The objectives of this study were (1) to evaluate the computational feasibility of the multitrait test-day single-step SNP-BLUP (ssSNP-BLUP) model using phenotypic records of genotyped and ...nongenotyped animals, and (2) to compare accuracies (coefficient of determination; R2) and bias of genomic estimated breeding values (GEBV) and de-regressed proofs as response variables in 3 Australian dairy cattle breeds (i.e., Holstein, Jersey, and Red breeds). Additive genomic random regression coefficients for milk, fat, protein yield and somatic cell score were predicted in the first, second, and third lactation. The predicted coefficients were used to derive 305-d GEBV and were compared with the traditional parent averages obtained from a BLUP model without genomic information. Cow fertility traits were evaluated from the 5-trait repeatability model (i.e., calving interval, days from calving to first service, pregnancy diagnosis, first service nonreturn rate, and lactation length). The de-regressed proofs were only for calving interval. Our results showed that ssSNP-BLUP using multitrait test-day model increased reliability and reduced bias of breeding values of young animals when compared with parent average from traditional BLUP in Australian Holsten, Jersey, and Red breeds. The use of a custom selection of approximately 46,000 SNP (custom XT SNP list) increased the reliability of GEBV compared with the results obtained using the commercial Illumina 50K chip (Illumina, San Diego, CA). The use of the second preconditioner substantially improved the convergence rate of the preconditioned conjugate gradient method, but further work is needed to improve the efficiency of the computation of the Kronecker matrix product by vector. Application of ssSNP-BLUP to multitrait random regression models is computationally feasible.
The variation in structure and function of gene regulatory networks (GRNs) participating in organisms development is a key for understanding species-specific evolutionary strategies. Even the tiniest ...modification of developmental GRN might result in a substantial change of a complex morphogenetic pattern. Great variety of trichomes and their accessibility makes them a useful model for studying the molecular processes of cell fate determination, cell cycle control and cellular morphogenesis. Nowadays, a large number of genes regulating the morphogenesis of A. thaliana trichomes are described. Here we aimed at a study the evolution of the GRN defining the trichome formation, and evaluation its importance in other developmental processes.
In study of the evolution of trichomes formation GRN we combined classical phylogenetic analysis with information on the GRN topology and composition in major plants taxa. This approach allowed us to estimate both times of evolutionary emergence of the GRN components which are mainly proteins, and the relative rate of their molecular evolution. Various simplifications of protein structure (based on the position of amino acid residues in protein globula, secondary structure type, and structural disorder) allowed us to demonstrate the evolutionary associations between changes in protein globules and speciations/duplications events. We discussed their potential involvement in protein-protein interactions and GRN function.
We hypothesize that the divergence and/or the specialization of the trichome-forming GRN is linked to the emergence of plant taxa. Information about the structural targets of the protein evolution in the GRN may predict switching points in gene networks functioning in course of evolution. We also propose a list of candidate genes responsible for the development of trichomes in a wide range of plant species.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The eastern boundary of the Siberian Craton was formed as a result of rifting that split the continent late in the Middle Paleozoic. The paleomagnetic data derived from the Middle Paleozoic ...kimberlites and basites that were formed in the zone of the dynamic effect of the Vilyui paleorift attest to the clockwise rotation of the Aldan terrane relative to the Angara–Anabar terrane during the post-Late Devonian time. The amount of rotation of the terranes increases gradually eastward and reaches 22° on the eastern flank of the Chara–Sinsk dyke belt.
Safety of open pit mining in complicated geological conditions can be improved using the multilevel geomechanical monitoring of pitwall and adjacent rock mass. The domestic and foreign practices of ...pitwall stability monitoring are reviewed. The proposed approach need the operating mines to be equipped with advanced control equipment, procedures and services in order to jointly expand essentially the geomechanical monitoring possibilities.
Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing ...substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology.
We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore
using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species.
The protist belongs to the genus
based on the 18S rRNA sequence analysis. We designated the isolated protist as
. The closest species with the genome assembly is
. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes.
Our findings suggest that the
is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.
Quiescent cells have a low level of gene activity compared to growing cells. Using a yeast model for cellular quiescence, we defined the genome-wide profiles of three species of histone methylation ...associated with active transcription between growing and quiescent cells, and correlated these profiles with the presence of RNA polymerase II and transcripts.
Quiescent cells retained histone methylations normally associated with transcriptionally active chromatin and had many transcripts in common with growing cells. Quiescent cells also contained significant levels of RNA polymerase II, but only low levels of the canonical initiating and elongating forms of the polymerase. The RNA polymerase II associated with genes in quiescent cells displayed a distinct occupancy profile compared to its pattern of occupancy across genes in actively growing cells. Although transcription is generally repressed in quiescent cells, analysis of individual genes identified a period of active transcription during the development of quiescence.
The data suggest that the transcript profile and histone methylation marks in quiescent cells were established both in growing cells and during the development of quiescence and then retained in these cells. Together, this might ensure that quiescent cells can rapidly adapt to a changing environment to resume growth.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Bread wheat (
Triticum aestivum
L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance ...to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.
The results of study of primary melt inclusions in сhromium spinel of kimberlites of the middle Paleozoic Zapolyarnaya pipe (Upper Muna field, Siberian Craton) are presented. The inclusions are ...composed of an aggregate of daughter minerals: calcite, dolomite, nyerereite Na
2
Ca(CO
3
)
2
, gregoryite (Na,K)
2
CO
3
, northupite Na
3
Mg(CO
3
)
2
Cl, bradleyite Na
3
Mg(PO
4
)(CO
3
), apatite, chlorides (sylvite and/or halite), phlogopite, olivine, magnetite, and djerfisherite K
6
(Fe,Cu,Ni)
25
S
26
Cl. Carbonates are dominant over silicates. The assemblage of daughter minerals in the inclusions indicates a Si-depleted and alkali- (both Na and K) and CO
2
-rich, probably, alkali-carbonatitic parental kimberlite melt for the Zapolyarnaya pipe.
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