Population size,habitat fragmentation,and the nature of adaptive variation in a stream fish

Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analysing coding-gene, single-nucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest.     

One-step zero-background IgG reformatting of phage-displayed antibody fragments enabling rapid and high-throughput lead identification

We describe a novel cloning method, referred to as insert-tagged (InTag) positive selection, for the rapid one-step reformatting of phage-displayed antibody fragments to full-length immunoglobulin Gs (IgGs). InTag positive selection enables recombinant clones of interest to be directly selected without cloning background, bypassing the laborious process of plating out cultures and colony screening and enabling the cloning procedure to be automated and performed in a high-throughput format. This removes a significant bottleneck in the functional screening of phage-derived antibody candidates and enables a large number of clones to be directly reformatted into IgG without the intermediate step of Escherichia coli expression and testing of soluble antibody fragments. The use of InTag positive selection with the Dyax Fab-on-phage antibody library is demonstrated, and optimized methods for the small-scale transient expression of IgGs at high levels are described. InTag positive selection cloning has the potential for wide application in high-throughput DNA cloning involving multiple inserts, markedly improving the speed and quality of selections from protein libraries.     

Temporally dynamic habitat suitability predicts genetic relatedness among caribou

Landscape heterogeneity plays a central role in shaping ecological and evolutionary processes. While species utilization of the landscape is usually viewed as constant within a year, the spatial distribution of individuals is likely to vary in time in relation to particular seasonal needs. Understanding temporal variation in landscape use and genetic connectivity has direct conservation implications. Here, we modelled the daily use of the landscape by caribou in Quebec and Labrador, Canada and tested its ability to explain the genetic relatedness among individuals. We assessed habitat selection using locations of collared individuals in migratory herds and static occurrences from sedentary groups. Connectivity models based on habitat use outperformed a baseline isolation-by-distance model in explaining genetic relatedness, suggesting that variations in landscape features such as snow, vegetation productivity and land use modulate connectivity among populations. Connectivity surfaces derived from habitat use were the best predictors of genetic relatedness. The relationship between connectivity surface and genetic relatedness varied in time and peaked during the rutting period. Landscape permeability in the period of mate searching is especially important to allow gene flow among populations. Our study highlights the importance of considering temporal variations in habitat selection for optimizing connectivity across heterogeneous landscape and counter habitat fragmentation.     

Volatile Compounds of Viola odorata Absolutes: Identification of Odorant Active Markers to Distinguish Plants Originating from France and Egypt

Absolutes isolated from Viola odorata leaves, valuable materials for the flavor and fragrance industry, were studied. Violets are mainly cultivated in France and Egypt and extracted locally. The absolutes of the two origins showed different olfactory profiles both in top and heart notes, as evidenced by sensory analysis. The aims of this study were i) to characterize the volatile compounds, ii) to determine the odorant‐active ones, and iii) to identify some markers of the plant origin. Two complementary analytical methods were used for these purposes, i.e., headspace solid‐phase microextraction (HS‐SPME) using different fiber coatings followed by GC/MS analysis and gas chromatography – olfactometry/mass spectrometry (GC‐O/MS) applied to violet leaf extracts. From a total of 70 identified compounds, 61 have never been reported so far for this species, 17 compounds were characterized by both techniques (with seven among them known from the literature), 23 compounds were solely identified by HS‐SPME GC/MS (among them only two being already mentioned as components of violet absolutes in the literature), and, finally, 30 compounds were only identified by GC‐O/MS. According to the HS‐SPME GC/MS analyses, ethyl hexanoate and (2E,6Z)‐nona‐2,6‐dienol were specific volatile compounds of the sample with French origin, while (E,E)‐hepta‐2,4‐dienal, hexanoic acid, limonene, tridecane, and eugenol were specific of the samples with Egyptian origin. Additional compounds that were not detected by HS‐SPME GC/MS analysis were revealed by GC‐O analyses, some of them being markers of origin. Pent‐1‐en‐3‐ol, 3‐methylbut‐2‐enal, 2‐methoxy‐3‐(1‐methylethyl)pyrazine, 4‐ethylbenzaldehyde, β‐phenethyl formate, and 2‐methoxy‐3‐(2‐methylpropyl)pyrazine revealed to be odorant markers of the French sample, whereas cis‐rose oxide, trans‐rose oxide, and 3,5,5‐trimethylcyclohex‐2‐enone were odorant markers of the Egyptian samples.     

