DNA repair profiles of disease-associated isolates of Neisseria meningitidis

Neisseria meningitidis, or the meningococcus, is the source of significant morbidity and mortality in humans worldwide. Even though mutability has been linked to the occurrence of outbreaks of epidemic disease, meningococcal DNA repair pathways are poorly delineated. For the first time, a collection of meningococcal disease-associated isolates has been demonstrated to express constitutively the DNA glycosylases MutY and Fpg in vivo. DNA sequence analysis showed considerable variability in the deduced amino acid sequences of MutS and Fpg, while MutY and RecA were highly conserved. Interestingly, multi-locus sequence typing demonstrated a putative link between the pattern of amino acid substitutions and levels of spontaneous mutagenicity in meningococcal strains. These results provide a basis for further studies aimed at resolving the genotype/phenotype relationships of meningococcal genome variability and mutator activity.     

Okazaki fragment maturation involves α-segment error editing by the mammalian FEN1/MutSα functional complex

During nuclear DNA replication, proofreading-deficient DNA polymerase α (Pol α) initiates Okazaki fragment synthesis with lower fidelity than bulk replication by proofreading-proficient Pol δ or Pol ε. Here, we provide evidence that the exonuclease activity of mammalian flap endonuclease (FEN1) excises Pol α replication errors in a MutSα-dependent, MutLα-independent mismatch repair process we call Pol α-segment error editing (AEE). We show that MSH2 interacts with FEN1 and facilitates its nuclease activity to remove mismatches near the 5′ ends of DNA substrates. Mouse cells and mice encoding FEN1 mutations display AEE deficiency, a strong mutator phenotype, enhanced cellular transformation, and increased cancer susceptibility. The results identify a novel role for FEN1 in a specialized mismatch repair pathway and a new cancer etiological mechanism.     

A meta‐analysis reveals a positive correlation between genetic diversity metrics and environmental status in the long‐lived seagrass Posidonia oceanica

The seagrass Posidonia oceanica is a key engineering species structuring coastal marine systems throughout much of the Mediterranean basin. Its decline is of concern, leading to the search for short‐ and long‐term indicators of seagrass health. Using ArcGIS maps from a recent, high‐resolution (1–4 km) modelling study of 18 disturbance factors affecting coastal marine systems across the Mediterranean (Micheli et al. 2013, http://globalmarine.nceas.ucsb.edu/mediterranean/ ), we tested for correlations with genetic diversity metrics (allelic diversity, genotypic/clonal diversity and heterozygosity) in a meta‐analysis of 56 meadows. Contrary to initial predictions, weak but significantly positive correlations were found for commercial shipping, organic pollution (pesticides) and cumulative impact. This counterintuitive finding suggests greater resistance and resilience of individuals with higher genetic and genotypic diversity under disturbance (at least for a time) and/or increased sexual reproduction under an intermediate disturbance model. We interpret the absence of low and medium levels of genetic variation at impacted locations as probable local extinctions of individuals that already exceeded their resistance capacity. Alternatively, high diversity at high‐impact sites is likely a temporal artefact, reflecting the mismatch with pre‐environmental impact conditions, especially because flowering and sexual recruitment are seldom observed. While genetic diversity metrics are a valuable tool for restoration and mitigation, caution must be exercised in the interpretation of correlative patterns as found in this study, because the exceptional longevity of individuals creates a temporal mismatch that may falsely suggest good meadow health status, while gradual deterioration of allelic diversity might go unnoticed.     

Artificial light at night desynchronizes strictly seasonal reproduction in a wild mammal

Change in day length is an important cue for reproductive activation in seasonally breeding animals to ensure that the timing of greatest maternal investment (e.g. lactation in mammals) coincides with favourable environmental conditions (e.g. peak productivity). However, artificial light at night has the potential to interfere with the perception of such natural cues. Following a 5-year study on two populations of wild marsupial mammals exposed to different night-time levels of anthropogenic light, we show that light pollution in urban environments masks seasonal changes in ambient light cues, suppressing melatonin levels and delaying births in the tammar wallaby. These results highlight a previously unappreciated relationship linking artificial light at night with induced changes in mammalian reproductive physiology, and the potential for larger-scale impacts at the population level.     

Temperature seasonality during fry out‐migration influences the survival of hatchery‐reared chum salmon Oncorhynchus keta

Among years, fry‐to‐adult survival of hatchery‐reared chum salmon Oncorhynchus keta was positively correlated with the length (in days) of the fry out‐migration period with temperatures suitable for migration. Furthermore, survival decreased with increasing difference in mean temperature between May and June. Thus, prolonged out‐migration periods increased the probability of survival from fry to adult, lending support to the hypothesis that long migration periods decrease the risk of mortality (bet‐hedging), and increase the probability of migration when environmental conditions in fresh water and the ocean are suitable (match–mismatch).     

