The three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution-adaptation to a freshwater environment. Although genetic adaptations to freshwater ...environments are well-studied, epigenetic adaptations have attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of the marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into a freshwater environment and freshwater sticklebacks placed into seawater. We showed that the DNA methylation profile after placing a marine stickleback into fresh water partially converged to that of a freshwater stickleback. For six genes including ATP4A ion pump and NELL1, believed to be involved in skeletal ossification, we demonstrated similar changes in DNA methylation in both evolutionary and short-term adaptation. This suggested that an immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. For the first time, we demonstrated that genes encoding ion channels KCND3, CACNA1FB, and ATP4A were differentially methylated between the marine and the freshwater populations. Other genes encoding ion channels were previously reported to be under selection in freshwater populations. Nevertheless, the genes that harbor genetic and epigenetic changes were not the same, suggesting that epigenetic adaptation is a complementary mechanism to selection of genetic variants favorable for freshwater environment.
Anthropogenic activity is the top factor directly related to the extinction of several animal species. The last Steller's sea cow (Hydrodamalis gigas) population on the Commander Islands (Russia) was ...wiped out in the second half of the 18
century due to sailors and fur traders hunting it for the meat and fat. However, new data suggests that the extinction process of this species began much earlier. Here, we present a nuclear de novo assembled genome of H. gigas with a 25.4× depth coverage. Our results demonstrate that the heterozygosity of the last population of this animal is low and comparable to the last woolly mammoth population that inhabited Wrangel Island 4000 years ago. Besides, as a matter of consideration, our findings also demonstrate that the extinction of this marine mammal starts along the North Pacific coastal line much earlier than the first Paleolithic humans arrived in the Bering sea region.
The Steller's sea cow – Hydrodamalis gigas (Dugongidae: Sirenia) – is an extinct herbivorous marine mammal which inhabited the North Pacific Ocean during the Pleistocene and Holocene. H. gigas was ...the largest member of the Sirenia order and disappeared in the middle of the 18th century. Here, we present the complete sequence of the mitochondrial genome of this extinct animal. The Steller's sea cow mitochondrial DNA (mtDNA) is 16,872 base pairs (bp) in length and contains a set of mitochondrial genes typical for mammals. Phylogenetic analysis based on complete mitochondrial genomes of the sirenian species allows accurate assessment of the degree of their mitogenomic diversification during millions of years of evolution.
•The modern methods of historical DNA analysis are fruitful for reconstructing the mitogenomic phylogeny of extinct species•The complete mitogenome of Hydrodamalis gigas was sequenced and annotated•The mitogenomic phylogeny of Sirenia order was reconstructed and the sister relationships of Hydrodamalis gigas and Dugong dugon were confirmed
Common carp (Cyprinus carpio) has an outstanding economic importance in freshwater aquaculture due to its high adaptive capacity to both food and environment. In fact, it is the third most farmed ...fish species worldwide according to the Food and Agriculture Organization. More than four million tons of common carp are produced annually in aquaculture, and more than a hundred thousand tons are caught from the wild. Historically, the common carp was also the first fish species to be domesticated in ancient China, and now, there is a huge variety of domestic carp strains worldwide. In the present study, we used double digestion restriction site‐associated DNA sequencing to genotype several European common carp strains and showed that they are divided into two distinct groups. One of them includes central European common carp strains as well as Ponto–Caspian wild common carp populations, whereas the other group contains several common carp strains that originated in the Soviet Union, mostly as cold‐resistant strains. We believe that breeding with wild Amur carp and subsequent selection of the hybrids for resistance to adverse environmental conditions was the attribute of the second group. We assessed the contribution of wild Amur carp inheritance to the common carp strains and discovered discriminating genes, which differed in allele frequencies between groups. Taken together, our results improve our current understanding of the genetic variability of common carp, namely the structure of natural and artificial carp populations, and the contribution of wild carp traits to domestic strains.
