 2 release, physical activity, food consumption and fasted blood glucose. However, YAC128 mice were heavier and had more body fat compared with WT mice. Overall, our data argue against respiratory deficiency in YAC128 mice and, consequently, suggest that mitochondrial respiratory dysfunction is not essential for HD pathogenesis.

Description: Leucine-rich repeat kinase 2 (LRRK2) is the causative molecule of the autosomal dominant hereditary form of Parkinson's disease (PD), PARK8, which was originally defined in a study of a Japanese family (the Sagamihara family) harboring the I2020T mutation in the kinase domain. Although a number of reported studies have focused on cell death mediated by mutant LRRK2, details of the pathogenetic effect of LRRK2 still remain to be elucidated. In the present study, to elucidate the mechanism of neurodegeneration in PD caused by LRRK2, we generated induced pluripotent stem cells (iPSC) derived from fibroblasts of PD patients with I2020T LRRK2 in the Sagamihara family. We found that I2020T mutant LRRK2 iPSC-derived neurons released less dopamine than control-iPSC-derived neurons. Furthermore, we demonstrated that patient iPSC-derived neurons had a lower phospho-AKT level than control-iPSC-derived neurons, and that the former showed an increased incidence of apoptosis relative to the controls. Interestingly, patient iPSC-derived neurons exhibited activation of glycogen synthase kinase-3β (GSK-3β) and high Tau phosphorylation. In addition, the postmortem brain of the patient from whom the iPSC had been established exhibited deposition of neurofibrillary tangles as well as increased Tau phosphorylation in neurons. These results suggest that I2020T LRRK2-iPSC could be a promising new tool for reproducing the pathology of PD in the brain caused by the I2020T mutation, and applicable as a model in studies of targeted therapeutics.

Description: SOX10 is a transcription factor with well-known functions in neural crest and oligodendrocyte development. Mutations in SOX10 were first associated with Waardenburg–Hirschsprung disease (WS4; deafness, pigmentation defects and intestinal aganglionosis). However, variable phenotypes that extend beyond the WS4 definition are now reported. The neurological phenotypes associated with some truncating mutations are suggested to be the result of escape from the nonsense-mediated mRNA decay pathway; but, to date, no mechanism has been suggested for missense mutations, of which approximately 20 have now been reported, with about half of the latter shown to be redistributed to nuclear bodies of undetermined nature and function in vitro . Here, we report that p54NRB, which plays a crucial role in the regulation of gene expression during many cellular processes including differentiation, interacts synergistically with SOX10 to regulate several target genes. Interestingly, this paraspeckle protein, as well as two other members of the Drosophila behavior human splicing (DBHS) protein family, co-localize with SOX10 mutants in nuclear bodies, suggesting the possible paraspeckle nature of these foci or re-localization of the DBHS members to other subnuclear compartments. Remarkably, the co-transfection of wild-type and mutant SOX10 constructs led to the sequestration of wild-type protein in mutant-induced foci. In contrast to mutants presenting with additional cytoplasmic re-localization, those exclusively found in the nucleus alter synergistic activity between SOX10 and p54NRB. We propose that such a dominant negative effect may contribute to or be at the origin of the unique progressive and severe neurological phenotype observed in affected patients.

Description: Huntington's disease (HD) is a hereditary neurodegenerative disorder characterized by motor and cognitive impairments, involving striatum, cortex and hippocampus. Synaptic and memory dysfunction in HD mouse models have been related to low levels of brain-derived neurotrophic factor (BDNF) and imbalance between TrkB and p75 NTR receptors. In addition, astrocyte over-activation has also been suggested to contribute to HD cognitive deficits. Fingolimod (FTY720), a modulator of sphingosine-1 phosphate (S1P) receptors, has been shown to increase BDNF levels and to reduce astrogliosis, proving its potential to regulate trophic support and inflammatory response. In this view, we have investigated whether FTY720 improves synaptic plasticity and memory in the R6/1 mouse model of HD, through regulation of BDNF signaling and astroglial reactivity. Chronic administration of FTY720 from pre-symptomatic stages ameliorated long-term memory deficits and dendritic spine loss in CA1 hippocampal neurons from R6/1 mice. Furthermore, FTY720 delivery prevented astrogliosis and over-activation of nuclear factor kappa beta (NF-B) signaling in the R6/1 hippocampus, reducing tumor necrosis factor alpha (TNFα) and induced nitric oxide synthase (iNOS) levels. TNFα decrease correlated with the normalization of p75 NTR expression in the hippocampus of FTY720-treated R6/1 mice, thus preventing p75 NTR /TrkB imbalance. In addition, FTY720 increased cAMP levels and promoted phosphorylation of CREB and RhoA in the hippocampus of R6/1 mice, further supporting its role in the enhancement of synaptic plasticity. Our findings provide new insights into the mechanism of action of FTY720 and reveal a novel therapeutic strategy to treat memory deficits in HD.

Description: DDX11 was recently identified as a cause of Warsaw breakage syndrome (WABS). However, the functional mechanism of DDX11 and the contribution of clinically described mutations to the pathogenesis of WABS are elusive. Here, we show that DDX11 is a novel nucleolar protein that preferentially binds to hypomethylated active ribosomal DNA (rDNA) gene loci, where it interacts with upstream binding factor (UBF) and the RNA polymerase I (Pol I). DDX11 knockdown changed the epigenetic state of rDNA loci from euchromatic structures to more heterochromatic structures, reduced the activity of UBF, decreased the recruitment of UBF and RPA194 (a subunit of Pol I) to rDNA promoter, suppressed rRNA transcription and thereby inhibited growth and proliferation of HeLa cells. Importantly, two indentified WABS-derived mutants, R263Q and K897del, and a Fe–S deletion construct demonstrated significantly reduced binding abilities to rDNA promoters and lowered DNA-dependent ATPase activities compared with wild-type DDX11. Knockdown of the zebrafish ortholog of human DDX11 by morpholinos resulted in growth retardation and vertebral and craniofacial malformations in zebrafish, concomitant with the changes in histone epigenetic modifications at rDNA loci, the reduction of Pol I recruitment to the rDNA promoter and a significant decrease in nascent pre-RNA levels. These growth disruptions in zebrafish in response to DDX11 reduction showed similarities to the clinically described developmental abnormalities found in WABS patients for the first time in any vertebrate. Thus, our results indicate that DDX11 functions as a positive regulator of rRNA transcription and provides a novel insight into the pathogenesis of WABS.

