Improved mitochondrial amino acid substitution models for metazoan evolutionary studies

Abstract Background Amino acid substitution models play an essential role in inferring phylogenies from mitochondrial protein data. However, only few empirical models have been estimated from restricted mitochondrial protein data of a hundred species. The existing models are unlikely to represent appropriately the amino acid substitutions from hundred thousands metazoan mitochondrial protein sequences. Results We selected 125,935 mitochondrial protein sequences from 34,448 species in the metazoan kingdom to estimate new amino acid substitution models targeting metazoa, vertebrates and invertebrate groups. The new models help to find significantly better likelihood phylogenies in comparison with the existing models. We noted remarkable distances from phylogenies with the existing models to the maximum likelihood phylogenies that indicate a considerable number of incorrect bipartitions in phylogenies with the existing models. Finally, we used the new models and mitochondrial protein data to certify that Testudines, Aves, and Crocodylia form one separated clade within amniotes. Conclusions We introduced new mitochondrial amino acid substitution models for metazoan mitochondrial proteins. The new models outperform the existing models in inferring phylogenies from metazoan mitochondrial protein data. We strongly recommend researchers to use the new models in analysing metazoan mitochondrial protein data

Residual Cardiovascular Risk Factors in Dyslipidemia

Cardiovascular disease poses a major challenge for the 21st century. Although good control of blood pressure and type 2 diabetes and reducing low-density lipoprotein-cholesterol levels can improve cardiovascular outcomes, a substantial residual risk remains existed after treatment in most patient populations. Recently, many efforts have been directed at finding the important role of low high-density-lipoprotein cholesterol, high triglycerides, especially triglyceride-rich lipoproteins and lipoprotein (a) in the metabolism of atherosclerotic plaque formation Therefore, based on the recent evidence, identification and treatment of these risk factors may play a role in optimizing therapeutic strategy, particularly in high risk subjects along with conventional treatment. In clinical practice, adequate attention should be paid when screening and managing residual cardiovascular risk factors in dyslipidemia in term of individualized approach. The ongoing trials will give more answers to elucidate this important area

Cardiovascular magnetic resonance by non contrast T1-mapping allows assessment of severity of injury in acute myocardial infarction

BACKGROUND: Current cardiovascular magnetic resonance (CMR) methods, such as late gadolinium enhancement (LGE) and oedema imaging (T2W) used to depict myocardial ischemia, have limitations. Novel quantitative T1-mapping techniques have the potential to further characterize the components of ischemic injury. In patients with myocardial infarction (MI) we sought to investigate whether state-of the art pre-contrast T1-mapping (1) detects acute myocardial injury, (2) allows for quantification of the severity of damage when compared to standard techniques such as LGE and T2W, and (3) has the ability to predict long term functional recovery. METHODS: 3T CMR including T2W, T1-mapping and LGE was performed in 41 patients [of these, 78% were ST elevation MI (STEMI)] with acute MI at 12-48 hour after chest pain onset and at 6 months (6M). Patients with STEMI underwent primary PCI prior to CMR. Assessment of acute regional wall motion abnormalities, acute segmental damaged fraction by T2W and LGE and mean segmental T1 values was performed on matching short axis slices. LGE and improvement in regional wall motion at 6M were also obtained. RESULTS: We found that the variability of T1 measurements was significantly lower compared to T2W and that, while the diagnostic performance of acute T1-mapping for detecting myocardial injury was at least as good as that of T2W-CMR in STEMI patients, it was superior to T2W imaging in NSTEMI. There was a significant relationship between the segmental damaged fraction assessed by either by LGE or T2W, and mean segmental T1 values (P < 0.01). The index of salvaged myocardium derived by acute T1-mapping and 6M LGE was not different to the one derived from T2W (P = 0.88). Furthermore, the likelihood of improvement of segmental function at 6M decreased progressively as acute T1 values increased (P < 0.0004). CONCLUSIONS: In acute MI, pre-contrast T1-mapping allows assessment of the extent of myocardial damage. T1-mapping might become an important complementary technique to LGE and T2W for identification of reversible myocardial injury and prediction of functional recovery in acute MI

Results of magnetotelluric survey for studying geothermal system in the Bang area, Quang Binh province

