Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome

A Novel Strategy to Reveal the Landscape of Crossovers in an F1 Hybrid Population of Populus deltoides and Populus simonii

Although the crossover (CO) patterns of different species have been extensively investigated, little is known about the landscape of CO patterns in Populus because of its high heterozygosity and long-time generation. A novel strategy was proposed to reveal the difference of CO rate and interference between Populus deltoides and Populus simonii using their F1 hybrid population. We chose restriction site-associated DNA (RAD) tags that contained two SNPs, one only receiving the CO information from the female P. deltoides and the other from the male P. simonii. These RAD tags allowed us to investigate the CO patterns between the two outbred species, instead of using the traditional backcross populations in inbred lines. We found that the CO rate in P. deltoides was generally greater than that in P. simonii, and that the CO interference was a common phenomenon across the two genomes. The COs landscape of the different Populus species facilitates not only to understand the evolutionary mechanism for adaptability but also to rebuild the statistical model for precisely constructing genetic linkage maps that are critical in genome assembly in Populus. Additionally, the novel strategy could be applied in other outbred species for investigating the CO patterns.

Heterogeneity of synonymous substitution rates in the Xenopus frog genome

With the increasing availability of high quality genomic data, there is opportunity to deeply explore the genealogical relationships of different gene loci between closely related species. In this study, we utilized genomes of Xenopus laevis (XLA, a tetraploid species with (L) and (S) sub-genomes) and X. tropicalis (XTR, a diploid species) to investigate whether synonymous substitution rates among orthologous or homoeologous genes displayed any heterogeneity. From over 1500 orthologous/homoeologous genes collected, we calculated proportion of synonymous substitutions between genomes/sub-genomes (k) and found variation within and between chromosomes. Within most chromosomes, we identified higher k with distance from the centromere, likely attributed to higher substitution rates and recombination in these regions. Using maximum likelihood methods, we identified further evidence supporting rate heterogeneity, and estimated species divergence times and ancestral population sizes. Estimated species divergence times (XLA.L-XLA.S: ~25.5 mya; XLA-XTR: ~33.0 mya) were slightly younger compared to a past study, attributed to consideration of population size in our study. Meanwhile, we found very large estimated population size in the ancestral populations of the two species (N_A = 2.55 x 10⁶). Local hybridization and population structure, which have not yet been well elucidated in frogs, may be a contributing factor to these possible large population sizes.

An Overview of Chitosan Nanofibers and their Applications in the Drug Delivery Process

Chitosan is a polycationic natural polymer which is abundant in nature. Chitosan has gained much attention as natural polymer in the biomedical field. The up to date drug delivery as well as the nanotechnology in controlled release of drugs from chitosan nanofibers are focused in this review. Electrospinning is one of the most established and widely used techniques for preparing nanofibers. This method is versatile and efficient for the production of continuous nanofibers. The chitosan-based nanofibers are emerging materials in the arena of biomaterials. Recent studies revealed that various drugs such as antibiotics, chemotherapeutic agents, proteins and anti-inflammatory analgesic drugs were successfully loaded onto electrospun nanofibers. Chitosan nanofibers have several outstanding properties for different significant pharmaceutical applications such as wound dressing, tissue engineering, enzyme immobilization, and drug delivery systems. This review highlights different issues of chitosan nanofibers in drug delivery applications, starting from the preparation of chitosan nanofibers, followed by giving an idea about the biocompatibility and degradation of chitosan nanofibers, then describing how to load the drug into the nanofibers. Finally, the major applications of chitosan nanofibers in drug delivery systems.

Adsorption efficiency enhancing of electrospun polycaprolactone nanofibers towards acidic polar drugs through the incorporation of a composite of graphene oxide nanosheets and Al30 polyoxocations: a comparative study

The main objective of this study focuses on exploration of the feasibility of Al30 polyoxocations for preparation of a novel sorbent material for a solid-phase extraction (SPE) method by selective adsorption and extraction of a class of compounds considering the type of interactions involved in the adsorption process. Accordingly, first Al30 polyoxocations were synthesized and their composite was prepared with graphene oxide (GO) nanosheets as a suitable substrate to be introduced as a SPE sorbent material. Then, the prepared composite was incorporated into polycaprolactone (PCL) nanofibers via electrospinning to present an alternative sorbent for SPE-based on a GO/Al30 nanocomposite (GO/Al30 NC) creating no need for filtering or centrifuging steps. Intercalation of Al30 polyoxocations into the GO layers and the incorporation of GO/Al30 NC into PCL nanofibers was successfully confirmed through FE-SEM, TEM, EDX, XRD, BET, TGA, IR spectroscopy, and zeta potential determination. For investigating the types of probable interactions involved in the adsorption process of different compounds on the proposed sorbents, four statin drugs, cholesterol-lowering agents with various polarity and ionization properties, were selected as model analytes. Factors affecting the extraction efficiency of dispersive SPE and immersed SPE methods using GO/Al30 NC and GO/Al30 NC-PCL nanofibers, respectively, were investigated and optimized. Under optimal conditions, acceptable analytical figures of merit were obtained for both SPE methods. A comparison of extraction efficiencies of the target drugs by the two proposed sorbents, as well as GO nanosheets and PCL nanofibers, was accomplished to study the types of interactions as well as the adsorption mechanism. The results revealed that GO/Al30 NC, having many polar and anion exchange sites caused by Al30 polyoxocations, is a good selective sorbent for acidic polar compounds which their extraction by nonpolar sorbents is not desirable. Additionally, GO/Al30 NC-PCL nanofibers exhibited extraction capability for a wide range of compounds from acidic polar to nonpolar and nonionizable ones.