Description: Motivation: Very large studies are required to provide sufficiently big sample sizes for adequately powered association analyses. This can be an expensive undertaking and it is important that an accurate sample size is identified. For more realistic sample size calculation and power analysis, the impact of unmeasured aetiological determinants and the quality of measurement of both outcome and explanatory variables should be taken into account. Conventional methods to analyse power use closed-form solutions that are not flexible enough to cater for all of these elements easily. They often result in a potentially substantial overestimation of the actual power. Results: In this article, we describe the Estimating Sample-size and Power in R by Exploring Simulated Study Outcomes tool that allows assessment errors in power calculation under various biomedical scenarios to be incorporated. We also report a real world analysis where we used this tool to answer an important strategic question for an existing cohort. Availability and implementation: The software is available for online calculation and downloads at http://espresso-research.org . The code is freely available at https://github.com/ESPRESSO-research . Contact: louqman@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Given the importance of non-coding RNAs to cellular regulatory functions, it would be highly desirable to have accurate computational prediction of RNA 3D structure, a task which remains challenging. Even for a short RNA sequence, the space of tertiary conformations is immense; existing methods to identify native-like conformations mostly resort to random sampling of conformations to achieve computational feasibility. However, native conformations may not be examined and prediction accuracy may be compromised due to sampling. State-of-the-art methods have yet to deliver satisfactory predictions for RNAs of length beyond 50 nucleotides. Results: This paper presents a method to tackle a key step in the RNA 3D structure prediction problem, the prediction of the nucleotide interactions that constitute the desired 3D structure. The research is based on a novel graph model, called a backbone k-tree , to tightly constrain the nucleotide interaction relationships considered for RNA 3D structures. It is shown that the new model makes it possible to efficiently predict the optimal set of nucleotide interactions (including the non-canonical interactions in all recently revealed families) from the query sequence along with known or predicted canonical basepairs. The preliminary results indicate that in most cases the new method can predict with a high accuracy the nucleotide interactions that constitute the 3D structure of the query sequence. It thus provides a useful tool for the accurate prediction of RNA 3D structure. Availability and Implementation: The source package for BkTree is available at http://rna-informatics.uga.edu/index.php?f=software&p=BkTree . Contact: lding@uga.edu or cai@cs.uga.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: RNAs fold into complex structures that are integral to the diverse mechanisms underlying RNA regulation of gene expression. Recent development of transcriptome-wide RNA structure profiling through the application of structure-probing enzymes or chemicals combined with high-throughput sequencing has opened a new field that greatly expands the amount of in vitro and in vivo RNA structural information available. The resultant datasets provide the opportunity to investigate RNA structural information on a global scale. However, the analysis of high-throughput RNA structure profiling data requires considerable computational effort and expertise. Results: We present a new platform, StructureFold, that provides an integrated computational solution designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and analysis of raw high-throughput RNA structure profiling data, allowing the seamless incorporation of wet-bench structural information from chemical probes and/or ribonucleases to restrain RNA secondary structure prediction via the RNAstructure and ViennaRNA package algorithms. StructureFold performs reads mapping and alignment, normalization and reactivity derivation, and RNA structure prediction in a single user-friendly web interface or via local installation. The variation in transcript abundance and length that prevails in living cells and consequently causes variation in the counts of structure-probing events between transcripts is accounted for. Accordingly, StructureFold is applicable to RNA structural profiling data obtained in vivo as well as to in vitro or in silico datasets. StructureFold is deployed via the Galaxy platform. Availability and Implementation: StructureFold is freely available as a component of Galaxy available at: https://usegalaxy.org/ . Contact: yxt148@psu.edu or sma3@psu.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Structural variations (SVs) are large genomic rearrangements that vary significantly in size, making them challenging to detect with the relatively short reads from next-generation sequencing (NGS). Different SV detection methods have been developed; however, each is limited to specific kinds of SVs with varying accuracy and resolution. Previous works have attempted to combine different methods, but they still suffer from poor accuracy particularly for insertions. We propose MetaSV, an integrated SV caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of SVs. It also analyzes soft-clipped reads from alignment to detect insertions accurately since existing tools underestimate insertion SVs. Local assembly in combination with dynamic programming is used to improve breakpoint resolution. Paired-end and coverage information is used to predict SV genotypes. Using simulation and experimental data, we demonstrate the effectiveness of MetaSV across various SV types and sizes. Availability and implementation: Code in Python is at http://bioinform.github.io/metasv/ . Contact: rd@bina.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : We present a web server to predict the functional effect of single or multiple amino acid substitutions, insertions and deletions using the prediction tool PROVEAN. The server provides rapid analysis of protein variants from any organisms, and also supports high-throughput analysis for human and mouse variants at both the genomic and protein levels. Availability and implementation : The web server is freely available and open to all users with no login requirements at http://provean.jcvi.org . Contact: achan@jcvi.org Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: In attempts to determine the genetic causes of human disease, researchers are often faced with a large number of candidate genes. Linkage studies can point to a genomic region containing hundreds of genes, while the high-throughput sequencing approach will often identify a great number of non-synonymous genetic variants. Since systematic experimental verification of each such candidate gene is not feasible, a method is needed to decide which genes are worth investigating further. Computational gene prioritization presents itself as a solution to this problem, systematically analyzing and sorting each gene from the most to least likely to be the disease-causing gene, in a fraction of the time it would take a researcher to perform such queries manually. Results: Here, we present Gene TIssue Expression Ranker (GeneTIER), a new web-based application for candidate gene prioritization. GeneTIER replaces knowledge-based inference traditionally used in candidate disease gene prioritization applications with experimental data from tissue-specific gene expression datasets and thus largely overcomes the bias toward the better characterized genes/diseases that commonly afflict other methods. We show that our approach is capable of accurate candidate gene prioritization and illustrate its strengths and weaknesses using case study examples. Availability and Implementation: Freely available on the web at http://dna.leeds.ac.uk/GeneTIER/. Contact: umaan@leeds.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The role of personalized medicine and target treatment in the clinical management of cancer patients has become increasingly important in recent years. This has made the task of precise histological substratification of cancers crucial. Increasingly, genomic data are being seen as a valuable classifier. Specifically, copy number alteration (CNA) profiles generated by next-generation sequencing (NGS) can become a determinant for tumours subtyping. The principle purpose of this study is to devise a model with good prediction capability for the tumours histological subtypes as a function of both the patients covariates and their genome-wide CNA profiles from NGS data. Results: We investigate a logistic regression for modelling tumour histological subtypes as a function of the patients’ covariates and their CNA profiles, in a mixed model framework. The covariates, such as age and gender, are considered as fixed predictors and the genome-wide CNA profiles are considered as random predictors. We illustrate the application of this model in lung and oral cancer datasets, and the results indicate that the tumour histological subtypes can be modelled with a good fit. Our cross-validation indicates that the logistic regression exhibits the best prediction relative to other classification methods we considered in this study. The model also exhibits the best agreement in the prediction between smooth-segmented and circular binary-segmented CNA profiles. Availability and implementation: An R package to run a logistic regression is available in http://www1.maths.leeds.ac.uk/~arief/R/CNALR/ . Contact: a.gusnanto@leeds.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Metabolic network mapping is a widely used approach for integration of metabolomic experimental results with biological domain knowledge. However, current approaches can be limited by biochemical domain or pathway knowledge which results in sparse disconnected graphs for real world metabolomic experiments. MetaMapR integrates enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate richly connected metabolic networks. This open source, web-based or desktop software, written in the R programming language, leverages KEGG and PubChem databases to derive associations between metabolites even in cases where biochemical domain or molecular annotations are unknown. Network calculation is enhanced through an interface to the Chemical Translation System, which allows metabolite identifier translation between 〉200 common biochemical databases. Analysis results are presented as interactive visualizations or can be exported as high-quality graphics and numerical tables which can be imported into common network analysis and visualization tools. Availability and Implementation: Freely available at http://dgrapov.github.io/MetaMapR/ . Requires R and a modern web browser. Installation instructions, tutorials and application examples are available at http://dgrapov.github.io/MetaMapR/ . Contact: ofiehn@ucdavis.edu

Description: Motivation: The Cellular Phenotype Database (CPD) is a repository for data derived from high-throughput systems microscopy studies. The aims of this resource are: (i) to provide easy access to cellular phenotype and molecular localization data for the broader research community; (ii) to facilitate integration of independent phenotypic studies by means of data aggregation techniques, including use of an ontology and (iii) to facilitate development of analytical methods in this field. Results: In this article we present CPD, its data structure and user interface, propose a minimal set of information describing RNA interference experiments, and suggest a generic schema for management and aggregation of outputs from phenotypic or molecular localization experiments. The database has a flexible structure for management of data from heterogeneous sources of systems microscopy experimental outputs generated by a variety of protocols and technologies and can be queried by gene, reagent, gene attribute, study keywords, phenotype or ontology terms. Availability and implementation: CPD is developed as part of the Systems Microscopy Network of Excellence and is accessible at http://www.ebi.ac.uk/fg/sym . Contact: jes@ebi.ac.uk or ugis@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata , a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae–Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.

