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Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea
Qiu, H.,Price, D.C.,Weber, A.P.M.,Reeb, V.,Chan Yang, E.,Lee, J.M.,Kim, S.Y.,Yoon, H.S.,Bhattacharya, D. Current Biology Ltd ; Elsevier Science Ltd 2013 Current biology Vol.23 No.19
Thriving in the hot, acidic, and metal-rich environments associated with geothermal areas is possible for only a few eukaryotes, with the Cyanidiophytina red algae (Cyanidium, Galdieria, and Cyanidioschyzon) being a famous example. These unicellular taxa can live in pH 0-4 and temperatures reaching up to 56<SUP>o</SUP>C [1,2]. Because Cyanidiophytina is sister to a vast array of mesophilic red algae (the Rhodophytina), such as the unicellular Porphyridium and the seaweed Chondrus[3], the genetic basis of their adaptation to extreme environments is of great interest from both the perspective of biotechnology and of evolution. The recently completed 13.7 Mbp genome sequence from the hot-spring dwelling Galdieria sulphuraria demonstrated that horizontal gene transfer (HGT) from prokaryotic sources provided this taxon with remarkable metabolic versatility (e.g., glycerol metabolism) and the ability to survive in its hostile environment (e.g., genes to detoxify mercury and arsenic) [4]. To explore the role of HGT in other members of this genus, we generated an 11.4 Mbp draft genome assembly from the sister taxon G. phlegrea DBV 009 [5]. In contrast to G. sulphuraria, this species is adapted to dry habitats near fumaroles such as fissures between rocks or cryptoendolithic environments [5,6]. Here, we provide evidence for extensive gene loss in the common ancestor of Cyanidiophytina that includes the eukaryote-derived loci required for urea utilization. Surprisingly, we find that G. phlegrea has regained the complete set of genes required for urea hydrolysis through HGT from eubacteria. The unlinked nature of these genes is likely explained by multiple gene transfers that resulted in assembly of the pathway in G. phlegrea. Our study demonstrates that genome reduction, a common outcome in eukaryotes for adaptation to a specialized niche, can be ameliorated by the gain of once lost, or novel functions through HGT.
Ancient gene paralogy may mislead inference of plastid phylogeny.
Qiu, Huan,Yang, Eun Chan,Bhattacharya, Debashish,Yoon, Hwan Su University of Chicago Press 2012 Molecular biology and evolution Vol.29 No.11
<P>Because of its ancient origin more than 1 billion years ago, the highly reduced plastid genomes of Plantae (e.g., plant chloroplasts) provide limited insights into the initial stages of endosymbiont genome reduction. The photosynthetic amoeba Paulinella provides a more useful model to study this process because its alpha-cyanobacterium-derived plastid originated 60 Ma and the genome still contains 1,000 genes. Here, we compared and contrasted features associated with genome reduction due to primary endosymbiosis in Paulinella plastids and in marine, free-living strains of the picocyanobacterium, Prochlorococcus. Both types of genomes show gene inactivation, concerted evolution, and contraction of gene families that impact highly conserved single-copy phylogenetic markers in the plastid such as psbA, psbC, and psbD. Our data suggest that these photosystem II genes may provide misleading phylogenetic signal because each of the constituent Plantae lineages has likely undergone a different, independent series of events that led to their reduction to a single copy. This issue is most problematic for resolving basal Plantae relationships when differential plastid gene loss was presumably ongoing, as we observe in Paulinella species. Our work uncovers a key, previously unappreciated aspect of organelle genome reduction and demonstrates 'work-in-progress' models such as Paulinella to be critical to gain a fuller understanding of algal and plant genome evolution.</P>
Impact of Local Environment on Cooling Island Effect of Water Body: Case Study of Changsha, China
Xinyi Qiu,Sung-Ho Kil,Chan Park 강원대학교 산림과학연구소 2021 강원대학교 산림과학연구소 학술대회 Vol.2021 No.10
The deterioration of the urban thermal environment poses multiple threats to residents’ health and the ecological environment. The impact of the local environment on the water cooling island (WCI) effect is complex and non-negligible. In this study, 21 water bodies in Changsha, China, were selected to reveal the impact of the local environment on the WCI effect. The results showed the average cooling distance (WCI_D), cooling magnitude (WCI_M), and cooling gradient (WCI_G) of the water bodies are about 0.31 km, 2.36 °C, and 7.61 °C/km, respectively. The WCI effect changes with the type of land cover surrounding the water body: the greatest WCI effect occurs when the water body is surrounded by built-up land, followed by bare land, forest, and cropland. Shannon’s diversity index was the factor with the greatest effect on WCI_D and WCI_G, while the landscape shape index had the greatest effect on WCI_M. The wind direction has a significant impact on WCI_D and WCI_M. The influence of the wind direction on the WCI effect is obvious, e.g., the impact of prevailing wind in the downwind direction on the WCI effect is larger than that in the upwind direction, where WCI_D and WCI_M in the downwind direction were 0.15 km and 0.24 °C larger than those in the upwind direction, respectively.
