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Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae

PLANT PHYSIOLOGY 2019年第1期180卷 404-419页

作者： Schubert, Marian Gronvold, Lars Sandve, Simen R. Hvidsten, Torgeir R. Fjellheim, Siri Norwegian Univ Life Sci Dept Plant Sci NO-1432 As Norway Norwegian Univ Life Sci Fac Chem Biotechnol & Food Sci NO-1432 As Norway Norwegian Univ Life Sci Dept Anim & Aquacultural Sci Ctr Integrat Genet NO-1432 As Norway Umea Univ Dept Plant Physiol Umea Plant Sci Ctr SE-90187 Umea Sweden

The grass subfamily Pooideae dominates the grass floras in cold temperate regions and has evolved complex physiological adaptations to cope with extreme environmental conditions like frost, winter, and seasonality. One such adaptation is cold acclimation, wherein plants increase their frost tolerance in response to gradually falling temperatures and shorter days in the autumn. However, understanding how complex traits like cold acclimation evolve remains a major challenge in evolutionary biology. Here, we investigated the evolution of cold acclimation in Pooideae and found that a phylogenetically diverse set of Pooideae species displayed cold acclimation capacity. However, comparing differential gene expression after cold treatment in transcriptomes of five phylogenetically diverse species revealed widespread species-specific responses of genes with conserved sequences. Furthermore, we studied the correlation between gene family size and number of cold-responsive genes as well as between selection pressure on coding sequences of genes and their cold responsiveness. We saw evidence of protein-coding and regulatory sequence evolution as well as the origin of novel genes and functions contributing toward evolution of a cold response in Pooideae. Our results reflect that selection pressure resulting from global cooling must have acted on already diverged lineages. Nevertheless, conservation of cold-induced gene expression of certain genes indicates that the Pooideae ancestor may have possessed some molecular machinery to mitigate cold stress. Evolution of adaptations to seasonally cold climates is regarded as particularly difficult. How Pooideae evolved to transition from tropical to temperate biomes sheds light on how complex traits evolve in the light of climate changes.

关键词： Biome Family Size Molecular machinery Transcriptome subfamily selection pressure Cold Climate coding sequence regulatory sequences Global cooling Cold acclimation Genes frost resistance Grasses Cold treatment

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Spectrum of ENU-induced mutations in phenotype-driven and gene-driven screens in the mouse

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ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2007年第2期48卷 124-142页

作者： Barbaric, Ivana Wells, Sara Russ, Andreas Dear, T. Neil Univ Sheffield Mammalian Genet Dis Unit Sch Med & Biomed Sci Sheffield S10 2RX S Yorkshire England Univ Sheffield Dept Biomed Sci Sheffield S10 2TN S Yorkshire England Mary Lyon Ctr MRC Harwell Berks England Univ Oxford Dept Biochem Genet Unit Oxford OX1 3QU England

N-ethyl-N-nitrosourea (ENU) mutagenesis in mice has become a standard tool for (i) increasing the pool of mutants in many areas of biology, (ii) identifying novel genes involved in physiological processes and disease, and (iii) in assisting in assigning functions to genes. ENU is assumed to cause random mutations throughout the mouse genome, but this presumption has never been analyzed. This is a crucial point, especially for large-scale mutagenesis, as a bias would reflect a constraint on identifying possible genetic targets. There is a significant body of published data now available from both phenotype-driven and gene-driven ENU mutagenesis screens in the mouse that can be used to reveal the effectiveness and limitations of an ENU mutagenesis approach. Analysis of the published data is presented in this paper. As expected for a randomly acting mutagen, ENU-induced mutations identified in phenotype-driven screens were in genes that had higher coding sequence length and higher exon number than the average for the mouse genome. Unexpectedly, the data showed that ENU-induced mutations were more likely to be found in genes that had a higher G + C content and neighboring base analysis revealed that the identified ENU mutations were more often directly flanked by G or C nucleotides. ENU mutations from phenotypedriven and gene-driven screens were dominantly A:T to T:A transversions or A:T to G:C transitions. Knowledge of the spectrum of mutations that ENU elicits will assist in positional cloning of ENU-induced mutations by allowing prioritization of candidate genes based on some of their inherent features.

