scholarly journals Molecular evolution of PCSK family: Analysis of natural selection rate and gene loss

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259085
Author(s):  
Najmeh Parvaz ◽  
Zahra Jalali
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Gene Loss ◽  
Experimental Studies ◽  
Bile Acid Metabolism ◽  
Future Studies ◽  
Accelerated Evolution ◽  
Family Analysis ◽  
Bioinformatics Study ◽  
Functional Relevance

Proprotein convertases subtilisin kexins are serine endoproteases, playing critical roles in the biological functions, including lipid, glucose, and bile acid metabolism, as well as cell proliferation, migration, and metastasis. Experimental studies have demonstrated the physiological functions of PCSKs and their association with diseases; however, studies on the evolutionary history and diversification of these proteins are missing. In the present research, a bioinformatics study was conducted on the molecular evolution of several PCSKs family members and gene loss events across placental mammalian. In order to detect evolutionary constraints and positive selection, the CodeML program of the PAML package was used. The results showed the positive selection to occur in PCSK1, PCSK3, PCSK5, and PCSK7. A decelerated rate of evolution was observed in PCSK7, PCSK3, and MBTPS1 in Carnivores compared to the rest of phylogeny, and an accelerated evolution of PCSK1, PCSK7, and MBTPS1 in Muridae family of rodents was found. Additionally, our results indicated pcsk9 gene loss in 12 species comprising Carnivores and bats (Chiroptera). Future studies are required to evaluate the functional relevance and selective evolutionary advantages associated with these modifications in PCSK proteins during evolution.

scholarly journals Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 667-677
Author(s):  
Hitoshi Araki ◽  
Nobuyuki Inomata ◽  
Tsuneyuki Yamazaki
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Natural Populations ◽  
Sliding Window ◽  
Selective Constraint ◽  
Proximal Region ◽  
Coding Regions ◽  
Asian Populations ◽  
Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

scholarly journals Molecular Evolution of Cytochrome c Oxidase Subunit IV: Evidence for Positive Selection in Simian Primates

1997 ◽  
Vol 44 (5) ◽  
pp. 477-491 ◽  
Author(s):  
Wei Wu ◽  
Morris Goodman ◽  
Margaret I. Lomax ◽  
Lawrence I. Grossman
Keyword(s):  
Molecular Evolution ◽  
Cytochrome C ◽  
Positive Selection ◽  
Cytochrome C Oxidase ◽  
Oxidase Subunit

scholarly journals Multiple Origins and nrDNA Internal Transcribed Spacer Homeologue Evolution in the Glycine tomentella (Leguminosae) Allopolyploid Complex

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 987-998 ◽  
Author(s):  
Jason T Rauscher ◽  
Jeff J Doyle ◽  
A H D Brown
Keyword(s):  
Molecular Evolution ◽  
Concerted Evolution ◽  
Internal Transcribed Spacer ◽  
Direct Sequencing ◽  
Nuclear Ribosomal Dna ◽  
Nucleolar Dominance ◽  
Future Studies ◽  
Complex Interactions ◽  
Multiple Origins ◽  
Glycine Tomentella

Abstract Despite the importance of polyploidy in the evolution of plants, patterns of molecular evolution and genomic interactions following polyploidy are not well understood. Nuclear ribosomal DNA is particularly complex with respect to these genomic interactions. The composition of nrDNA tandem arrays is influenced by intra- and interlocus concerted evolution and their expression is characterized by patterns such as nucleolar dominance. To understand these complex interactions it is important to study them in diverse natural polyploid systems. In this study we use direct sequencing to isolate and characterize nrDNA internal transcribed spacer (ITS) homeologues from multiple accessions of six different races in the Glycine tomentella allopolyploid complex. The results indicate that in most allopolyploid accessions both homeologous nrDNA repeats are present, but that there are significant biases in copy number toward one homeologue, possibly resulting from interlocus concerted evolution. The predominant homeologue often differs between races and between accessions within a race. A phylogenetic analysis of ITS sequences provides evidence for multiple origins in several of the polyploid races. This evidence for diverse patterns of nrDNA molecular evolution and multiple origins of polyploid races will provide a useful system for future studies of natural variation in patterns of nrDNA expression.

scholarly journals New exon ignites accelerated evolution of placental gene Nrk in the ancestral lineage of eutherians

2021 ◽  
Author(s):  
Guopeng Liu ◽  
Chunxiao Zhang ◽  
Yuting Wang ◽  
Guangyi Dai ◽  
Shu-Qun Liu ◽  
...  
Keyword(s):  
Positive Selection ◽  
Fitness Landscape ◽  
Induction Of Labor ◽  
Placental Development ◽  
Terrestrial Vertebrates ◽  
Regulatory Domains ◽  
Ancestral Lineage ◽  
Accelerated Evolution ◽  
Rate Test ◽  
Chorioallantoic Placenta

