Molecular diversity and phylogenetic analysis of domestic and wild Bactrian camel populations based on the mitochondrial ATP8 and ATP6 genes

Phthalates and phthalate metabolites in urine from Tianjin and implications for platelet mitochondrial DNA methylation

Background

Phthalates (PAEs) are important synthetic substances in plastics, attracting much attention due to their potential effects on the cardiovascular system.

Methods

In this study, urine and blood samples from 39 individuals were collected in Tianjin, China. Phthalates and phthalate metabolites (mPAEs) were analyzed using gas chromatography-mass spectrometry (GC-MS) and high-performance liquid chromatography-mass spectrometry (HPLC-MS), respectively. The polymerase chain reaction (PCR) products from bisulfite-treated mitochondrial DNA (mtDNA) samples were analyzed using pyrosequencing technology.

Results

The detection frequencies for 9 PAEs varied from 2.56 to 92.31%, and those for 10 mPAEs varied from 30.77 to 100%. The estimated daily intakes (EDIs) and cumulative risk of PAEs were calculated based on the experimental statistics of urinary PAEs and mPAEs. For PAEs, the HIRfD (hazard index corresponding to reference doses) values of 10.26% of participants and the HITDI (hazard index corresponding to tolerable daily intake) values of 30.77% of participants were estimated to exceed 1, suggesting a relatively high exposure risk. The mtDNA methylation levels in the MT-ATP8 and MT-ND5 were observed to be lower than in the MT-ATP6. Mono-ethyl phthalate (MEP) and MT-ATP8 were positively correlated with triglyceride levels (p < 0.05). Based on the association of PAEs, mtDNA methylation, and triglycerides, the mediating role of mtDNA methylation between PAEs and cardiovascular diseases (CVDs) was analyzed in this study, but no mediated effect was observed.

Conclusion

The effects of PAE exposure on cardiovascular diseases (CVDs) should be investigated further.

Full Mitochondrial Genomes Reveal Species Differences between the Venerid Clams Ruditapes philippinarum and R. variegatus

In natural sea areas along the coast of China, venerid clams Ruditapes philippinarum and R. variegatus exhibit similar adult shell forms and are especially difficult to distinguish as spat and juveniles. This study used comparative mitochondrial genome analysis to reveal differences between these species. The results showed that: (1) the mitochondrial genomes of R. philippinarum and R. variegatus share a large number of similar gene clusters arranged in consistent order, yet they also display noncommon genes, with both gene rearrangements and random losses found; (2) the 13 protein-coding genes in R. philippinarum as well as two-fold and four-fold degenerate sites in R. variegatus have an evident AT bias; (3) the Ka/Ks ratio of the mitochondrial ATP8 gene was significantly higher in R. philippinarum than in R. variegatus, and an analysis of selection pressure revealed that the mitochondrial NADH dehydrogenase subunit 2 gene and NADH dehydrogenase subunit 6 gene of R. variegatus were under great selective pressure during its evolution; and finally, (4) the two species clustered into one branch on a phylogenetic tree, further affirming their phylogenetic closeness. Based on these results, we speculate that the species differences between R. variegatus and R. philippinarum are largely attributable to adaptive evolution to the environment. The present findings provide a reference for the development of germplasm identification.

The exposure levels and health risk assessment of antibiotics in urine and its association with platelet mitochondrial DNA methylation in adults from Tianjin, China: A preliminary study

There has been extensive research on antibiotics exposure in adults by biomonitoring, but the biological mechanisms and potential risks to human health remain limited. In this study, 102 adults aged 26-44 years in Tianjin were studied and 23 common antibiotics in urine were analyzed by Liquid chromatography-mass spectrometry (LC-MS). All antibiotics were detected in urine, with an overall detection frequency of 40.4% (the detection frequencies of phenothiazines, quinolones, sulfonamides, tetracyclines, and chloramphenicol were 77%, 54%, 24%, 28%, and 49%, respectively.). Ofloxacin and enrofloxacin had the highest detection frequencies (85% and 81%), with median concentrations of 0.26 (IQR: 0.05-1.36) and 0.09 (IQR: 0.03-0.14) ng/mL, respectively. Based on health risk assessment, the predicted estimated daily exposures (EDEs) ranged from 0 μg/kg/day to 13.98 μg/kg/day. The hazard quotient (HQ) values of all the antibiotics except ofloxacin and ciprofloxacin were bellow one, which are considered safe. For all blood samples, the mitochondrial DNA (mtDNA) methylation levels in the MT-ATP6 (ranging between 3.86% and 34.18%) were slightly higher than MT-ATP8 and MT-ND5 (ranging between 0.57% and 9.32%, 1.08% and 19.62%, respectively). Furthermore, mtDNA methylation from MT-ATP6, MT-ATP8 and MT-ND5 were measured by bisulfite-PCR pyrosequencing. The association (P < 0.05) was found between mtDNA methylation level (MT-ATP8 and MT-ND5) and individual antibiotics including chlorpromazine, ciprofloxacin, enrofloxacin, norfloxacin, pefloxacin, sulfaquinoxaline, sulfachloropyridazine, chloramphenicol, and thiamphenicol, indicating that persistent exposure to low-dose multiple antibiotics may affect the mtDNA methylation level and in turn pose health risks.

