Tidal and seasonal effects on survival rates of the endangered California clapper rail: does invasive Spartina facilitate greater survival in a dynamic environment?

Invasive species frequently degrade habitats, disturb ecosystem processes, and can increase the likelihood of extinction of imperiled populations. However, novel or enhanced functions provided by invading species may reduce the impact of processes that limit populations. It is important to recognize how invasive species benefit endangered species to determine overall effects on sensitive ecosystems. For example, since the 1990s, hybrid Spartina (Spartina foliosa × alterniflora) has expanded throughout South San Francisco Bay, USA, supplanting native vegetation and invading mudflats. The endangered California clapper rail (Rallus longirostris obsoletus) uses the tall, dense hybrid Spartina for cover and nesting, but the effects of hybrid Spartina on clapper rail survival was unknown. We estimated survival rates of 108 radio-marked California clapper rails in South San Francisco Bay from January 2007 to March 2010, a period of extensive hybrid Spartina eradication, with Kaplan–Meier product limit estimators. Clapper rail survival patterns were consistent with hybrid Spartina providing increased refuge cover from predators during tidal extremes which flood native vegetation, particularly during the winter when the vegetation senesces. Model averaged annual survival rates within hybrid Spartina dominated marshes before eradication (? = 0.466) were greater than the same marshes posttreatment (? = 0.275) and a marsh dominated by native vegetation (? = 0.272). However, models with and without marsh treatment as explanatory factor for survival rates had nearly equivalent support in the observed data, lending ambiguity as to whether hybrid Spartina facilitated greater survival rates than native marshland. Conservation actions to aid in recovery of this endangered species should recognize the importance of available of high tide refugia, particularly in light of invasive species eradication programs and projections of future sea-level rise.     

BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells

Genome maintenance by homologous recombination depends on coordinating many proteins in time and space to assemble at DNA break sites. To understand this process, we followed the mobility of BRCA2, a critical recombination mediator, in live cells at the single-molecule level using both single-particle tracking and fluorescence correlation spectroscopy. BRCA2-GFP and -YFP were compared to distinguish diffusion from fluorophore behavior. Diffusive behavior of fluorescent RAD51 and RAD54 was determined for comparison. All fluorescent proteins were expressed from endogenous loci. We found that nuclear BRCA2 existed in oligomeric clusters, and exhibited heterogeneous mobility. DNA damage increased BRCA2 transient binding, presumably including binding to damaged sites. Despite its very different size, RAD51 displayed mobility similar to BRCA2, which indicates physical interaction between these proteins both before and after induction of DNA damage. We propose that BRCA2-mediated sequestration of nuclear RAD51 serves to prevent inappropriate DNA interactions and that all RAD51 is delivered to DNA damage sites in association with BRCA2.     

Histone H4K20 tri‐methylation at late‐firing origins ensures timely heterochromatin replication

Among other targets, the protein lysine methyltransferase PR‐Set7 induces histone H4 lysine 20 monomethylation (H4K20me1), which is the substrate for further methylation by the Suv4‐20h methyltransferase. Although these enzymes have been implicated in control of replication origins, the specific contribution of H4K20 methylation to DNA replication remains unclear. Here, we show that H4K20 mutation in mammalian cells, unlike in Drosophila, partially impairs S‐phase progression and protects from DNA re‐replication induced by stabilization of PR‐Set7. Using Epstein–Barr virus‐derived episomes, we further demonstrate that conversion of H4K20me1 to higher H4K20me2/3 states by Suv4‐20h is not sufficient to define an efficient origin per se, but rather serves as an enhancer for MCM2‐7 helicase loading and replication activation at defined origins. Consistent with this, we find that Suv4‐20h‐mediated H4K20 tri‐methylation (H4K20me3) is required to sustain the licensing and activity of a subset of ORCA/LRWD1‐associated origins, which ensure proper replication timing of late‐replicating heterochromatin domains. Altogether, these results reveal Suv4‐20h‐mediated H4K20 tri‐methylation as a critical determinant in the selection of active replication initiation sites in heterochromatin regions of mammalian genomes.     

