Phylogeny and evolution of mycophagy in the Zygothrica genus group (Diptera: Drosophilidae)

Пономаренко

Kozhemyakina

et al. 2021

Animals

Belyaev’s concept of destabilizing selection during domestication was a major achievement in the XX century. Its practical value has been realized in commercial colors of the domesticated fox that never occur in the wild and has been confirmed in a wide variety of pet breeds. Many human disease models involving animals allow to test drugs before human testing. Perhaps this is why investigators doing transcriptomic profiling of domestic versus wild animals have searched for breed-specific patterns. Here we sequenced hypothalamic transcriptomes of tame and aggressive rats, identified their differentially expressed genes (DEGs), and, for the first time, applied principal component analysis to compare them with all the known DEGs of domestic versus wild animals that we could find. Two principal components, PC1 and PC2, respectively explained 67% and 33% of differential-gene-expression variance (hereinafter: log2 value) between domestic and wild animals. PC1 corresponded to multiple orthologous DEGs supported by homologs; these DEGs kept the log2 value sign from species to species and from tissue to tissue (i.e., a common domestication pattern). PC2 represented stand-alone homologous DEG pairs reversing the log2 value sign from one species to another and from tissue to tissue (i.e., representing intraspecific and interspecific variation).

Section: Discussionmentioning

confidence: 99%

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

Пономаренко

Kozhemyakina

et al. 2021

Animals

“…From among the 39 novel PAG-related rat DEGs ( Table 2 ) and these 2866 known animal DEGs ( Table 8 ), we selected seven animal genes homologous to the rat Fcgr2b gene (the right half of Table 9 ). Furthermore, we transformed the log 2 value characterizing the animal DEGs into either underexpression or overexpression of these animal genes after the domestic and wild animals split from their most recent common ancestor, according to the commonly accepted phylogeny concept [ 212 , 213 , 214 , 215 , 216 ]) ( Table 9 ).…”

Section: Resultsmentioning

confidence: 99%

Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases

Shikhevich

Khandaev

et al. 2023

IJMS

Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine and helps understand how, why, when, and what ARDs one can develop depending on their genetic background. Within this mainstream paradigm, we wanted to find out whether the known ARD-linked DEGs available in PubMed can reveal a molecular marker that will serve the purpose in anyone’s any tissue at any time. We sequenced the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats, identified rat-behavior-related DEGs, and compared them with their known homologous animal ARD-linked DEGs. This analysis yielded statistically significant correlations between behavior-related and ARD-susceptibility-related fold changes (log2 values) in the expression of these DEG homologs. We found principal components, PC1 and PC2, corresponding to the half-sum and the half-difference of these log2 values, respectively. With the DEGs linked to ARD susceptibility and ARD resistance in humans used as controls, we verified these principal components. This yielded only one statistically significant common molecular marker for ARDs: an excess of Fcγ receptor IIb suppressing immune cell hyperactivation.

“…Using the 42 DEGs (from the hippocampus of the tame versus aggressive rats) identified here ( Table 2 ), together with these 2393 DEGs of domestic versus wild animals ( Table 8 ), we revealed three β-protocadherin DEGs and seven hemoglobin subunit DEGs, which are compared in Table 9 with the human homologous genes ( HBB , HBD , and PCDHB9 ) , annotated with respect to hypertension in Table S3 . Within columns viii and ix of this table, we transformed the log2 value characterizing the animal hemoglobin subunit and β-protocadherin DEGs into either underexpression or overexpression of the corresponding gene during divergence of domestic and wild animals from their most recent common ancestor, which is the most widely used phylogeny concept [ 194 , 195 , 196 , 197 , 198 ]. Downregulation of human genes HBB and HBD reduces blood viscosity [ 199 ] and corresponds to downregulation of the homologous genes Hbb-b1 , Hbbl , Hba1 , Hbad , Hbm, and Hbz1 in the tame rat, domestic chicken, or dog during their divergence from their most recent ancestors with respect to their wild congeners ( Table 9 ).…”

Section: Resultsmentioning

confidence: 99%

Stress Reactivity, Susceptibility to Hypertension, and Differential Expression of Genes in Hypertensive Compared to Normotensive Patients

Oshchepkov

Kozhemyakina

et al. 2022

IJMS

Although half of hypertensive patients have hypertensive parents, known hypertension-related human loci identified by genome-wide analysis explain only 3% of hypertension heredity. Therefore, mainstream transcriptome profiling of hypertensive subjects addresses differentially expressed genes (DEGs) specific to gender, age, and comorbidities in accordance with predictive preventive personalized participatory medicine treating patients according to their symptoms, individual lifestyle, and genetic background. Within this mainstream paradigm, here, we determined whether, among the known hypertension-related DEGs that we could find, there is any genome-wide hypertension theranostic molecular marker applicable to everyone, everywhere, anytime. Therefore, we sequenced the hippocampal transcriptome of tame and aggressive rats, corresponding to low and high stress reactivity, an increase of which raises hypertensive risk; we identified stress-reactivity-related rat DEGs and compared them with their known homologous hypertension-related animal DEGs. This yielded significant correlations between stress reactivity-related and hypertension-related fold changes (log2 values) of these DEG homologs. We found principal components, PC1 and PC2, corresponding to a half-difference and half-sum of these log2 values. Using the DEGs of hypertensive versus normotensive patients (as the control), we verified the correlations and principal components. This analysis highlighted downregulation of β-protocadherins and hemoglobin as whole-genome hypertension theranostic molecular markers associated with a wide vascular inner diameter and low blood viscosity, respectively.