Description: : Specific recognition of DNA by proteins is a crucial step of many biological processes. PDIviz is a plugin for the PyMOL molecular visualization system that analyzes protein–DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free DNA. The plugin provides three distinct three-dimensional visualization modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type (hydrogen bond donors/acceptors, hydrophobic and thymine methyl). Each mode comes in three styles to focus the visual analysis on the protein or DNA side of the interface, or on the nucleotide sequence. PDIviz allows for the generation of publication quality images, all calculated data can be written to disk, and a command line interface is provided for automating tasks. The plugin may be helpful for the detailed identification of regions involved in DNA base and shape readout, and can be particularly useful in rapidly pinpointing the overall mode of interaction. Availability and implementation: Freely available at http://melolab.org/pdiviz/ as a PyMOL plugin. Tested with incentive, educational, and open source versions of PyMOL on Windows, Mac and Linux systems. Contact: aschueller@bio.puc.cl Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: We report the identification of a novel gene family (named MgCRP-I) encoding short secreted cysteine-rich peptides in the Mediterranean mussel Mytilus galloprovincialis . These peptides display a highly conserved pre-pro region and a hypervariable mature peptide comprising six invariant cysteine residues arranged in three intramolecular disulfide bridges. Although their cysteine pattern is similar to cysteines-rich neurotoxic peptides of distantly related protostomes such as cone snails and arachnids, the different organization of the disulfide bridges observed in synthetic peptides and phylogenetic analyses revealed MgCRP-I as a novel protein family. Genome- and transcriptome-wide searches for orthologous sequences in other bivalve species indicated the unique presence of this gene family in Mytilus spp. Like many antimicrobial peptides and neurotoxins, MgCRP-I peptides are produced as pre-propeptides, usually have a net positive charge and likely derive from similar evolutionary mechanisms, that is, gene duplication and positive selection within the mature peptide region; however, synthetic MgCRP-I peptides did not display significant toxicity in cultured mammalian cells, insecticidal, antimicrobial, or antifungal activities. The functional role of MgCRP-I peptides in mussel physiology still remains puzzling.

Description: Most sequenced eukaryotic genomes show a large excess of recent duplicates. As duplicates age, both the population genetic process of failed fixation and the mutation-driven process of nonfunctionalization act to reduce the observed number of duplicates. Understanding the processes generating the age distributions of recent duplicates is important to also understand the role of duplicate genes in the functional divergence of genomes. To date, mechanistic models for duplicate gene retention only account for the mutation-driven nonfunctionalization process. Here, a neutral model for the distribution of synonymous substitutions in duplicated genes which are segregating and expected to never fix in a population is introduced. This model enables differentiation of neutral loss due to failed fixation from loss due to mutation-driven nonfunctionalization. The model has been validated on simulated data and subsequent analysis with the model on genomic data from human and mouse shows that conclusions about the underlying mechanisms for duplicate gene retention can be sensitive to consideration of population genetic processes.

Description: : In next generation sequencing (NGS)-based genetic studies, researchers typically perform genotype calling first and then apply standard genotype-based methods for association testing. However, such a two-step approach ignores genotype calling uncertainty in the association testing step and may incur power loss and/or inflated type-I error. In the recent literature, a few robust and efficient likelihood based methods including both likelihood ratio test (LRT) and score test have been proposed to carry out association testing without intermediate genotype calling. These methods take genotype calling uncertainty into account by directly incorporating genotype likelihood function (GLF) of NGS data into association analysis. However, existing LRT methods are computationally demanding or do not allow covariate adjustment; while existing score tests are not applicable to markers with low minor allele frequency (MAF). We provide an LRT allowing flexible covariate adjustment, develop a statistically more powerful score test and propose a combination strategy (UNC combo) to leverage the advantages of both tests. We have carried out extensive simulations to evaluate the performance of our proposed LRT and score test. Simulations and real data analysis demonstrate the advantages of our proposed combination strategy: it offers a satisfactory trade-off in terms of computational efficiency, applicability (accommodating both common variants and variants with low MAF) and statistical power, particularly for the analysis of quantitative trait where the power gain can be up to ~60% when the causal variant is of low frequency (MAF 〈 0.01). Availability and implementation : UNC combo and the associated R files, including documentation, examples, are available at http://www.unc.edu/~yunmli/UNCcombo/ Contact: yunli@med.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation : Recombined T- and B-cell receptor repertoires are increasingly being studied using next generation sequencing (NGS) in order to interrogate the repertoire composition as well as changes in the distribution of receptor clones under different physiological and disease states. This type of analysis requires efficient and unambiguous clonotype assignment to a large number of NGS read sequences, including the identification of the incorporated V and J gene segments and the CDR3 sequence. Current tools have deficits with respect to performance, accuracy and documentation of their underlying algorithms and usage. Results : We present IMSEQ, a method to derive clonotype repertoires from NGS data with sophisticated routines for handling errors stemming from PCR and sequencing artefacts. The application can handle different kinds of input data originating from single- or paired-end sequencing in different configurations and is generic regarding the species and gene of interest. We have carefully evaluated our method with simulated and real world data and show that IMSEQ is superior to other tools with respect to its clonotyping as well as standalone error correction and runtime performance. Availability and implementation: IMSEQ was implemented in C++ using the SeqAn library for efficient sequence analysis. It is freely available under the GPLv2 open source license and can be downloaded at www.imtools.org . Supplementary information : Supplementary data are available at Bioinformatics online. Contact: lkuchenb@inf.fu-berlin.de or peter.robinson@charite.de

Description: Motivation: Interactions between amino acids are important determinants of the structure, stability and function of proteins. Several tools have been developed for the identification and analysis of such interactions in proteins based on the extensive studies carried out on high-resolution structures from Protein Data Bank (PDB). Although these tools allow users to identify and analyze interactions, analysis can only be performed on one structure at a time. This makes it difficult and time consuming to study the significance of these interactions on a large scale. Results: SpeeDB is a web-based tool for the identification of protein structures based on structural properties. SpeeDB queries are executed on all structures in the PDB at once, quickly enough for interactive use. SpeeDB includes standard queries based on published criteria for identifying various structures: disulphide bonds, catalytic triads and aromatic–aromatic, sulphur–aromatic, cation– and ionic interactions. Users can also construct custom queries in the user interface without any programming. Results can be downloaded in a Comma Separated Value (CSV) format for further analysis with other tools. Case studies presented in this article demonstrate how SpeeDB can be used to answer various biological questions. Analysis of human proteases revealed that disulphide bonds are the predominant type of interaction and are located close to the active site, where they promote substrate specificity. When comparing the two homologous G protein-coupled receptors and the two protein kinase paralogs analyzed, the differences in the types of interactions responsible for stability accounts for the differences in specificity and functionality of the structures. Availability and implementation: SpeeDB is available at http://www.parallelcomputing.ca as a web service. Contact: d@drobilla.net Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: : Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores. It is designed to isolate systematic disturbances and common biological underpinnings from next-generation sequencing (NGS) data. Seq2pathway offers Bioconductor users enhanced capability in discovering collective pathway effects caused by both coding genes and cis-regulation of non-coding elements. Availability and implementation: The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html . Contact : xyang2@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Aggregation plots are frequently used to evaluate signal distributions at user-interested points in ChIP-Seq data analysis. agplus, a new and simple command-line tool, enables rapid and flexible generation of text tables tailored for aggregation plots from which users can easily design multiple groups based on user-definitions such as regulatory regions or transcription initiation sites. Availability and Implementation: This software is implemented in Ruby, supported on Linux and Mac OSX, and freely available at http://github.com/kazumits/agplus Contact: yohkawa@epigenetics.med.kyushu-u.ac.jp