Des gènes à la culture : réflexions finales

Imagination pushes humanity well beyond its natural biological capacities. An approach of co-evolution, between molecular biology and behaviour, is thus required to explain these combined processes. Technological performances define spiritual conquests and formulas whose sole function is cultural. Humanity operates according to intentional social modes defined by the group, but these immediately become conditions for their own evolution. These choices are the motor for the history of humanity, and thus humanity can itself choose its own path. Anatomic modernisation is only a distant reflection of bipedalism, but freeing the hands leads to the development of abstract thought. The relationship between anatomy and awareness allows infinite variations in the harmonious adaptation to nature, animals and other societies. In Europe, humanity arrived in abrupt bursts because it was the result of external evolution, continuous and distant, dispersed across Asia. By its unceasing audacity, humanity combats biological determinism, imposing “moral” rules, or imperatives. The balance between biology and culture is reflected in the rules for sharing food: the biological life itself is coded by social sharing. These systems take on ternary values as soon as they include animal behaviours. Built shelters integrate societies with the cosmos because they delimit cultural spaces within natural chaos. Mastery of cognitive mechanisms gives humanity an entirely new responsibility, that of being able to define its destiny. Our united disciplines are transformed into ethical requirements.     

Parentage and host preference in the common cuckoo Cuculus canorus

Microsatellite DNA markers were used to investigate parentage relationships in a population of common cuckoo Cuculus canorus. Thirty adults and 55 nestlings were genotyped at six loci from blood samples collected over a four‐year period. To test whether each cuckoo female specialises in parasitising one single host species (Host Preference Hypothesis), the maternal relationships were used to record each female's host choice. The results supported the Host Preference Hypothesis since no female (N=3) was recorded to have parasitised more than one of four congeneric host species breeding in the area. In contrast, the males (N=4) did not show such specialisation since two of them sired offspring reared by different host species.     

A complete collection of single‐gene deletion mutants of Acinetobacter baylyi ADP1

We have constructed a collection of single‐gene deletion mutants for all dispensable genes of the soil bacterium Acinetobacter baylyi ADP1. A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. This essentiality data set is 88% consistent with the Escherichia coli data set inferred from the Keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as essential in Pseudomonas aeruginosa are also essential in ADP1. Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2‐3 butanediol, glucose, etc.). This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches.     

Neurotransmitter modulation of small-conductance Ca2+-activated K+ channels by regulation of Ca2+ gating

Small-conductance Ca2+-activated K+ (SK) channels are widely expressed in neuronal tissues where they underlie post-spike hyperpolarizations, regulate spike-frequency adaptation, and shape synaptic responses. SK channels constitutively interact with calmodulin (CaM), which serves as Ca2+ sensor, and with protein kinase CK2 and protein phosphatase 2A, which modulate their Ca2+ gating. By recording coupled activities of Ca2+ and SK2 channels, we showed that SK2 channels can be inhibited by neurotransmitters independently of changes in the activity of the priming Ca2+ channels. This inhibition involvesSK2-associated CK2 and results from a 3-fold reduction in the Ca2+ sensitivity of channel gating. CK2phosphorylated SK2-bound CaM but not KCNQ2-bound CaM, thereby selectively regulating SK2 channels. We extended these observations to sensory neurons by showing that noradrenaline inhibits SK current and increases neuronal excitability in aCK2-dependent fashion. Hence, neurotransmitter-initiated signaling cascades can dynamically regulate Ca2+ sensitivity of SK channels and directly influence somatic excitability.     

An edge-centric perspective on the human connectome: link communities in the brain

Brain function depends on efficient processing and integration of information within a complex network of neural interactions, known as the connectome. An important aspect of connectome architecture is the existence of community structure, providing an anatomical basis for the occurrence of functional specialization. Typically, communities are defined as groups of densely connected network nodes, representing clusters of brain regions. Looking at the connectome from a different perspective, instead focusing on the interconnecting links or edges, we find that the white matter pathways between brain regions also exhibit community structure. Eleven link communities were identified: five spanning through the midline fissure, three through the left hemisphere and three through the right hemisphere. We show that these link communities are consistently identifiable and investigate the network characteristics of their underlying white matter pathways. Furthermore, examination of the relationship between link communities and brain regions revealed that the majority of brain regions participate in multiple link communities. In particular, the highly connected and central hub regions showed a rich level of community participation, supporting the notion that these hubs play a pivotal role as confluence zones in which neural information from different domains merges.