Charge changes in protein evolution

The number of charge changes relative to total amino acid replacements for each of seven protein sequences (cytochrome c, hemoglobin alpha, hemoglobin beta, myoglobin, insulin, and fibrinopeptides A and B) has been studied. This number was compared with the expected value obtained under the assumption of random nucleotide substitution. The results obtained indicate that four proteins--hemoglobin alpha, hemoglobin beta, myoglobin, and insulin--are accumulating charge changes at rates slower than those predicted by a model of random substitution. Cytochrome c and fibrinopeptides A and B are accumulating charge changes at rates similar to those predicted by a random model.     

Step changes in end-tidal CO2: methods and implications.

A dynamic end-tidal forcing technique for producing step changes in end-tidal CO2 with end-tidal O2 held constant independent of the ventilation response or the mixed venous return is introduced for characterizing the human ventilation response to end-tidal CO2 step changes for both normoxic (PAO2 = 125 Torr) and hypoxic (PAO2 = 60 Torr) conditions. The ventilation response approaches a steady state within 5 min. In normoxia, the on-transient is faster than the off-transient, presumably reflecting the action of cerebral blood flow. The hypoxic step response is faster than the normoxic response presumably reflecting the increased contribution from the carotid body. The delay in the ventilation response after the change in end-tidal CO2 is less in hypoxia than in normoxia and reflects the action of a transport delay and that of a virtual delay. These delays are interpreted with respect to the high-frequency phase shift data for the same subject, generated using sinusoidal end-tidal forcing. The methods of others for experiments utilizing step changes in inspired CO2 are considered with respect to our methods.     

Estimating changes in mutational mechanisms of evolution

By considering three DNA sequences simultaneously there is sufficient information to recover a full Markov model with three transition matrices from the root to each of the sequences. It is necessary to have relatively long sequences because, for nucleotides, the full model requires 39 parameters that are estimated from 63 observable values. This triplet Markov method is evaluated for the protein coding genes of mammalian vertebrate mitochondrial genomes, and, in addition, version for two-state-characters (such as R/Y coding) is implemented. A key finding is that some changes in mutational mechanism differentially affect the mutation rate between pairs of nucleotides: there does not appear to be a universal change in "rate" of evolution. It remains to be explored whether detecting changes in certain nucleotide interchanges can be localized to a particular part of the DNA replication/repair system. In order to estimate divergence dates it may eventually be advantageous to use the nucleotide interchanges that show little rate change.     

Extreme differences in charge changes during protein evolution

Summary The maintenance of a proper distribution of charged amino acid residues might be expected to be an important factor in protein evolution. We therefore compared the inferred changes in charge during the evolution of 43 protein families with the changes expected on the basis of random base substitutions. It was found that certain proteins, like the eye lens crystallins and most histones, display an extreme avoidance of changes in charge. Other proteins, like phospholipase A2 and ferredoxin, apparently have sustained more charged replacements than expected, suggesting a positive selection for changes in charge. Depending on function and structure of a protein, charged residues apparently can be important targets for selective forces in protein evolution. It appears that actual biased codon usage tends to decrease the proportion of charged amino acid replacements. The influence of nonrandomness of mutations is more equivocal. Genes that use the mitochondrial instead of the universal code lower the probability that charge changes will occur in the encoded proteins.     

Conformational changes in the globin family during evolution

Summary Conformational restrictions imposed on the fixation of insertions and deletions by the three-dimensional structure of globins during evolution are analyzed. An evolutionary tree for the primary structure of 38 taxonomically distant globins was constructed by a computer method. Based on this tree, the calculated fixation frequency of point mutations was 50-fold higher than that established jointly for deletions and insertions, and the fixation frequency of deletions was more than three times that established for insertions. It was also found that deletions and insertions are predominantly fixed in the interhelical sections and at the ends of the -helices of the globin molecules. Conformational analysis of the packing of the -helices in the spatial structure of globins demonstrated that the fixation of deletions and insertions in the center of an -helix produces a marked distortion of their normal packing. The possible role of deletions and insertions in the evolution of protein families is discussed.     

Metabolic changes in schizophrenia and human brain evolution

Background

Despite decades of research, the molecular changes responsible for the evolution of human cognitive abilities remain unknown. Comparative evolutionary studies provide detailed information about DNA sequence and mRNA expression differences between humans and other primates but, in the absence of other information, it has proved very difficult to identify molecular pathways relevant to human cognition.