Description: : We devise a novel inference algorithm to effectively solve the cancer progression model reconstruction problem. Our empirical analysis of the accuracy and convergence rate of our algorithm, CAncer PRogression Inference (CAPRI), shows that it outperforms the state-of-the-art algorithms addressing similar problems. Motivation: Several cancer-related genomic data have become available (e.g. The Cancer Genome Atlas , TCGA) typically involving hundreds of patients. At present, most of these data are aggregated in a cross-sectional fashion providing all measurements at the time of diagnosis. Our goal is to infer cancer ‘progression’ models from such data. These models are represented as directed acyclic graphs (DAGs) of collections of ‘selectivity’ relations, where a mutation in a gene A ‘selects’ for a later mutation in a gene B. Gaining insight into the structure of such progressions has the potential to improve both the stratification of patients and personalized therapy choices. Results: The CAPRI algorithm relies on a scoring method based on a probabilistic theory developed by Suppes, coupled with bootstrap and maximum likelihood inference. The resulting algorithm is efficient, achieves high accuracy and has good complexity, also, in terms of convergence properties. CAPRI performs especially well in the presence of noise in the data, and with limited sample sizes. Moreover CAPRI, in contrast to other approaches, robustly reconstructs different types of confluent trajectories despite irregularities in the data. We also report on an ongoing investigation using CAPRI to study atypical Chronic Myeloid Leukemia , in which we uncovered non trivial selectivity relations and exclusivity patterns among key genomic events. Availability and implementation: CAPRI is part of the TRanslational ONCOlogy R package and is freely available on the web at: http://bimib.disco.unimib.it/index.php/Tronco Contact: daniele.ramazzotti@disco.unimib.it Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Model organisms play critical roles in biomedical research of human diseases and drug development. An imperative task is to translate information/knowledge acquired from model organisms to humans. In this study, we address a trans-species learning problem: predicting human cell responses to diverse stimuli, based on the responses of rat cells treated with the same stimuli. Results: We hypothesized that rat and human cells share a common signal-encoding mechanism but employ different proteins to transmit signals, and we developed a bimodal deep belief network and a semi-restricted bimodal deep belief network to represent the common encoding mechanism and perform trans-species learning. These ‘deep learning’ models include hierarchically organized latent variables capable of capturing the statistical structures in the observed proteomic data in a distributed fashion. The results show that the models significantly outperform two current state-of-the-art classification algorithms. Our study demonstrated the potential of using deep hierarchical models to simulate cellular signaling systems. Availability and implementation: The software is available at the following URL: http://pubreview.dbmi.pitt.edu/TransSpeciesDeepLearning/ . The data are available through SBV IMPROVER website, https://www.sbvimprover.com/challenge-2/overview , upon publication of the report by the organizers. Contact : xinghua@pitt.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Identification of differentially expressed genes is an important step in extracting knowledge from gene expression profiling studies. The raw expression data from microarray and other high-throughput technologies is deposited into the Gene Expression Omnibus (GEO) and served as Simple Omnibus Format in Text (SOFT) files. However, to extract and analyze differentially expressed genes from GEO requires significant computational skills. Results: Here we introduce GEO2Enrichr, a browser extension for extracting differentially expressed gene sets from GEO and analyzing those sets with Enrichr, an independent gene set enrichment analysis tool containing over 70 000 annotated gene sets organized into 75 gene-set libraries. GEO2Enrichr adds JavaScript code to GEO web-pages; this code scrapes user selected accession numbers and metadata, and then, with one click, users can submit this information to a web-server application that downloads the SOFT files, parses, cleans and normalizes the data, identifies the differentially expressed genes, and then pipes the resulting gene lists to Enrichr for downstream functional analysis. GEO2Enrichr opens a new avenue for adding functionality to major bioinformatics resources such GEO by integrating tools and resources without the need for a plug-in architecture. Importantly, GEO2Enrichr helps researchers to quickly explore hypotheses with little technical overhead, lowering the barrier of entry for biologists by automating data processing steps needed for knowledge extraction from the major repository GEO. Availability and implementation: GEO2Enrichr is an open source tool, freely available for installation as browser extensions at the Chrome Web Store and FireFox Add-ons. Documentation and a browser independent web application can be found at http://amp.pharm.mssm.edu/g2e/ . Contact: avi.maayan@mssm.edu

Description: : We report the creation of Drug Signatures Database (DSigDB), a new gene set resource that relates drugs/compounds and their target genes, for gene set enrichment analysis (GSEA). DSigDB currently holds 22 527 gene sets, consists of 17 389 unique compounds covering 19 531 genes. We also developed an online DSigDB resource that allows users to search, view and download drugs/compounds and gene sets. DSigDB gene sets provide seamless integration to GSEA software for linking gene expressions with drugs/compounds for drug repurposing and translational research. Availability and implementation: DSigDB is freely available for non-commercial use at http://tanlab.ucdenver.edu/DSigDB . Supplementary information: Supplementary data are available at Bioinformatics online. Contact: aikchoon.tan@ucdenver.edu

Description: : We describe the implementation of the method introduced by Chambaz et al. in 2012. We also demonstrate its genome-wide application to the integrative search of new regions with strong association between DNA copy number and gene expression accounting for DNA methylation in breast cancers. Availability and implementation: An open-source R package tmle.npvi is available from CRAN ( http://cran.r-project.org/ ). Contact: pierre.neuvial@genopole.cnrs.fr

Description: Stenotrophomonas maltophilia , a ubiquitous Gram-negative -proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain’s phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance–nodulation–division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.