We showed that the studied domestic strains are divided into two clearly distinct groups. One of the groups has traces of genomic introgression of wild Amur carp (Cyprinus carpio haematopterus). We defined genes with significantly different allele frequency between the groups and conducted functional gene set analyses to estimate gene categories, enriched in the gene set that discriminates between strains.
Recently, the plasma cytokines FGF‐21 and GDF‐15 were described as cellular metabolic regulators. They share an endocrine function and are highly expressed in the liver under stress and during ...starvation. Several studies found that these markers have high sensitivity and specificity for the diagnosis of mitochondrial diseases, especially those with prominent muscular involvement. In our study, we aimed to determine whether these markers could help distinguish mitochondrial diseases from other groups of inherited diseases. We measured plasma FGF‐21 and GDF‐15 concentrations in 122 patients with genetically confirmed primary mitochondrial disease and 127 patients with non‐mitochondrial inherited diseases. Although GDF‐15 showed better analytical characteristics (sensitivity = 0.66, specificity = 0.64, area under the curve AUC = 0.88) compared to FGF‐21 (sensitivity = 0.51, specificity = 0.76, AUC = 0.78) in the pediatric group of mitochondrial diseases, both markers were also elevated in a variety of non‐mitochondrial diseases, especially those with liver involvement (Gaucher disease, galactosemia, glycogenosis types 1a, 1b, 9), organic acidurias and some leukodystrophies. Thus, the overall positive and negative predictive values were not acceptable for these measurements to be used as diagnostic tests for mitochondrial diseases (FGF‐21 positive predictive value PPV = 34%, negative predictive value NPV = 73%; GDF‐15 PPV = 47%, NPV = 28%). We suggest that FGF‐21 and GDF‐15 increase in patients with metabolic diseases with metabolic or oxidative stress and inflammation.
Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals conquer new ecological niches. ...However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect-the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, compared to other chalcid wasps the gene content of M. amalphitanum is remarkably conserved. Intriguingly, we observed significant changes in M. amalphitanum transposable element dynamics over time, in which an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Overall, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.
The enigmatic and poorly studied sturgeon genus Pseudoscaphirhynchus (Scaphirhynchinae: Acipenseridae) comprises three species: the Amu Darya shovelnose sturgeon (Pseudoscaphirhynchus kaufmanni ...(Bogdanow)), dwarf Amu Darya shovelnose sturgeon P. hermanni (Kessler), and Syr Darya shovelnose sturgeon (P. fedtschenkoi (Bogdanow). Two species - P. hermanni and P. kaufmanni - are critically endangered due to the Aral Sea area ecological disaster, caused by massive water use for irrigation to support cotton agriculture, subsequent pesticide pollution and habitat degradation. For another species - P. fedtschenkoi - no sightings have been reported since 1960-s and it is believed to be extinct, both in nature and in captivity. In this study, complete mitochondrial (mt) genomes of these three species of Pseudoscaphirhynchus were characterized using Illumina and Sanger sequencing platforms. Phylogenetic analyses showed the significant divergence between Amu Darya and Syr Darya freshwater sturgeons and supported the monophyletic origin of the Pseudoscaphirhynchus species. We confirmed that two sympatric Amu Darya species P. kaufmanni and P. hermanni form a single genetic cluster, which may require further morphological and genetic study to assess possible hybridization, intraspecific variation and taxonomic status and to develop conservation measures to protect these unique fishes.
Glycan-binding profile of DC-like cells Rapoport, Eugenia M.; Moiseeva, Ekaterina V.; Aronov, Dmitry A. ...