Sleep intensity and the evolution of human cognition

Over the past four decades, scientists have made substantial progress in understanding the evolution of sleep patterns across the Tree of Life. 1 , 2 Remarkably, the specifics of sleep along the human lineage have been slow to emerge. This is surprising, given our unique mental and behavioral capacity and the importance of sleep for individual cognitive performance. 3 - 5 One view is that our species' sleep architecture is in accord with patterns documented in other mammals. 6 We promote an alternative view, that human sleep is highly derived relative to that of other primates. Based on new and existing evidence, we specifically propose that humans are more efficient in their sleep patterns than are other primates, and that human sleep is shorter, deeper, and exhibits a higher proportion of REM than expected. Thus, we propose the sleep intensity hypothesis: Early humans experienced selective pressure to fulfill sleep needs in the shortest time possible. Several factors likely served as selective pressures for more efficient sleep, including increased predation risk in terrestrial environments, threats from intergroup conflict, and benefits arising from increased social interaction. Less sleep would enable longer active periods in which to acquire and transmit new skills and knowledge, while deeper sleep may be critical for the consolidation of those skills, leading to enhanced cognitive abilities in early humans.     

An amplified surface plasmon resonance "turn-on" sensor for mercury ion using gold nanoparticles

Inorganic mercury ion (Hg²⁺) has been shown to coordinate to DNA duplexes that feature thymine–thymine (T–T) base pair mismatches. This observation suggests that an Hg²⁺-induced conformational change in a single-stranded DNA molecule can be used to detect aqueous Hg²⁺. Here, we have developed an analytical method using surface plasmon resonance (SPR) to develop a highly selective and sensitive detection technique for Hg²⁺ that takes advantage of T–Hg²⁺–T coordination chemistry. The general concept used in this approach is that the “turn-on” reaction of a hairpin probe via coordination of Hg²⁺ by the T–T base pair results in a substantial increase in the SPR response, followed by specific hybridization with a gold nanoparticle probe to amplify the sensor performance. Meanwhile, the limit of detection is 1 nM, which is lower than other recently developed techniques. A linear correlation is observed between the measured SPR reflectivity and the logarithm of the Hg²⁺ concentration over the concentration range of 5–5000 nM. Additionally, the SPR system provides high selectivity for Hg²⁺ in the presence of other divalent metal ions up to micromolar concentration levels. The proposed approach is also successfully utilized for the determination of Hg²⁺ in water samples.     

Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia

Sundaland has a dynamic geographic history because its landmasses were periodically interconnected when sea levels fell during glacial periods. Superimposed on this geographic dynamism were environmental changes related to climatic oscillations. To investigate how tropical taxa responded to such changes, we studied the divergence and demographic history of two co-distributed rainforest passerine species, Arachnothera longirostra and Malacocincla malaccensis. We sampled birds primarily from Borneo and the Malay Peninsula, which straddle the now-submerged Sunda shelf, and analysed multilocus DNA data with a variety of coalescent and gene genealogy methods. Cross-shelf divergence in both species occurred well before the last glacial maximum, i.e., before the most recent land connection. However, post-divergence gene flow occurred, and it was more pronounced in A. longirostra (a highly vagile nectarivore/insectivore) than in M. malaccensis (an understory insectivore). Despite current habitat continuity on Borneo, the population of M. malaccensis in northeastern Borneo is substantially divergent from that on the rest of the island. The NE population experienced dramatic demographic fluctuations, probably because of competition with the other population, which expanded from western Borneo after the mid-Pleistocene. In contrast, the Borneo population of A. longirostra has little structure and appears to have experienced demographic expansion 16 kya, long after it had diverged from the Malay Peninsula population (630-690 kya). Malay Peninsula populations of both species have remained relatively stable. Overall, the most recent glacial period was not the chief determinant of the evolutionary dynamics of our study species, and in this respect, they are different from temperate species.     

Identifying climatic niche shifts using coarse‐grained occurrence data: a test with non‐native freshwater fish

Aim We tested whether coarse‐grained occurrence data can be used to detect climatic niche shifts between native and non‐native ranges for a set of widely introduced freshwater fishes. Location World‐wide. Methods We used a global database of freshwater fish occurrences at the river basin scale to identify native and non‐native ranges for 18 of the most widely introduced fish species. We also examined climatic conditions within each river basin using fine‐grained climate data. We combined this information to test whether climatic niche shifts have occurred between native and non‐native ranges. We defined climatic niche shifts as instances where the ranges of a climatic variable within native and non‐native basins exhibit zero overlap. Results We detected at least one climatic niche shift for each of the 18 studied species. However, we did not detect common patterns in the thermal preference or biogeographic origin of the non‐native fish, hence suggesting a species‐specific response. Main conclusions Coarse‐grained occurrence data can be used to detect climatic niche shifts. They also enable the identification of the species experiencing niche shifts, although the mechanisms responsible for these shifts (e.g. local adaptation, dispersal limitation or physiological constraints) have yet to be determined. Furthermore, the coarse‐grained approach, which highlights regions where climatic niche shifts have occurred, can be used to select specific river basins for more detailed, fine‐grained studies.