Description: Motivation: Genes with indispensable functions are identified as essential; however, the traditional gene-level studies of essentiality have several limitations. In this study, we characterized gene essentiality from a new perspective of protein domains, the independent structural or functional units of a polypeptide chain. Results: To identify such essential domains, we have developed an Expectation–Maximization (EM) algorithm-based Essential Domain Prediction (EDP) Model. With simulated datasets, the model provided convergent results given different initial values and offered accurate predictions even with noise. We then applied the EDP model to six microbial species and predicted 1879 domains to be essential in at least one species, ranging 10–23% in each species. The predicted essential domains were more conserved than either non-essential domains or essential genes. Comparing essential domains in prokaryotes and eukaryotes revealed an evolutionary distance consistent with that inferred from ribosomal RNA. When utilizing these essential domains to reproduce the annotation of essential genes, we received accurate results that suggest protein domains are more basic units for the essentiality of genes. Furthermore, we presented several examples to illustrate how the combination of essential and non-essential domains can lead to genes with divergent essentiality. In summary, we have described the first systematic analysis on gene essentiality on the level of domains. Contact: huilu.bioinfo@gmail.com or Long.Lu@cchmc.org Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Information-theoretic and compositional analysis of biological sequences, in terms of k -mer dictionaries, has a well established role in genomic and proteomic studies. Much less so in epigenomics, although the role of k -mers in chromatin organization and nucleosome positioning is particularly relevant. Fundamental questions concerning the informational content and compositional structure of nucleosome favouring and disfavoring sequences with respect to their basic building blocks still remain open. Results: We present the first analysis on the role of k -mers in the composition of nucleosome enriched and depleted genomic regions (NER and NDR for short) that is: (i) exhaustive and within the bounds dictated by the information-theoretic content of the sample sets we use and (ii) informative for comparative epigenomics. We analize four different organisms and we propose a paradigmatic formalization of k -mer dictionaries, providing two different and complementary views of the k -mers involved in NER and NDR. The first extends well known studies in this area, its comparative nature being its major merit. The second, very novel, brings to light the rich variety of k -mers involved in influencing nucleosome positioning, for which an initial classification in terms of clusters is also provided. Although such a classification offers many insights, the following deserves to be singled-out: short poly(dA:dT) tracts are reported in the literature as fundamental for nucleosome depletion, however a global quantitative look reveals that their role is much less prominent than one would expect based on previous studies. Availability and implementation: Dictionaries, clusters and Supplementary Material are available online at http://math.unipa.it/rombo/epigenomics/ . Contact: simona.rombo@unipa.it Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The number of reported genetic variants is rapidly growing, empowered by ever faster accumulation of next-generation sequencing data. A major issue is comparability. Standards that address the combined problem of inaccurately predicted breakpoints and repeat-induced ambiguities are missing. This decisively lowers the quality of ‘consensus’ callsets and hampers the removal of duplicate entries in variant databases, which can have deleterious effects in downstream analyses. Results: We introduce a sound framework for comparison of deletions that captures both tool-induced inaccuracies and repeat-induced ambiguities. We present a maximum matching algorithm that outputs virtual duplicates among two sets of predictions/annotations. We demonstrate that our approach is clearly superior over ad hoc criteria, like overlap, and that it can reduce the redundancy among callsets substantially. We also identify large amounts of duplicate entries in the Database of Genomic Variants, which points out the immediate relevance of our approach. Availability and implementation: Implementation is open source and available from https://bitbucket.org/readdi/readdi Contact: roland.wittler@uni-bielefeld.de or t.marschall@mpi-inf.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated produces an opportunity to detect species even at very low levels, provided that computational tools can effectively profile the relevant metagenomic communities. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. Here we present metaMix, a Bayesian mixture model framework for resolving complex metagenomic mixtures. We show that the use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture. Results: We demonstrate the greater accuracy of metaMix compared with relevant methods, particularly for profiling complex communities consisting of several related species. We designed metaMix specifically for the analysis of deep transcriptome sequencing datasets, with a focus on viral pathogen detection; however, the principles are generally applicable to all types of metagenomic mixtures. Availability and implementation: metaMix is implemented as a user friendly R package, freely available on CRAN: http://cran.r-project.org/web/packages/metaMix Contact: sofia.morfopoulou.10@ucl.ac.uk Supplementary information: Supplementary data are available at Bionformatics online.

Description: Motivation: A detailed analysis of multidimensional NMR spectra of macromolecules requires the identification of individual resonances (peaks). This task can be tedious and time-consuming and often requires support by experienced users. Automated peak picking algorithms were introduced more than 25 years ago, but there are still major deficiencies/flaws that often prevent complete and error free peak picking of biological macromolecule spectra. The major challenges of automated peak picking algorithms is both the distinction of artifacts from real peaks particularly from those with irregular shapes and also picking peaks in spectral regions with overlapping resonances which are very hard to resolve by existing computer algorithms. In both of these cases a visual inspection approach could be more effective than a ‘blind’ algorithm. Results: We present a novel approach using computer vision (CV) methodology which could be better adapted to the problem of peak recognition. After suitable ‘training’ we successfully applied the CV algorithm to spectra of medium-sized soluble proteins up to molecular weights of 26 kDa and to a 130 kDa complex of a tetrameric membrane protein in detergent micelles. Our CV approach outperforms commonly used programs. With suitable training datasets the application of the presented method can be extended to automated peak picking in multidimensional spectra of nucleic acids or carbohydrates and adapted to solid-state NMR spectra. Availability and implementation: CV-Peak Picker is available upon request from the authors. Contact : gsw@mol.biol.ethz.ch ; michal.walczak@mol.biol.ethz.ch ; adam.gonczarek@pwr.edu.pl Supplementary information : Supplementary data are available at Bioinformatics online.

Description: : PsyGeNET (Psychiatric disorders and Genes association NETwork) is a knowledge platform for the exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of a database and a web interface supporting data search, visualization, filtering and sharing. PsyGeNET integrates information from DisGeNET and data extracted from the literature by text mining, which has been curated by domain experts. It currently contains 2642 associations between 1271 genes and 37 psychiatric disease concepts. In its first release, PsyGeNET is focused on three psychiatric disorders: major depression, alcohol and cocaine use disorders. PsyGeNET represents a comprehensive, open access resource for the analysis of the molecular mechanisms underpinning psychiatric disorders and their comorbidities. Availability and implementation: The PysGeNET platform is freely available at http://www.psygenet.org/ . The PsyGeNET database is made available under the Open Database License ( http://opendatacommons.org/licenses/odbl/1.0/ ). Contact: lfurlong@imim.es Supplementary information : Supplementary data are available at Bioinformatics online.

Description: Genome-wide association studies (GWAS) have identified several common loci contributing to non-obstructive azoospermia (NOA). However, a substantial fraction of NOA heritability remains undefined, especially those low-frequency [defined here as having a minor allele frequency (MAF) between 0.5 and 5%] and rare (MAF below 0.5%) variants. Here, we performed a 3-stage exome-wide association study in Han Chinese men to evaluate the role of low-frequency or rare germline variants in NOA development. The discovery stage included 962 NOA cases and 1348 healthy male controls genotyped by exome chips and was followed by a 2-stage replication with an additional 2168 cases and 5248 controls. We identified three low-frequency variants located at 6p22.2 (rs2298090 in HIST1H1E encoding p.Lys152Arg: OR = 0.30, P = 2.40 x 10 –16 ) and 6p21.33 (rs200847762 in FKBPL encoding p.Pro137Leu: OR = 0.11, P = 3.77 x 10 –16 ; rs11754464 in MSH5 : OR = 1.78, P = 3.71 x 10 –7 ) associated with NOA risk after Bonferroni correction. In summary, we report an instance of newly identified signals for NOA risk in genes previously undetected through GWAS on 6p22.2–6p21.33 in a Chinese population and highlight the role of low-frequency variants with a large effect in the process of spermatogenesis.