Non-coding RNA gene families in the genomes of anopheline mosquitoes

Background

Only a small fraction of the mosquito species of the genus Anopheles are able to transmit malaria, one of the biggest killer diseases of poverty, which is mostly prevalent in the tropics. This diversity has genetic, yet unknown, causes. In a further attempt to contribute to the elucidation of these variances, the international “Anopheles Genomes Cluster Consortium” project (a.k.a. “16 Anopheles genomes project”) was established, aiming at a comprehensive genomic analysis of several anopheline species, most of which are malaria vectors. In the frame of the international consortium carrying out this project our team studied the genes encoding families of non-coding RNAs (ncRNAs), concentrating on four classes: microRNA (miRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and in particular small nucleolar RNA (snoRNA) and, finally, transfer RNA (tRNA).

Results

Our analysis was carried out using, exclusively, computational approaches, and evaluating both the primary NGS reads as well as the respective genome assemblies produced by the consortium and stored in VectorBase; moreover, the results of RNAseq surveys in cases in which these were available and meaningful were also accessed in order to obtain supplementary data, as were “pre-genomic era” sequence data stored in nucleic acid databases. The investigation included the identification and analysis, in most species studied, of ncRNA genes belonging to several families, as well as the analysis of the evolutionary relations of some of those genes in cross-comparisons to other members of the genus Anopheles.

Conclusions

Our study led to the identification of members of these gene families in the majority of twenty different anopheline taxa. A set of tools for the study of the evolution and molecular biology of important disease vectors has, thus, been obtained.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1038) contains supplementary material, which is available to authorized users.     

Selection and Combustion of Ni-Hyperaccumulators for the Phytomining Process

Ni recovery from serpentine soils by phytomining has proved feasible. Phytomining involves the crop of hyperaccumulating plants with high Ni contents and the valorization of Ni by pyro or hydrometallurgical process. In order to evaluate the Ni content of different plants, we analyzed the organs of 14 hyperaccumulators from three genera: Alyssum, Leptoplax and Bornmuellera. The highest concentration was recorded in the leaves of Leptoplax (34.3 ± 0.7 mg g^?1 _DM). Additionally, we investigated biomass combustion which is the first step of the process we designed to obtain a nickel salt. We showed that temperature and duration were important parameters to ensure a good quality of ashes. At the bench scale, the best conditions were 550°C and 3 h. In this way, we obtained ashes in which Ni could reach 20 wt%. Biomass ashes can be considered as a bio-ore for recovering metal value.     

The Codes of Recognition

This paper is divided into two parts. Part I focuses on the manner in which the components of the face recognition system work together so that a perceiver, within several hundred milliseconds after seeing a familiar face, is able to both identify the face of the perceived and recall elements of the history of past encounters with the perceived. Face recognition plays a crucial role in enabling both human and nonhuman primates to interact in collaborative social groups. This critical function is accomplished through the unidirectional coded transfer of informational elements from one component to another. Although these informational elements themselves are not meaningful to the perceiving agent, they do nevertheless contain essential bits of information that are necessary for the final formation of the meaningful message. The structural components of the system are identified and the manner in which informational elements are coded and transferred sequentially from component to component in the brain of the perceiver is described. The independent, physically separated components in the face recognition system are bridged by an additional component, an “adaptor”, that mediates the transfer of informational elements from one component to another. The nature of the independent systems, and the manner by which the bridging or adaptor apparatus enables coded information transfer from one system to another is discussed. Part II focuses on the analysis of recognition in human-designed sign systems such as Braille and Morse code. Recognition in human-designed sign systems is notable for the stability of the link between sign and meaning. Face recognition is characterized as being subjective, indicating that the meaning of a sign (face) to a perceiver is variable and dependent on context, whereas human-devised sign recognition is characterized as being objective, indicating that the meaning of a sign is context independent and invariant. Human-designed sign systems require the presence in brain of a referent world. An example of a referent world is the set of letters of the alphabet. Representations of this set are installed in the brain through social mediated learning. Human-designed sets of signs (e.g., Braille, and written text) are created to correspond, via a code enabling adaptor structure, to referent worlds in the brain. Human-designed sign systems are the foundations for literacy, a capability only found in humans.