关键词： forward genetics exon coding sequence specific locus test

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Energy Cost Minimization of a Compressor Station by Modified Genetic Algorithms

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ENGINEERING LETTERS 2015年第4期23卷 258-268页

作者： Zhang, X. Wu, C. China Univ Petr Natl Engn Lab Pipeline Safety Beijing 102200 Peoples R China

Energy cost minimization of a compressor station is an integral part of operation optimization for gas pipelines. Given the suction flow rate, the suction pressure and temperature, and the required discharge pressure of a compressor station, the operator needs to figure out the optimal compressor combination and load distribution of the station. To investigate the feasibility of genetic algorithms for solving this problem and to examine how the coding sequence of a genetic algorithm influences its performance, four genetic algorithms which are different in aspect of coding method and coding sequence were devised for this problem. These four algorithms are tested on multiple case problems of two in-service compressor stations. Comparison of the four algorithms shows that the coding sequence of a genetic algorithm influences its ability to find a feasible solution. The weaker this ability is, the more severely the algorithm is impacted. However, once any feasible solution is found, the coding sequence just impacts slightly on how steady a genetic algorithm performs in solving a problem multiple times, and no obvious bias is observed. According to the comparison, one of the four genetic algorithms was chosen to compare with two global optimization approaches, and the results show that the genetic algorithm is comparable with these global optimization methods.

关键词： coding sequence compressor station genetic algorithm power optimization

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Keratin 16-Null Mice Develop Palmoplantar Keratoderma, a Hallmark Feature of Pachyonychia Congenita and Related Disorders

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JOURNAL OF INVESTIGATIVE DERMATOLOGY 2012年第5期132卷 1384-1391页

作者： Lessard, Juliane C. Coulombe, Pierre A. Johns Hopkins Univ Dept Biochem & Mol Biol Bloomberg Sch Publ Hlth Baltimore MD USA Johns Hopkins Univ Dept Biol Chem Baltimore MD USA Johns Hopkins Univ Sch Med Dept Dermatol Baltimore MD 21205 USA

Keratin 16 (KRT16 in human, Krt16 in mouse), a type I intermediate filament protein, is constitutively expressed in epithelial appendages and is induced in the epidermis upon wounding and other stressors. Mutations altering the coding sequence of KRT16 cause pachyonychia congenita (PC), a rare autosomal dominant disorder characterized by hypertrophic nail dystrophy, oral leukokeratosis, and palmoplantar keratoderma (PPK). PPK associated with PC is extremely painful and compromises patient mobility, making it the most debilitating PC symptom. In this study, we show that, although inherited in a recessive manner, the inactivation of Krt16 in mice consistently causes oral lesions as well as PPK-like hyperkeratotic calluses on Krt16(-/-) front and hind paws, which severely compromise the animals' ability to walk. Our findings call into question the view that PC-related PPK arises exclusively as a gain-of-function on account of dominantly acting mutated keratins, and highlight the key role of modifiers in the clinical heterogeneity of PC symptoms.

关键词： Pachyonychia Congenita KRT16 gene Onychodystrophy Keratins Oral lesions KLKB1 gene coding sequence palmoplantar keratoderma

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Compactness of human housekeeping genes: selection for economy or genomic design? (vol 20, pg 248, 2004)

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TRENDS IN GENETICS 2004年第11期20卷 543-543页

作者： Vinogradov, AE Institute of Cytology Russian Academy of Sciences Tikhoretsky Ave 4 St Petersburg 194064 Russia

The short length of human housekeeping genes, compared with tissue-specificgenes, has been attributed to selection for economy in transcription and translation. In thisarticle, I show that the non-transcribed intergenic spacer around housekeeping genes is also short,which suggests that short housekeeping genes are a result of local genome ***-specific genes are longer than housekeeping genes because they have more functional domains,which is an indication of their more-complex protein architecture.