This paper presents the first results from the application of magnetotelluric method (MT) using the new equipment MTU 2000 (Canada) and analysis software to investigate the structure of geothermal area around the Bang hot water source (Quang Binh province). Results of data analysis by MT 1D and 2D models to a depth of 20 km show low resistivity zone in the southwest of Bang hot water (100°C) and allow for interpreting the structural elements of athehydro- geothermal system. This includes a very low resistivity layer at depth of 2 km suggesting a clay cap (heat resistive shield), a relatively low resistivity zone at depth ≥ 2 km reflecting  fractured rocks containing geothermal fluid and hot steam. A lower resistivity body at depth of 12-14 km located about 1.5 km from the hot water source indicates the existence of a heat source or a hot mass of intrusive magma., commonly thought to be sources of typical hydro- geothermal systems potential for energy exploitation. The obtained results not only provide new information for better understanding geothermal resource in the surveyed area, but also point out the methods and technology needed to improve the effectiveness for assessing potential of geothermal resources elsewhere in Vietnam.ReferencesBản đồ Địa chất và khoáng sản Việt Nam tỷ lệ 1:1.000.000. Cục Địa chất và Khoáng sản Việt Nam xuất bản 2004. Lưu trữ Địa chất. Cumming W., 2009: Geothermal resource conceptual models using surface exploration data. In: proceedings, 34th workshop on geothermal reservoir engineering, Stanford University. Data Processing User guide. Phoenix Geophysic Ltd. 2005, 201p. Di Pippo R., 2012: Geothermal Power plant. Principles, applications, case studies. 3rd edition. Elseverdirect, 579p. Doan Van Tuyen, Tran Anh Vu, Nguyen Thi Kim Thuong, 2014: Geochemical Characteristics of Geothermal Hot Water Sources on the Territory of Vietnam. Proceeding, Thirty-Eighth Workshop on Geothermal Reservoir Engineering Stanford University, Stanford, California, February 24-26, 2014 SGP-TR-202. Duchkov A.D., Nguyen Trong Yem, Dinh Van Toan, and Trinh Viet Bac, 1992: First estimations of heat flow in northern Vietnam. Soviet Geology and Geophysics, Vol. 33, No. 5, pp 92-96. Flynn T., Quy H. H., 1997: Assessment of the geothermal resources of Socialist Republic of Vietnam. Geothermal resources Council Transactions, vol.21, 341-345. IGA report, 2013: Geothermal Exploration best practices: A Guide to resource data collection, analysis, and presentation for Geothermal projects. He Lijuan, 1999: Analysis of heat flow along a transect across the South China Sea. Geothermal Training Programme, Reports 1999, Number 5, 125-140. Hoang Huu Quy, 1998: Overview of the Geothermal potential of Vietnam. Geothermics, Vol.27, n.1, 109-115. Koenig J. et al., 1981: Evaluation of the potential for Geothermal Energy Resources in the SR of Vietnam. Berkeley, CA. Kulinich G.G., Zabolotnikov A.A, Markov Yu., 1989: Cenozoic evalution of the Earth crust and orogeny in South- Eastern Asia (Tiếng Nga). MTU2000: User guide. Phoenix Geophysic Ltd. 2000, 36p. Munoz Gerard, 2014: Exploring for Geothermal Resources with Electromagnetic Methods. Surv Geophys (2014) 35:101-122, Springer, DOI 10.1007/s10712-013-9236-0. Pellerin et al., Johnston M, Hohmann W., 1996: A numerical evaluation of electromagnetic methods in geothermal exploration. Geophysics 61(1996):121-130. Thomas Mathews, et al., 2008: Study on the sozio-economic framework for the use Geothermal energy in Vietnam. Proceedings of the 8th Asian Geothermal Symposium, Hanoi. Trần Huyên, Trương Minh, Nguyễn Tiến Bào, 1999: Về chế độ địa nhiệt ở các bể trầm tích thềm lục địa Việt Nam. Tạp chí Kinh tế Địa chất và Nguyên liệu khoáng. Cục Địa chất và Khoáng sản Việt Nam. Số 18 tháng 2 năm 1999, tr.16-25. Võ Công Nghiệp (chủ biên), 1998: Danh bạ các nguồn nước khoáng và nước nóng Việt Nam. Cục Địa chất và Khoáng sản Việt Nam. Hà Nội, 300tr. Zhdanov M., 2009: Geophysical Electromagnetic Theory and Methods. Methods in Geochemistry and Geophysics, Volume 43. ISSN: 0076-6895 Elsevier, 831pp. WinGLink User guide. Geosystem 200, 182p. www.geosystem.net.

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θsil=~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (πtot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4Ne generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role