Results

Here, we compare changes in gene expression and metabolite concentrations in the human brain and compare them to the changes seen in a disorder known to affect human cognitive abilities, schizophrenia. We find that both genes and metabolites relating to energy metabolism and energy-expensive brain functions are altered in schizophrenia and, at the same time, appear to have changed rapidly during recent human evolution, probably as a result of positive selection.

Conclusion

Our findings, along with several previous studies, suggest that the evolution of human cognitive abilities was accompanied by adaptive changes in brain metabolism, potentially pushing the human brain to the limit of its metabolic capabilities.     

Multiple changes in sialic acid biology during human evolution

Humans are genetically very similar to “great apes”, (chimpanzees, bonobos, gorillas and orangutans), our closest evolutionary relatives. We have discovered multiple genetic and biochemical differences between humans and these other hominids, in relation to sialic acids and in Siglecs (Sia-recognizing Ig superfamily lectins). An inactivating mutation in the CMAH gene eliminated human expression of N-glycolylneuraminic acid (Neu5Gc) a major sialic acid in “great apes”. Additional human-specific changes have been found, affecting at least 10 of the <60 genes known to be involved in the biology of sialic acids. There are potential implications for unique features of humans, as well as for human susceptibility or resistance to disease. Additionally, metabolic incorporation of Neu5Gc from animal-derived materials occurs into biotherapeutic molecules and cellular preparations - and into human tissues from dietary sources, particularly red meat and milk products. As humans also have varying and sometime high levels of circulating anti-Neu5Gc antibodies, there are implications for biotechnology products, and for some human diseases associated with chronic inflammation.     

Investigating the causes of changes in allele frequency during evolution

The use of models as teaching aids in the study of the causes of changes of gene frequency during evolution is now a well established practice in school and degree courses. The effects of migration, selection and genetic drift may all be investigated. This paper extends the range of procedures which may be used with sixth form and more advanced students by discussing possible migration models, by describing an improved selection model where selection is applied unconsciously and the selection coefficient can be calculated from the data and by comparing single and multiple generation models.

In each case there is a brief discussion of points to be extracted from class results.

An overall teaching programme is suggested which should enable the students to investigate all three factors while spending a minimum of time on repetitive manual procedures.

Finally, there is a brief discussion of the roles of migration, drift and selection in evolution.     

Proteogenomic review of the changes in primate apoC-I during evolution

Apolipoprotein C-I has evolved more rapidly than any of the other soluble apolipoproteins. During the course of primate evolution, the gene for this apolipoprotein was duplicated. Prompted by our observation that the two resulting genes encode two distinct forms of apoC-I in great apes, we have reviewed both the genomic and proteomic data to examine what changes have occurred during the course of primate evolution. We have found data showing that one of the duplicated genes, known to be a pseudogene in humans, was also a pseudogene in Denisovans and Neandertals. Using genomic and proteomic data for primates, we will provide in this review evidence that the duplication took place after the divergence of New World monkeys from the human lineage and that the formation of the pseudogene took place after the divergence of the bonobos and chimpanzees from the human lineage.     

Developmental evolution: Hox proteins ring the changes

The evolution of body form is believed to involve changes in expression of developmental genes, largely through changes in cis-regulatory elements. Recent studies suggest that changes in the sequences of key developmental regulators, such as the Hox proteins, may also play an important role.     

Contribution of ambient ozone to changes in Scots pine defoliation. Step II of Lithuanian studies

This study aimed to explore if changes in peak ozone (O3) concentrations may reinforce the phytotoxic effects of air concentration of acidifying compounds and their deposition, as well as unfavorable climatic factors on pine crown defoliation. Forty-eight pine stands with more than 8000 sample pine trees have been monitored annually. The impact of sulfur dioxide (SO2) on pine defoliation was found to be the most significant. The impacts of peak O3 concentrations, acid deposition, and amount of precipitation were considerably lower, whereas the impact of air temperature, the least. Contribution of peak O3 concentrations to the integrated impact of acid deposition and amount of precipitation on pine defoliation was most significant, whereas the contribution to the impact of acidifying air compounds, mainly SO2, was the least. No synergetic effect between peak O3 concentrations and high temperature during vegetation period was detected.