Non-coding regulatory elements: potential roles in disease and the case of epilepsy

Non-coding DNA (ncDNA) refers to the portion of the genome that does not code for proteins and accounts for the greatest physical proportion of the human genome. ncDNA includes sequences that are transcribed into RNA molecules, such as ribosomal RNAs (rRNAs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and un-transcribed sequences that have regulatory functions, including gene promoters and enhancers. Variation in non-coding regions of the genome have an established role in human disease, with growing evidence from many areas, including several cancers, Parkinson's disease and autism. Here, we review the features and functions of the regulatory elements that are present in the non-coding genome and the role that these regions have in human disease. We then review the existing research in epilepsy and emphasise the potential value of further exploring non-coding regulatory elements in epilepsy. In addition, we outline the most widely used techniques for recognising regulatory elements throughout the genome, current methodologies for investigating variation and the main challenges associated with research in the field of non-coding DNA

Genome annotation for clinical genomic diagnostics: strengths and weaknesses

The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number of patients, the genetic basis remains unclear. As clinicians begin to consider whole-genome sequencing, an understanding of the processes and tools involved and the factors to consider in the annotation of the structure and function of genomic elements that might influence variant identification is crucial. Here, we discuss and illustrate the strengths and weaknesses of approaches for the annotation and classification of important elements of protein-coding genes, other genomic elements such as pseudogenes and the non-coding genome, comparative-genomic approaches for inferring gene function, and new technologies for aiding genome annotation, as a practical guide for clinicians when considering pathogenic sequence variation. Complete and accurate annotation of structure and function of genome features has the potential to reduce both false-negative (from missing annotation) and false-positive (from incorrect annotation) errors in causal variant identification in exome and genome sequences. Re-analysis of unsolved cases will be necessary as newer technology improves genome annotation, potentially improving the rate of diagnosis

(1S)-1-Phenylethanaminium 4-{[(1S,2S)-1-hydroxy-2,3-dihydro-1H,1\u27H-[2,2\u27-biinden]-2-yl]methyl}benzoate

The title molecular salt, C(8)H(12)N(+)·C(26)H(21)O(3)(-), contains a dimeric indane pharmacophore that demonstrates potent anti-inflammatory activity. The indane group of the anion exhibits some disorder about the α-C atom, which appears common to many structures containing this group. A model to account for the slight disorder was attempted, but this was deemed unsuccessful because applying bond-length constraints to all the bonds about the α-C atom led to instability in the refinement. The absolute configuration was determined crystallographically as S,S,S by anomalous dispersion methods with reference to both the Flack parameter and Bayesian statistics on Bijvoet differences. The configuration was also determined by an a priori knowledge of the absolute configuration of the (1S)-1-phenylethanaminium counter-ion. The molecules pack in the crystal structure to form an infinite two-dimensional hydrogen-bond network in the (100) plane of the unit cell

Movements and diving behaviour of white-chinned petrels: Diurnal variation and implications for bycatch mitigation

Many seabirds dive to forage, and the ability to use this hunting technique varies according to such factors as morphology, physiology, prey availability, and ambient light levels. Proficient divers are more able to seize sinking baits deployed by longline fishing vessels and may return them to the surface, increasing exposure of other species. Hence, diving ability has major implications for mitigating incidental mortality (bycatch) in fisheries. Here, the diving behaviour and activity patterns of the most bycaught seabird species worldwide, the white-chinned petrel (Procellaria aequinoctialis), tracked from Bird Island (South Georgia), are analysed. Three data sources (dives, spatial movements, and immersion events) are combined to examine diverse aspects of at-sea foraging behaviour, and their implications for alternative approaches to bycatch mitigation are considered. The tracked white-chinned petrels (n = 14) mostly performed shallow dives (<3 m deep) of very short duration (<5 s), predominantly during darkness, but only 7 and 10% of landings in daylight and darkness, respectively, involved diving, suggesting that surface-seizing is the preferred foraging technique. Nonetheless, individuals were able to dive to considerable depth (max = 14.5 m) and at speed (max = 2.0 m·s−1), underlining the importance of using heavy line-weighting to maximize hook sink rates, and bird-scaring lines (Tori lines) that extend for long distances behind vessels to protect hooks until beyond diving depths

The origins, evolution, and functional potential of alternative splicing in vertebrates.

Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the contribution of AS to the generation of phenotypic complexity and to study the evolution of splicing patterns. We have compared the AS of 309 protein-coding genes in the human ENCODE pilot regions against their mouse orthologs in unprecedented detail, utilizing traditional transcriptomic and RNAseq data. The conservation status of every transcript has been investigated, and each functionally categorized as coding (separated into coding sequence [CDS] or nonsense-mediated decay [NMD] linked) or noncoding. In total, 36.7% of human and 19.3% of mouse coding transcripts are species specific, and we observe a 3.6 times excess of human NMD transcripts compared with mouse; in contrast to previous studies, the majority of species-specific AS is unlinked to transposable elements. We observe one conserved CDS variant and one conserved NMD variant per 2.3 and 11.4 genes, respectively. Subsequently, we identify and characterize equivalent AS patterns for 22.9% of these CDS or NMD-linked events in nonmammalian vertebrate genomes, and our data indicate that functional NMD-linked AS is more widespread and ancient than previously thought. Furthermore, although we observe an association between conserved AS and elevated sequence conservation, as previously reported, we emphasize that 30% of conserved AS exons display sequence conservation below the average score for constitutive exons. In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution

Effects of age on foraging behavior in two closely related albatross species

Abstract: Background: Foraging performance is widely hypothesized to play a key role in shaping age-specific demographic rates in wild populations, yet the underlying behavioral changes are poorly understood. Seabirds are among the longest-lived vertebrates, and demonstrate extensive age-related variation in survival, breeding frequency and success. The breeding season is a particularly critical phase during the annual cycle, but it remains unclear whether differences in experience or physiological condition related to age interact with the changing degree of the central-place constraint in shaping foraging patterns in time and space. Methods: Here we analyze tracking data collected over two decades from congeneric black-browed (BBA) and grey-headed (GHA) albatrosses, Thalassarche melanophris and T. chrysostoma, breeding at South Georgia. We compare the foraging trip parameters, at-sea activity (flights and landings) and habitat preferences of individuals aged 10–45 years and contrast these patterns between the incubation and early chick-rearing stages. Results: Young breeders of both species showed improvements in foraging competency with age, reducing foraging trip duration until age 26. Thereafter, there were signs of foraging senescence; older adults took gradually longer trips, narrowed their habitat preference (foraging within a smaller range of sea surface temperatures) (GHA), made fewer landings and rested on the water for longer (BBA). Some age-specific effects were apparent for each species only in certain breeding stages, highlighting the complex interaction between intrinsic drivers in determining individual foraging strategies. Conclusions: Using cross-sectional data, this study highlighted clear age-related patterns in foraging behavior at the population-level for two species of albatrosses. These trends are likely to have important consequences for the population dynamics of these threatened seabirds, as young or old individuals may be more vulnerable to worsening environmental conditions

Bioactive Indanes: Development and Validation of a Bioanalytical Method of LC-MS/MS for the Determination of PH46A, a New Potential Anti-Inflammatory Agent, in Human Plasma, Urine and Faeces

PH46A, a new chemical entity developed by our group, has shown potent anti-inflammatory activities through various pre-preclinical studies. The aim of this work was to develop and validate a sensitive and robust LC-MS/MS analytical method to determine the levels of PH46 in human plasma, urine and faeces. The linearity (0.5–500 ng/mL for plasma/urine, and 10–2000 ng/g for human faeces), accuracy (within 100 ± 15% for plasma/urine or 100 ± 20% for faeces), precision (≤ 15% CV for plasma/urine or ≤ 20% CV for faeces) and the method’s specificity were demonstrated to be acceptable. No significant matrix effects or carry-over was observed for PH46 and IStd, and the recovery was consistent. About 10- and 100-fold dilutions in control matrix were found not to affect the assays’ performance. PH46 was proven to be stable: at room temperature for >24 hrs in plasma through 3 freeze-thaw cycles, at –20°C for 83 days in plasma/32 days in urine/33 days in faeces, and at –80°C for 154 days in plasma/33 days in faeces. The re-injection reproducibility of PH46 in matrix extracts was at least 239 hrs at 4°C in plasma/25 days in urine/6.5 days in faeces. This method was successfully applied to the pharmacokinetic evaluation of the Phase I clinical studies

Business experience and start-up size: buying more lottery tickets next time around?

This paper explores the determinants of start-up size by focusing on a cohort of 6247 businesses that started trading in 2004, using a unique dataset on customer records at Barclays Bank. Quantile regressions show that prior business experience is significantly related with start-up size, as are a number of other variables such as age, education and bank account activity. Quantile treatment effects (QTE) estimates show similar results, with the effect of business experience on (log) start-up size being roughly constant across the quantiles. Prior personal business experience leads to an increase in expected start-up size of about 50%. Instrumental variable QTE estimates are even higher, although there are concerns about the validity of the instrument

Environmental drivers of movement in a threatened seabird: insights from a mechanistic model and implications for conservation

Determining the drivers of movement of different life‐history stages is crucial for understanding age‐related changes in survival rates and, for marine top predators, the link between fisheries overlap and incidental mortality (bycatch), which is driving population declines in many taxa. Here, we combine individual tracking data and a movement model to investigate the environmental drivers and conservation implications of divergent movement patterns in juveniles (fledglings) and adults of a threatened seabird, the white‐chinned petrel (Procellaria aequinoctialis)

Rafting behaviour of albatrosses and petrels at South Georgia

Seabirds often spend time on the water in the vicinity of their breeding colonies at the start or end of foraging trips, which may be for bathing, social interaction, information transfer, or to reduce predation risk for small petrels that prefer to return to land in darkness. Although such behaviour (hereafter rafting) is common, there are few data on variation in its incidence or timing across species, or analyses of relationships with intrinsic or extrinsic factors such as breeding stage (reflecting central-place foraging constraints) or weather. Here, we use GPS and immersion data collected over multiple years at Bird Island, South Georgia, to investigate rafting behaviour of four albatross and one burrow-nesting petrel species. Nearly all tracked birds (89%) landed within 10 km of the colony at the start of foraging trips for ~ 30 min, whereas only 17% did so at the end, suggesting they likely use rafting mainly for plumage maintenance after extended breeding shifts on land. Rafting duration, distance and bearing from the colony varied markedly according to species, wind speeds and period of the day (daylight vs. darkness), which may reflect differences in foraging direction, time constraints, degree of plumage soiling, diel activity patterns, or the requirement for high wind speeds for efficient flight. Given that all the study populations are decreasing, and most individuals make extensive use of nearshore waters during the breeding season, effective marine spatial planning is required that eliminates or mitigates human risks around their colonies