Description: For cancer and many other complex diseases, a large number of gene signatures have been generated. In this study, we use cancer as an example and note that other diseases can be analyzed in a similar manner. For signatures generated in multiple independent studies on the same cancer type and outcome, and for signatures on different cancer types, it is of interest to evaluate their degree of overlap. Many of the existing studies simply count the number (or percentage) of overlapped genes shared by two signatures. Such an approach has serious limitations. In this study, as a demonstrating example, we consider cancer prognosis data under the Cox model. Lasso, which is representative of a large number of regularization methods, is adopted for generating gene signatures. We examine two families of measures for quantifying the degree of overlap. The first family is based on the Cox-Lasso estimates at the optimal tunings, and the second family is based on estimates across the whole solution paths. Within each family, multiple measures, which describe the overlap from different perspectives, are introduced. The analysis of TCGA (The Cancer Genome Atlas) data on five cancer types shows that the degree of overlap varies across measures, cancer types and types of (epi)genetic measurements. More investigations are needed to better describe and understand the overlaps among gene signatures.

Description: Loss-of-function mutations in the X-linked gene Methyl-CpG-binding protein 2 ( MECP2 ) cause a devastating pediatric neurological disorder called Rett syndrome. In males, these mutations typically result in severe neonatal encephalopathy and early lethality. On the other hand, owing to expression of the normal allele in ~50% of cells, females do not suffer encephalopathy but instead develop Rett syndrome. Typically females with Rett syndrome exhibit a delayed onset of neurologic dysfunction that manifests around the child's first birthday and progresses over the next few years. Features of this disorder include loss of acquired language and motor skills, intellectual impairment and hand stereotypies. The developmental regression observed in patients with Rett syndrome arises from altered neuronal function and is not the result of neurodegeneration. Maintenance of an appropriate level of MeCP2 appears integral to the function of healthy neurons as patients with increased levels of MeCP2, owing to duplication of the Xq28 region encompassing the MECP2 locus, also present with intellectual disability and progressive neurologic symptoms. Despite major efforts over the past two decades to elucidate the molecular functions of MeCP2, the mechanisms underlying the delayed appearance of symptoms remain unclear. In this review, we will highlight recent findings that have expanded our knowledge of MeCP2's functions, and we will discuss how epigenetic regulation, chromatin organization and circuit dynamics may contribute to the postnatal onset of Rett syndrome.

Description: Aims This study explores the patterns of niche differentiation in a group of seven closely related columbines (genus Aquilegia , Ranunculaceae) from the Iberian Peninsula. Populations of these columbines are subject to complex patterns of divergent selection across environments, which partly explain the taxonomic structure of the group. This suggests the hypothesis that niche divergence must have occurred along the process of diversification of the group. Methods We used MaxEnt to build environmental niche models of seven subspecies belonging to the three species of Aquilegia present in the Iberian Peninsula. From these models, we compared the environmental niches through two different approaches: ENMtools and multivariate methods. Important Findings MaxEnt distributions conformed closely to the actual distribution of the study taxa. ENMtools methods failed to uncover any clear patterns of niche differentiation or conservatism in Iberian columbines. Multivariate analyses indicate the existence of differentiation along altitudinal gradients and along a gradient of climatic conditions determined by the summer precipitation and temperatures. However, climatic conditions related to winter temperature and precipitation, as well as soil properties, were equally likely to show conservatism or divergence. The complex patterns of niche evolution we found suggest that Iberian Columbines have not been significantly constrained by forces of niche conservatism, so they could respond adaptively to the fast and profound climate changes in the Iberian Peninsula through the glacial cycles of the Pleistocene.

Description: Aims The pattern and driving factors of forest fires are of interest for fire occurrence prediction and forest fire management. The aims of the study were: (i) to describe the history of human-caused fires by season and size of burned area over time; (ii) to identify the spatial patterns of human-caused fires and test for the existence of ‘hotspots’ to determine their exact locations in the Daxing’an Mountains; (iii) to determine the driving factors that determine the spatial distribution and the possibility of human-caused fire occurrence. Methods In this study, K -function and Kernel density estimation were used to analyze the spatial pattern of human-caused fires. The analysis was conducted in S-plus and ArcGIS environments, respectively. The analysis of driving factors was performed in SPSS 19.0 based on a logistic regression model. The variables used to identify factors that influence fire occurrence included vegetation types, meteorological conditions, socioeconomic factors, topography and infrastructure factors, which were extracted and collected through the spatial analysis mode of ArcGIS and from official statistics, respectively. Important Findings The annual number of human-caused fires and the area burnt have declined since 1987 due to the implementation of a forest fire protection act. There were significant spatial heterogeneity and seasonal variations in the distribution of human-caused fires in the Daxing’an Mountains. The heterogeneity was caused by elevation, distance to the nearest railway, forest type and temperature. A logistic regression model was developed to predict the likelihood of human-caused fire occurrence in the Daxing’an Mountains; its global accuracy attained 64.8%. The model was thus comparable to other relevant studies.

Description: Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s 2 U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s 2 U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s 2 U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s 2 U:A and s 2 U:U pairs and their native counterparts. These results indicate that s 2 U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s 2 U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s 2 U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s 2 U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using 1 H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying.

Description: DNA interstrand crosslinks (ICLs) are the primary mechanism for the cytotoxic activity of many clinical anticancer drugs, and numerous strategies for forming ICLs have been developed. One such method is using crosslink-forming oligonucleotides (CFOs). In this study, we designed a 4-amino-6-oxo-2-vinylpyrimidine (AOVP) derivative with an acyclic spacer to react selectively with guanine. The AOVP CFO exhibited selective crosslinking reactivity with guanine and thymine in DNA, and with guanine in RNA. These crosslinking reactions with guanine were accelerated in the presence of CoCl 2 , NiCl 2 , ZnCl 2 and MnCl 2 . In addition, we demonstrated that the AOVP CFO was reactive toward 8-oxoguanine opposite AOVP in the duplex DNA. The structural analysis of each guanine and 8-oxoguanine adduct in the duplex DNA was investigated by high-resolution NMR. The results suggested that AOVP reacts at the N2 amine in guanine and at the N1 or N2 amines in 8-oxoguanine in the duplex DNA. This study demonstrated the first direct determination of the adduct structure in duplex DNA without enzyme digestion.

Description: The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the measurement of genome-wide gene expression. Despite its widespread use, challenges remain in RNA-seq data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety of factors or ‘batch effects’ can contribute unwanted variation to the data, commonly used RNA-seq normalization methods only correct for sequencing depth. The study of gene expression is particularly problematic when it is influenced simultaneously by a variety of biological factors in addition to the one of interest. Using examples from experimental neuroscience, we show that batch effects can dominate the signal of interest; and that the choice of normalization method affects the power and reproducibility of the results. While commonly used global normalization methods are not able to adequately normalize the data, more recently developed RNA-seq normalization can. We focus on one particular method, RUVSeq and show that it is able to increase power and biological insight of the results. Finally, we provide a tutorial outlining the implementation of RUVSeq normalization that is applicable to a broad range of studies as well as meta-analysis of publicly available data.

Description: Many antiproliferative G-quadruplexes (G4s) arise from the folding of GT-rich strands. Among these, the Thrombin Binding Aptamer (TBA), as a rare example, adopts a monomolecular well-defined G4 structure. Nevertheless, the potential anticancer properties of TBA are severely hampered by its anticoagulant action and, consequently, no related studies have appeared so far in the literature. We wish to report here that suitable chemical modifications in the TBA sequence can preserve its antiproliferative over anticoagulant activity. Particularly, we replaced one residue of the TT or TGT loops with a dibenzyl linker to develop seven new quadruplex-forming TBA based sequences (TBA-bs), which were studied for their structural (CD, CD melting, 1D NMR) and biological (fibrinogen, PT and MTT assays) properties. The three-dimensional structures of the TBA-bs modified at T13 (TBA-bs13) or T12 (TBA-bs12), the former endowed with selective antiproliferative activity, and the latter acting as potently as TBA in both coagulation and MTT assays, were further studied by 2D NMR restrained molecular mechanics. The comparative structural analyses indicated that neither the stability, nor the topology of the G4s, but the different localization of the two benzene rings of the linker was responsible for the loss of the antithrombin activity for TBA-bs13.