Genetic differentiation of Indian dromedary and Bactrian camel populations based on mitochondrial ATP8 and ATP6 genes

Camelids are acknowledged worldwide to endure hostile conditions prevalent in the hot as well cold deserts across the globe. Adaptations to climatic extremes have been associated with mitochondrial protein variants such as ATP8 and ATP6 in different species. The camel genetic resources of India are represented by 9 breeds of dromedary camels which inhabit hot arid and semi-arid zones of the country and a small population of Bactrian camels found in the cold desert of Ladakh. In this study, within and between breed genetic diversity in Indian dromedaries and their divergence from Bactrian camels was investigated based on ATP8/6 genes. Sequence analysis of a mitochondrial DNA fragment encompassing ATP8 and ATP6 genes identified 15 haplotypes in the dromedaries of India and 3 haplotypes in Bactrian camels. The values of haplotype diversity and nucleotide diversity were 0.647 and 0.00187 in the former and 0.679 and 0.00098, respectively in the latter. AMOVA analysis revealed 97.81% variance between the two species. Median-Joining network delineated three distinct mitochondrial haplogroups for Camelus dromedarius, Camelus ferus and Camelus bactrianus. Clear demarcation of the old world (Dromedary and Bactrian camels) and new world camelids (Alpaca, llama, guanaco and vicugna) was evident through the phylogenetic analysis.

Mitochondrial DNA variation and phylogeography of Old World camels

Objective

Old World camels are a valuable genetic resource for many countries around the world due to their adaptation to the desert environment. At present, Old World camels have encountered the challenge of unprecedented loss of genetic resources. Through our research, we would reveal the population structure and genetic variation in Old World camel populations, which provides a theoretical basis for understanding the germplasm resources and origin and evolution of different Old World camel populations.

Methods

In the present study, we assessed mtDNA control region sequences of 182 individuals from Old World camels to unravel genetic diversity, phylogeography, and demographic dynamics.

Results

Thirty-two haplotypes confirmed by 54 polymorphic sites were identified in the 156 sequences, which included 129 domestic and 27 wild Bactrian camels. Meanwhile, 14 haplotypes were defined by 47 polymorphic sites from 26 sequences in the dromedaries. The wild Bactrian camel population showed the lowest haplotype and nucleotide diversity, while the dromedaries investigated had the highest. The phylogenetic analysis suggests that there are several shared haplotypes in different Bactrian camel populations, and that there has been genetic introgression between domestic Bactrian camels and dromedaries. In addition, positive values of Tajima’s D and Fu’s Fs test demonstrated a decrease in population size and/or balancing selection in the wild Bactrian camel population. In contrast, the negative values of Tajima’s D and Fu’s Fs test in East Asian Bactrian camel populations explained the demographic expansion and/or positive selection.

Conclusion

In summary, we report novel information regarding the genetic diversity, population structure and demographic dynamics of Old World camels. The findings obtained from the present study reveal that abundant genetic diversity occurs in domestic Bactrian camel populations and dromedaries, while there are low levels of haplotype and nucleotide diversity in the wild Bactrian camel population.

Old World camels in a modern world - a balancing act between conservation and genetic improvement

Old World camels have served humans in cross‐continental caravans, transporting people and goods, connecting different cultures and providing milk, meat, wool and draught since their domestication around 3000–6000 years ago. In a world of modern transport and fast connectivity, these beasts of burden seem to be out‐dated. However, a growing demand for sustainable milk and meat production, especially in countries affected by climate change and increasing desertification, brings dromedaries (Camelus dromedarius) and Bactrian camels (Camelus bactrianus) back onstage and into the focus of animal breeders and scientists. In this review on the molecular genetics of these economically important species we give an overview about the evolutionary history, domestication and dispersal of Old World camels, whereas highlighting the need for conservation of wild two‐humped camels (Camelus ferus) as an evolutionarily unique and highly endangered species. We provide cutting‐edge information on the current molecular resources and on‐going sequencing projects. We cannot emphasise enough the importance of balancing the need for improving camel production traits with maintaining the genetic diversity in two domestic species with specific physiological adaptation to a desert environment.