Surface-Functionalized Electrospun Titania Nanofibers for the Scavenging and Recycling of Precious Metal Ions

Precious metals are widely used as catalysts in industry. It is of critical importance to keep the precious metal ions leached from catalysts at a level below one part per million (ppm) in the final products and to recycle the expensive precious metals. Here we demonstrate a simple and effective method for scavenging precious metal ions from an aqueous solution and thereby reduce their concentrations down to the parts per billion (ppb) level. The key component is a filtration membrane comprised of titania (TiO₂ ) nanofibers whose surface has been functionalized with a silane bearing amino or thiol group. When operated under continuous flow at a rate of 1 mL min^-1 and at room temperature, up to 99.95 % of the Pd²⁺ ions could be removed from a stock solution with an initial concentration of 100 ppm. This work offers a viable strategy not only for the removal of precious metal ions but also for recovering and further recycling them for use as catalysts. For example, the captured Pd²⁺ ions could be converted to nanoparticles and used as catalysts for organic reactions such as Suzuki coupling in a continuous flow reactor. This system can be potentially applied to pharmaceutical industry and waste stream treatment.

Online stretching of directly electrospun nanofiber yarns

An online stretching during electrospinning of nanofiber yarn can considerably improve yarn production rate, quality and mechanical strength.

Electrospun polyurethane/keratin/AgNP biocomposite mats for biocompatible and antibacterial wound dressings

Keratin based biomaterials have emerged as potential candidates for various biomedical and biotechnological applications due to their intrinsic biocompatibility, biodegradability, mechanical durability, and natural abundance.

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations

The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya, and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes, both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.

Genomic signatures of selection at linked sites: unifying the disparity among species

Population genetics theory supplies powerful predictions about how natural selection interacts with genetic linkage to sculpt the genomic landscape of nucleotide polymorphism. Both the spread of beneficial mutations and the removal of deleterious mutations act to depress polymorphism levels, especially in low-recombination regions. However, empiricists have documented extreme disparities among species. Here we characterize the dominant features that could drive differences in linked selection among species--including roles for selective sweeps being 'hard' or 'soft'--and the concealing effects of demography and confounding genomic variables. We advocate targeted studies of closely related species to unify our understanding of how selection and linkage interact to shape genome evolution.

Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination

Background

Polymorphism is key to the evolutionary potential of populations. Understanding which factors shape levels of genetic diversity within genomes forms a central question in evolutionary genomics and is of importance for the possibility to infer episodes of adaptive evolution from signs of reduced diversity. There is an on-going debate on the relative role of mutation and selection in governing diversity levels. This question is also related to the role of recombination because recombination is expected to indirectly affect polymorphism via the efficacy of selection. Moreover, recombination might itself be mutagenic and thereby assert a direct effect on diversity levels.

Results

We used whole-genome re-sequencing data from domestic chicken (broiler and layer breeds) and its wild ancestor (the red jungle fowl) to study the relationship between genetic diversity and several genomic parameters. We found that recombination rate had the largest effect on local levels of nucleotide diversity. The fact that divergence (a proxy for mutation rate) and recombination rate were negatively correlated argues against a mutagenic role of recombination. Furthermore, divergence had limited influence on polymorphism.

Conclusions

Overall, our results are consistent with a selection model, in which regions within a short distance from loci under selection show reduced polymorphism levels. This conclusion lends further support from the observations of strong correlations between intergenic levels of diversity and diversity at synonymous as well as non-synonymous sites. Our results also demonstrate differences between the two domestic breeds and red jungle fowl, where the domestic breeds show a stronger relationship between intergenic diversity levels and diversity at synonymous and non-synonymous sites. This finding, together with overall lower diversity levels in domesticates compared to red jungle fowl, seem attributable to artificial selection during domestication.