Description: A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea.

Description: Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events.

Description: Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.

Description: Due to their high affinity and specificity, aptamers have been widely used as effective inhibitors in clinical applications. However, the ability to activate protein function through aptamer-protein interaction has not been well-elucidated. To investigate their potential as target-specific agonists, we used SELEX to generate aptamers to the insulin receptor (IR) and identified an agonistic aptamer named IR-A48 that specifically binds to IR, but not to IGF-1 receptor. Despite its capacity to stimulate IR autophosphorylation, similar to insulin, we found that IR-A48 not only binds to an allosteric site distinct from the insulin binding site, but also preferentially induces Y1150 phosphorylation in the IR kinase domain. Moreover, Y1150-biased phosphorylation induced by IR-A48 selectively activates specific signaling pathways downstream of IR. In contrast to insulin-mediated activation of IR, IR-A48 binding has little effect on the MAPK pathway and proliferation of cancer cells. Instead, AKT S473 phosphorylation is highly stimulated by IR-A48, resulting in increased glucose uptake both in vitro and in vivo . Here, we present IR-A48 as a biased agonist able to selectively induce the metabolic activity of IR through allosteric binding. Furthermore, our study also suggests that aptamers can be a promising tool for developing artificial biased agonists to targeted receptors.

Description: Ten eleven translocation (Tet) family-mediated DNA oxidation on 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) represents a novel epigenetic modification that regulates dynamic gene expression during embryonic stem cells (ESCs) differentiation. Through the role of Tet on 5hmC regulation in stem cell development is relatively defined, how the Tet family is regulated and impacts on ESCs lineage development remains elusive. In this study, we show non-coding RNA regulation on Tet family may contribute to epigenetic regulation during ESCs differentiation, which is suggested by microRNA-29b (miR-29b) binding sites on the Tet1 3' untranslated region (3' UTR). We demonstrate miR-29b increases sharply after embyoid body (EB) formation, which causes Tet1 repression and reduction of cellular 5hmC level during ESCs differentiation. Importantly, we show this miR-29b/Tet1 regulatory axis promotes the mesendoderm lineage formation both in vitro and in vivo by inducing the Nodal signaling pathway and repressing the key target of the active demethylation pathway, Tdg. Taken together, our findings underscore the contribution of small non-coding RNA mediated regulation on DNA demethylation dynamics and the differential expressions of key mesendoderm regulators during ESCs lineage specification. MiR-29b could potentially be applied to enrich production of mesoderm and endoderm derivatives and be further differentiated into desired organ-specific cells.

Description: The emergence of multidrug-resistant pathogens will make current antibiotics ineffective. For linezolid, a member of the novel oxazolidinone class of antibiotics, 10 nucleotide mutations in the ribosome have been described conferring resistance. Hypotheses for how these mutations affect antibiotics binding have been derived based on comparative crystallographic studies. However, a detailed description at the atomistic level of how remote mutations exert long-distance effects has remained elusive. Here, we show that the G2032A-C2499A double mutation, located 〉 10 Å away from the antibiotic, confers linezolid resistance by a complex set of effects that percolate to the binding site. By molecular dynamics simulations and free energy calculations, we identify U2504 and C2452 as spearheads among binding site nucleotides that exert the most immediate effect on linezolid binding. Structural reorganizations within the ribosomal subunit due to the mutations are likely associated with mutually compensating changes in the effective energy. Furthermore, we suggest two main routes of information transfer from the mutation sites to U2504 and C2452. Between these, we observe cross-talk, which suggests that synergistic effects observed for the two mutations arise in an indirect manner. These results should be relevant for the development of oxazolidinone derivatives that are active against linezolid-resistant strains.

Description: Genes from yeast to mammals are frequently subject to non-coding transcription of their antisense strand; however the genome-wide role for antisense transcription remains elusive. As transcription influences chromatin structure, we took a genome-wide approach to assess which chromatin features are associated with nascent antisense transcription, and contrast these with features associated with nascent sense transcription. We describe a distinct chromatin architecture at the promoter and gene body specifically associated with antisense transcription, marked by reduced H2B ubiquitination, H3K36 and H3K79 trimethylation and increased levels of H3 acetylation, chromatin remodelling enzymes, histone chaperones and histone turnover. The difference in sense transcription between genes with high or low levels of antisense transcription is slight; thus the antisense transcription-associated chromatin state is not simply analogous to a repressed state. Using mutants in which the level of antisense transcription is reduced at GAL1 , or altered genome-wide, we show that non-coding transcription is associated with high H3 acetylation and H3 levels across the gene, while reducing H3K36me3. Set1 is required for these antisense transcription-associated chromatin changes in the gene body. We propose that nascent antisense and sense transcription have fundamentally distinct relationships with chromatin, and that both should be considered canonical features of eukaryotic genes.

Description: The expansion of Bantu-speaking agropastoralist populations had a great impact on the genetic, linguistic, and cultural variation of sub-Saharan Africa. It is generally accepted that Bantu languages originated in an area around the present border between Cameroon and Nigeria approximately 5,000 years ago, from where they spread South and East becoming the largest African linguistic branch. The demic consequences of this event are reflected in the relatively high genetic homogeneity observed across most of sub-Saharan Africa populations. In this work, we explored genome-wide single nucleotide polymorphism data from 28 populations to characterize the genetic components present in sub-Saharan African populations. Combining novel data from four Southern African populations with previously published results, we reject the hypothesis that the "non-Bantu" genetic component reported in South-Eastern Africa (Mozambique) reflects extensive gene flow between incoming agriculturalist and resident hunter-gatherer communities. We alternatively suggest that this novel component is the result of demographic dynamics associated with the Bantu dispersal.

Description: Dietary shifts can drive molecular evolution in mammals and a major transition in human history, the agricultural revolution, favored carbohydrate consumption. We investigated the evolutionary history of nine genes encoding brush-border proteins involved in carbohydrate digestion/absorption. Results indicated widespread adaptive evolution in mammals, with several branches experiencing episodic selection, particularly strong in bats. Many positively selected sites map to functional protein regions (e.g., within glucosidase catalytic crevices), with parallel evolution at SI (sucrase-isomaltase) and MGAM (maltase-glucoamylase). In human populations, five genes were targeted by positive selection acting on noncoding variants within regulatory elements. Analysis of ancient DNA samples indicated that most derived alleles were already present in the Paleolithic. Positively selected variants at SLC2A5 (fructose transporter) were an exception and possibly spread following the domestication of specific fruit crops. We conclude that agriculture determined no major selective event at carbohydrate metabolism genes in humans, with implications for susceptibility to metabolic disorders.

Description: Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to 2X) for six fern species from the Polypodiales ( Ceratopteris , Pteridium , Polypodium , Cystopteris ), Cyatheales ( Plagiogyria ), and Gleicheniales ( Dipteris ). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.