Glycoconjugate journal,
02/2020, Letnik:
37, Številka:
1
Journal Article
Recenzirano
Modification of vaccine carriers by decoration with glycans can enhance binding to and even targeting of dendritic cells (DCs), thus augmenting vaccine efficacy. To find a specific glycan-“vector” it ...is necessary to know glycan-binding profile of DCs. This task is not trivial; the small number of circulating blood DCs available for isolation hinders screening and therefore advancement of the profiling. It would be more convenient to employ long-term cell cultures or even primary DCs from murine blood. We therefore examined whether THP-1 (human monocyte cell line) and DC2.4 (immature murine DC-like cell line) could serve as a model for human DCs. These cells were probed with a set of glycans previously identified as binding to circulating human CD14
low/-
CD16
+
CD83
+
DCs. In addition, we tested a subpopulation of murine CD14
low/-
CD80
+
СD11c
+
CD16
+
cells reported as relating to the human CD14
low/-
CD16
+
CD83
+
cells. Manα1–3(Manα1–6)Manβ1–4GlcNAcβ1–4GlcNAcβ bound to both the cell lines and the murine CD14
low/-
CD80
+
СD11c
+
CD16
+
cells. Primary cells, but not the cell cultures, were capable of binding GalNAcα1–3Galβ (A
di
), the most potent ligand for binding to human circulating DCs. In conclusion, not one of the studied cell lines proved an adequate model for DCs processes involving lectin binding. Although the glycan-binding profile of BYRB-Rb (8.17)1Iem mouse DCs could prove useful for assessing human DCs, important glycan interactions were missing, a situation which was aggravated when employing cells from the BALB/c strain. Accordingly, one must treat results from murine work with caution when seeking vaccine targeting of human DCs, and certainly should avoid cell lines such as THP-1 and DC2.4 cells.
Dendritic cells (DCs) play crucial roles in innate and adaptive immune response, for which reason targeting antigen to these cells is an important strategy for improvement of vaccine development. To ...this end, we explored recognition of DCs lectins by glycans. For selection of the glycan “vector”, a library of 229 fluorescent glycoprobes was employed to assess interaction with the CD14
low/-
CD16
+
CD83
+
blood mononuclear cell population containing the DCs known for their importance in antigen presentation to T-lymphocytes. It was found that: 1) the glycan-binding profiles of this CD14
low/-
CD16
+
CD83
+
subpopulation were similar but not identical to DCs of monocyte origin (moDCs); 2) the highest percentage of probe-positive cells in this CD14
low/-
CD16
+
CD83
+
subpopulation was observed for GalNAcα1-2Galβ (A
di
), (Neu5Acα)
3
and three mannose-reach glycans; 3) subpopulation of CD14
low/-
CD16
+
cells preferentially bound 4’-O-Su-LacdiNAc. Considering the published data on specificity of DCs binding, the glycans showing particular selectivity for the CD14
low/-
CD16
+
CD83
+
cells are likely interacting with macrophage galactose binding lectin (MGL), siglec-7 and dectin-2. In contrast, DC-SIGN is not apparently involved, even in case of mannose-rich glycans. Taking into consideration potential
in vivo
competition between glycan “vectors” and glycans within glycocalyx, attempting to target vaccine to DCs glycan-binding receptors should focus on A
di
and (Neu5Acα)
3
as the most promising vectors.
The high-capacity DNA analysis of museum samples opens new opportunities, associated with the investigation of extinct species evolution. Here, the complete mitochondrial genome of the presumably ...extinct bird species, the slender-billed curlew Numenius tenuirostris (Charadriiformes: Scolopacidae) is presented. Our results showed that mitochondrial DNA (mtDNA) is 16,705 base pairs (bp) in length and contain 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The overall base composition of the genome is 30.8% - A, 29.8% - C, 25.4% - T, 14.0% - G, and without a significant GC bias of 43.7%. Phylogenetic analyses based on the cytochrome B (cytB) gene and the whole mtDNA sequences revealed that N. tenuirostris had a close genetic relationship to Eurasian curlew (N. arquata), Far Eastern curlew (N. madagascariensis), and long-billed curlew - N. americanus. Besides, it reveals that Numenius genus is genetically distant from other Scolopacidae taxons. Together, these results provide a clear genetic perspective into the speciation process among the curlew genus members and points to a clear taxonomic position of N. tenuirostris.
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