The influence of recombination on SNP diversity in chickens

The association between recombination rate and diversity, but not divergence is considered to be driven mainly by natural selection: fixation of positively selected variants and associated hitchhiking effects and/or background selection eliminating deleterious alleles. In the present study, we investigated the relationship between recombination rate, SNP diversity and interspecies divergence for 29 loci in chickens. We found that recombination rate is positively correlated with nucleotide diversity but is not correlated with interspecies divergence. It appears that variation in recombination rate explains over 30% of the variation in levels of diversity among 29 loci. Our data suggested that natural selection is a main factor in shaping SNP diversity in chickens. Since SNP diversity is significantly lower at Z-linked than at autosomal loci, we argued that genetic hitchhiking might be more important than background selection in producing the observed correlation.

Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis)

Background

The level of nucleotide diversity observed across the genome is positively correlated with the local rate of recombination. Avian karyotypes are typified by large variation in chromosome size and the rate of recombination in birds has been shown to be negatively correlated with chromosome size. It has thus been predicted that nucleotide diversity is negatively correlated with chromosome size in aves. However, there is limited empirical evidence to support this prediction.

Results

Here we sequenced 27 autosomal and 12 sex chromosome-linked loci in the white-throated sparrow (Zonotrichia albicollis) to quantify and compare patterns of recombination, linkage disequilibrium (LD), and genetic diversity across the genome of this North American songbird. Genetic diversity on the autosomes varied up to 8-fold, with the lowest diversity observed on the macrochromosomes and the highest diversity on the microchromosomes. Genetic diversity on the sex chromosomes was reduced compared to the autosomes, the most extreme difference being a ~300-fold difference between the W chromosome and the microchromosomes. LD and population structure associated with a common inversion polymorphism (ZAL2/2^m) in this species were found to be atypical compared to other macrochromosomes, and nucleotide diversity within this inversion on the two chromosome arrangements was more similar to that observed on the Z chromosome.

Conclusions

A negative correlation between nucleotide diversity and autosome size was observed in the white-throated sparrow genome, as well as low levels of diversity on the sex chromosomes comparable to those reported in other birds. The population structure and extended LD associated with the ZAL2/2^m chromosomal polymorphism are exceptional compared to the rest of the white-throated sparrow genome.

Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken

Background

The chicken (Gallus gallus), like most avian species, has a very distinct karyotype consisting of many micro- and a few macrochromosomes. While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes. To this end we sampled four regions of ~1 cM each on macrochromosomes (GGA1 and GGA2), and four 1.5 -2 cM regions on microchromosomes (GGA26 and GGA27) at a high density of 1 SNP every 2 kb (total of 889 SNPs).

Results

At a similar physical distance, LD, haplotype homozygosity, haploblock structure, and haplotype sharing were all lower for the micro- as compared to the macrochromosomes. These differences were consistent across populations. Heterozygosity, genetic differentiation, and derived allele frequencies were also higher for the microchromosomes. Differences in LD, haplotype variation, and haplotype sharing between populations were largely in line with known demographic history of the commercial chicken. Despite very low levels of LD, as measured by r² for most populations, some haploblock structure was observed, particularly in the macrochromosomes, but the haploblock sizes were typically less than 10 kb.

Conclusion

Differences in LD between micro- and macrochromosomes were almost completely explained by differences in recombination rate. Differences in haplotype diversity and haplotype sharing between micro- and macrochromosomes were explained by differences in recombination rate and genotype variation. Haploblock structure was consistent with demography of the chicken populations, and differences in recombination rates between micro- and macrochromosomes. The limited haploblock structure and LD suggests that future whole-genome marker assays will need 100+K SNPs to exploit haplotype information. Interpretation and transferability of genetic parameters will need to take into account the size of chromosomes in chicken, and, since most birds have microchromosomes, in other avian species as well.

One-dimensional composite nanomaterials: synthesis by electrospinning and their applications

This Review provides an overview of the synthesis of one-dimensional (1D) composite nanomaterials by electrospinning and their applications. After a brief description of the development of the electrospinning technique, the transformation of an inorganic nanocomponent or polymer into another kind of polymer or inorganic matrix is discussed in terms of the electrospinning process, including the direct-dispersed method, gas-solid reaction, in situ photoreduction, sol-gel method, emulsion electrospinning method, solvent evaporation, and coaxial electrospinning. In addition, various applications of such 1D composite nanomaterials are highlighted in terms of electronic and optical nanodevices, chemical and biological sensors, catalysis and electrocatalysis, superhydrophobic surfaces, environment, energy, and biomedical fields. An increasing number of investigations show that electrospinning has been not only a focus of academic study in the laboratory but is also being applied in a great many technological fields.