Description: The evolution of heterogametic sex chromosomes is often—but not always—accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) species but not in female-heterogametic (ZW) species, which will consequently exhibit "incomplete" sex chromosome dosage compensation. However, recent results suggest that at least some Lepidoptera (moths and butterflies) may prove to be an exception to this prediction. Studies in bombycoid moths indicate the presence of a chromosome-wide epigenetic mechanism that effectively balances Z chromosome gene expression between the sexes by reducing Z-linked expression in males. In contrast, strong sex chromosome dosage effects without any reduction in male Z-linked expression were previously reported in a pyralid moth, suggesting a lack of any such dosage compensating mechanism. Here we report an analysis of sex chromosome dosage compensation in Heliconius butterflies, sampling multiple individuals for several different adult tissues (head, abdomen, leg, mouth, and antennae). Methodologically, we introduce a novel application of linear mixed-effects models to assess dosage compensation, offering a unified statistical framework that can estimate effects specific to chromosome, to sex, and their interactions (i.e., a dosage effect). Our results show substantially reduced Z-linked expression relative to autosomes in both sexes, as previously observed in bombycoid moths. This observation is consistent with an increasing body of evidence that some lepidopteran species possess an epigenetic dosage compensating mechanism that reduces Z chromosome expression in males to levels comparable with females. However, this mechanism appears to be imperfect in Heliconius , resulting in a modest dosage effect that produces an average 5–20% increase in male expression relative to females on the Z chromosome, depending on the tissue. Thus our results in Heliconius reflect a mixture of previous patterns reported for Lepidoptera. In Heliconius, a moderate pattern of incomplete dosage compensation persists apparently despite the presence of an epigenetic dosage compensating mechanism. The chromosomal distributions of sex-biased genes show an excess of male-biased and a dearth of female-biased genes on the Z chromosome relative to autosomes, consistent with predictions of sexually antagonistic evolution.

Description: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.

Description: Upon stable cell line generation, chromosomal integration site of the vector DNA has a major impact on transgene expression. Here we apply an active gene environment, rather than specified genetic elements, in expression vectors used for random integration. We generated a set of Bacterial Artificial Chromosome (BAC) vectors with different open chromatin regions, promoters and gene regulatory elements and tested their impact on recombinant protein expression in CHO cells. We identified the Rosa26 BAC as the most efficient vector backbone showing a nine-fold increase in both polyclonal and clonal production of the human IgG-Fc. Clonal protein production was directly proportional to integrated vector copy numbers and remained stable during 10 weeks without selection pressure. Finally, we demonstrated the advantages of BAC-based vectors by producing two additional proteins, HIV-1 glycoprotein CN54gp140 and HIV-1 neutralizing PG9 antibody, in bioreactors and shake flasks reaching a production yield of 1 g/l.

Description: Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data ( 3DBG ), and a 3D genome browser to visualize and explore 3D genome structures ( 3DGB ). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/ .

Description: Due to their relatively low-cost per sample and broad, gene-centric coverage of CpGs across the human genome, Illumina's 450k arrays are widely used in large scale differential methylation studies. However, by their very nature, large studies are particularly susceptible to the effects of unwanted variation. The effects of unwanted variation have been extensively documented in gene expression array studies and numerous methods have been developed to mitigate these effects. However, there has been much less research focused on the appropriate methodology to use for accounting for unwanted variation in methylation array studies. Here we present a novel 2-stage approach using RUV-inverse in a differential methylation analysis of 450k data and show that it outperforms existing methods.

Description: Telomerase is a reverse transcriptase that maintains telomeres on the ends of chromosomes, allowing rapidly dividing cells to proliferate while avoiding senescence and apoptosis. Understanding telomerase gene expression and splicing at the single cell level could yield insights into the roles of telomerase during normal cell growth as well as cancer development. Here we use droplet-based single cell culture followed by single cell or colony transcript abundance analysis to investigate the relationship between cell growth and transcript abundance of the telomerase genes encoding the RNA component (hTR) and protein component (hTERT) as well as hTERT splicing. Jurkat and K562 cells were examined under normal cell culture conditions and during exposure to curcumin, a natural compound with anti-carcinogenic and telomerase activity-reducing properties. Individual cells predominantly express single hTERT splice variants, with the α+/β– variant exhibiting significant transcript abundance bimodality that is sustained through cell division. Sub-lethal curcumin exposure results in reduced bimodality of all hTERT splice variants and significant upregulation of alpha splicing, suggesting a possible role in cellular stress response. The single cell culture and transcript abundance analysis method presented here provides the tools necessary for multiparameter single cell analysis which will be critical for understanding phenotypes of heterogeneous cell populations, disease cell populations and their drug response.

Description: Mycobacterium avium ( M. a. ) subsp. paratuberculosis (MAP)—the etiologic agent of Johne’s disease—affects cattle, sheep, and other ruminants worldwide. To decipher phenotypic differences among sheep and cattle strains (belonging to MAP-S [Type-I/III], respectively, MAP-C [Type-II]), comparative genome analysis needs data from diverse isolates originating from different geographic regions of the world. This study presents the so far best assembled genome of a MAP-S-strain: Sheep isolate JIII-386 from Germany. One newly sequenced cattle isolate (JII-1961, Germany), four published MAP strains of MAP-C and MAP-S from the United States and Australia, and M. a. subsp. hominissuis (MAH) strain 104 were used for assembly improvement and comparisons. All genomes were annotated by BacProt and results compared with NCBI (National Center for Biotechnology Information) annotation. Corresponding protein-coding sequences (CDSs) were detected, but also CDSs that were exclusively determined by either NCBI or BacProt. A new Shine–Dalgarno sequence motif (5'-AGCTGG-3') was extracted. Novel CDSs including PE-PGRS family protein genes and about 80 noncoding RNAs exhibiting high sequence conservation are presented. Previously found genetic differences between MAP-types are partially revised. Four of ten assumed MAP-S-specific large sequence polymorphism regions (LSP S s) are still present in MAP-C strains; new LSP S s were identified. Independently of the regional origin of the strains, the number of individual CDSs and single nucleotide variants confirms the strong similarity of MAP-C strains and shows higher diversity among MAP-S strains. This study gives ambiguous results regarding the hypothesis that MAP-S is the evolutionary intermediate between MAH and MAP-C, but it clearly shows a higher similarity of MAP to MAH than to Mycobacterium intracellulare .

Description: Eukaryotic organelles depend on nuclear genes to perpetuate their biochemical integrity. This is true for mitochondria in all eukaryotes and plastids in plants and algae. Then how do kleptoplasts, plastids that are sequestered by some sacoglossan sea slugs, survive in the animals’ digestive gland cells in the absence of the algal nucleus encoding the vast majority of organellar proteins? For almost two decades, lateral gene transfer (LGT) from algae to slugs appeared to offer a solution, but RNA-seq analysis, later supported by genome sequencing of slug DNA, failed to find any evidence for such LGT events. Yet, isolated reports continue to be published and are readily discussed by the popular press and social media, making the data on LGT and its support for kleptoplast longevity appear controversial. However, when we take a sober look at the methods used, we realize that caution is warranted in how the results are interpreted. There is no evidence that the evolution of kleptoplasty in sea slugs involves LGT events. Based on what we know about photosystem maintenance in embryophyte plastids, we assume kleptoplasts depend on nuclear genes. However, studies have shown that some isolated algal plastids are, by nature, more robust than those of land plants. The evolution of kleptoplasty in green sea slugs involves many promising and unexplored phenomena, but there is no evidence that any of these require the expression of slug genes of algal origin.