Yinghou He,Qiu-Sheng Li,Pakwai Chan,Li Zhang,Honglong Yang,Lei Li 한국풍공학회 2020 Wind and Structures, An International Journal (WAS Vol.30 No.6
The characteristics of winds associated with tropical cyclones are of great significance in many engineering fields. This paper presents an investigation of wind characteristics over a coastal urban terrain based on field measurements collected from multiple cup anemometers and ultrasonic anemometers equipped at 13 height levels on a 356-m-high meteorological tower in Shenzhen during severe Typhoon Hato. Several wind quantities, including wind spectrum, gust factor, turbulence intensity and length scale as well as wind profile, are presented and discussed. Specifically, the probability distributions of fluctuating wind speeds are analyzed in connection with the normal distribution and the generalized extreme value distribution. The von Karman spectral model is found to be suitable to depict the energy distributions of three-dimensionally fluctuating winds. Gust factors, turbulence intensity and length scale are determined and discussed. Moreover, this paper presents the wind profiles measured during the typhoon, and a comparative study of the vertical distribution of wind speeds from the field measurements and existing empirical models is performed. The influences of the topography features and wind speeds on the wind profiles were investigated based on the field-measured wind records. In general, the empirical models can provide reasonable predictions for the measured wind speed profiles over a typical coastal urban area during a severe typhoon.
Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants
Price, D. C.,Chan, C. X.,Yoon, H. S.,Yang, E. C.,Qiu, H.,Weber, A. P. M.,Schwacke, R.,Gross, J.,Blouin, N. A.,Lane, C.,Reyes-Prieto, A.,Durnford, D. G.,Neilson, J. A. D.,Lang, B. F.,Burger, G.,Steiner American Association for the Advancement of Scienc 2012 Science Vol.335 No.6070
Complex CAD surface shape design using semantic features
Fengbei Cheng,Zhenyu Liu,Guifang Duan,Chan Qiu,Bing Yi,Jianrong Tan 대한기계학회 2014 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.28 No.7
To a large extent, the success of the product shape design depends on whether the geometric modeling systems can satisfy more andmore complicated design demands in the engineering field. This paper proposes a shape design method based on semantic features forcomplex CAD surface. By the proposed method, we can easily meet the complicated design requirements, since the semantic can effectivelyrepresent the design intent. We discussed three aspects in shape design using semantic features, which are semantic design demandsof the target surface, geometric constraints in accordance with semantic features, and surface shape deformation under the geometricconstraints, respectively. The basic semantic features of geometric models drive the deformation of the target surface shape bychanging the related constraint, and the desirable features are added to the CAD surface shape. The examples of the car shape design arepresented to verify the effectives of our method.
Kim, Han Sung,Yeom, Yeon Soo,Nguyen, Thang Tat,Choi, Chansoo,Han, Min Cheol,Lee, Jai Ki,Kim, Chan Hyeong,Zankl, Maria,Petoussi-Henss, Nina,Bolch, Wesley E,Lee, Choonsik,Qiu, Rui,Eckerman, Keith,Chung, Institute of Physics in association with the Ameri 2017 Physics in medicine & biology Vol. No.
<P>It is not feasible to define very small or complex organs and tissues in the current voxel-type adult reference computational phantoms of the International Commission on Radiological Protection (ICRP), which limit dose coefficients for weakly penetrating radiations. To address the problem, the ICRP is converting the voxel-type reference phantoms into mesh-type phantoms. In the present study, as a part of the conversion project, the micrometer-thick target and source regions in the alimentary and respiratory tract systems as described in ICRP <I>Publications 100</I> and <I>66</I> were included in the mesh-type ICRP reference adult male and female phantoms. In addition, realistic lung airway models were simulated to represent the bronchial (BB) and bronchiolar (bb) regions. The electron specific absorbed fraction (SAF) values for the alimentary and respiratory tract systems were then calculated and compared with the values calculated with the stylized models of ICRP <I>Publications 100</I> and <I>66</I>. The comparisons show generally good agreement for the oral cavity, oesophagus, and BB, whereas for the stomach, small intestine, large intestine, extrathoracic region, and bb, there are some differences (e.g. up to ~9 times in the large intestine). The difference is mainly due to anatomical difference in these organs between the realistic mesh-type phantoms and the simplified stylized models. The new alimentary and respiratory tract models in the mesh-type ICRP reference phantoms preserve the topology and dimensions of the voxel-type ICRP phantoms and provide more reliable SAF values than the simplified models adopted in previous ICRP <I>Publications</I>.</P>