AbstractAccelerated evolution is often driven by the interaction between environmental factors and genes. However, it remains unclear whether accelerated evolution can be ignited. Here, we focused on adaptive events during the emergence of chorioallantoic placenta. We scanned the chromosome X and identified eight accelerated regions in the ancestral lineage of eutherian mammals. Five of these regions (P = 5.61 × 10−11 ~ 9.03 × 10−8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Moreover, a eutherian-specific exogenous exon lack of splice variant was found to be conserved. Structure modelling of NRK suggests that the accelerated exons and the eutherian-specific exon could change the enzymatic activity of eutherian NRK. Since the eutherian-specific exon was surrounded by accelerated exons, it indicates that the accelerated evolution of Nrk may be ignited by the emergence of the new exon in the ancestral lineage of eutherian mammals. The new exon might shift the function of Nrk and provide a new fitness landscape for eutherian species to explore. Although multiple exons were accelerated in both of the Nrk catalytic and regulatory domains, positive selection can only be revealed on the regulatory domain if the branch specific nonsynonymous and synonymous rate test was performed by PAML. Thus, it may be important to detect accelerated evolution when studying positive selection on coding regions. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection. Identifying positively selected placental genes provides insights into how eutherian mammals gain benefits from the invasive chorioallantoic placenta to form one of the most successful groups among terrestrial vertebrates.

scholarly journals Molecular Evolution of GYPC: Evidence for Recent Structural Innovation and Positive Selection in Humans

2009 ◽  
Vol 26 (12) ◽  
pp. 2679-2687 ◽  
Author(s):  
Jason A. Wilder ◽  
Elizabeth K. Hewett ◽  
Meredith E. Gansner
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Structural Innovation

scholarly journals Specific histone modifications associate with alternative exon selection during mammalian development

2020 ◽  
Vol 48 (9) ◽  
pp. 4709-4724
Author(s):  
Qiwen Hu ◽  
Casey S Greene ◽  
Elizabeth A Heller
Keyword(s):  
Alternative Splicing ◽  
Experimental Studies ◽  
Developmental Time ◽  
Transcriptional Elongation ◽  
Mammalian Development ◽  
Post Translational Modifications ◽  
Exon Splicing ◽  
Alternatively Spliced ◽  
Functional Relevance ◽  
Early Mouse

Abstract Alternative splicing (AS) is frequent during early mouse embryonic development. Specific histone post-translational modifications (hPTMs) have been shown to regulate exon splicing by either directly recruiting splice machinery or indirectly modulating transcriptional elongation. In this study, we hypothesized that hPTMs regulate expression of alternatively spliced genes for specific processes during differentiation. To address this notion, we applied an innovative machine learning approach to relate global hPTM enrichment to AS regulation during mammalian tissue development. We found that specific hPTMs, H3K36me3 and H3K4me1, play a role in skipped exon selection among all the tissues and developmental time points examined. In addition, we used iterative random forest model and found that interactions of multiple hPTMs most strongly predicted splicing when they included H3K36me3 and H3K4me1. Collectively, our data demonstrated a link between hPTMs and alternative splicing which will drive further experimental studies on the functional relevance of these modifications to alternative splicing.

Do Emotions Cause Eating? The Role of Previous Experiences and Social Context in Emotional Eating

2019 ◽  
Vol 28 (3) ◽  
pp. 234-240 ◽  
Author(s):  
Gizem Altheimer ◽  
Heather L. Urry
Keyword(s):  
Social Context ◽  
Emotional Eating ◽  
Negative Emotion ◽  
Negative Mood ◽  
Experimental Studies ◽  
Future Research ◽  
Discrete Emotions ◽  
Future Studies ◽  
Desire To Eat

Emotional eating is defined as an increase in eating following negative emotion. Self-reported emotional eating has been associated with physical-health concerns. However, experimental studies indicate that negative-mood inductions do not reliably lead to increased eating in healthy eaters, not even among those with a high desire to eat when emotional. We argue that experimental studies will help us understand emotional eating only if they account for the following ideas: (a) Emotional eating may require that people learn to associate emotion with eating, (b) emotional eating may follow only specific discrete emotions, and (c) emotional eating may depend on social context. Each of these points suggests a fruitful direction for future research. Specifically, future studies must acknowledge, identify, and account for variations in the extent to which people have learned to associate emotions with eating; assess or elicit strong discrete emotions; and systematically examine the effect of social context on emotional eating.

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