关键词： abbreviations CDS coding sequence UTRs untranslated regions

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High Suppression of Electromagnetic Wave Scattering Realized by Composite Absorption-Scattering Random coding Metamaterials

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IEEE ANTENNAS AND WIRELESS PROPAGATION LETTERS 2021年第12期20卷 2372-2376页

作者： Li, Weiduan Chen, Xu Yuan, Xujin Jin, Ming Chen, Mingji Fang, Daining Beijing Inst Technol Inst Adv Struct Technol Beijing Key Lab Lightweight Multifunct Composite Beijing 100081 Peoples R China Beijing Univ Chem Technol Coll Informat Sci & Technol Beijing 100029 Peoples R China

Electromagnetic wave scattering suppression has applications in many scenes, including radio communication and electromagnetic compatibility. A large amount of research focuses on absorber structures with reflection suppression at the -10 dB level, while scattering suppression beyond -10 dB level is rather rare. In order to study the formation of higher suppression, metamaterial with absorption and scattering composite function is presented based on the coding sequence of absorptive electromagnetic genetic components. The quantized experimental measurement result of scattering suppression reaches -22.4 dB in consecutive 7.152-16.184 GHz band (relative bandwidth 77.4%), which shows a consistent trend with simulation and validates the design process. Optimization with a small gene coding variation rate (4.7%) makes the scattering suppression effect surpass -30 dB line in 9.45-13.8 GHz in simulation. Besides camouflage function, this metamaterial could alter the scattering information in spatial distribution with a high suppression effect, which has a good chance to serve as a transmitter in a local area network with good privacy.

关键词： Metamaterials Encoding Electromagnetic scattering Absorption Bandwidth Reflection Periodic structures Absorption absorption-scattering metamaterial coding sequence electromagnetic scattering suppression

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Electrochemical Genetic Profiling of Single Cancer Cells

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ANALYTICAL CHEMISTRY 2017年第6期89卷 3378-3385页

作者： Acero Sanchez, Josep Ll. Joda, Hamdi Henry, Olivier Y. F. Solnestam, Beata W. Kvastad, Linda Akan, Pelin S. Lundeberg, Joakim Laddach, Nadja Ramakrishnan, Dheeraj Riley, Ian Schwind, Carmen Latta, Daniel O'Sullivan, Ciara K. Univ Rovira & Virgili Dept Engn Quim Av Paisos Catalans 26 Tarragona 43007 Spain KTH Royal Inst Technol Sch Biotechnol Div Gene Technol Sci Life Lab SciLifeLab Stockholm SE-17165 Solna Sweden MRC Holland Willem Schoutenstr 1 NL-1057 DL Amsterdam Netherlands Libman Automat Ltd Seamer Hill Stokesley TS9 5NQ North Yorkshire England Fraunhofer ICT IMM Carl Zeiss Str 18-20 D-55129 Mainz Germany Inst Catalana Recerca Estudis Avancats Passeig Lluis Co 23 Barcelona 08010 Spain

Recent understandings in the development and spread of cancer have led to the realization of novel single cell analysis platforms focused on circulating tumor cells (CTCs). A simple, rapid, and inexpensive analytical platform capable of providing genetic information on these rare cells is highly desirable to support clinicians and researchers alike to either support the selection or adjustment of therapy or provide fundamental insights into cell function and cancer progression mechanisms. We report on the genetic profiling of single cancer cells, exploiting a combination of multiplex ligation-dependent probe amplification (MLPA) and electrochemical detection. Cells were isolated using laser capture and lysed, and the mRNA was extracted and transcribed into DNA. Seven markers were amplified by MLPA, which allows for the simultaneous amplification of multiple targets with a single primer pair, using MLPA probes containing unique barcode sequences. Capture probes complementary to each of these barcode sequences were immobilized on a printed circuit board (PCB) manufactured electrode array and exposed to single-stranded MLPA products and subsequently to a single stranded DNA reporter probe bearing a HRP molecule, followed by substrate addition and fast electrochemical pulse amperometric detection. We present asimple, rapid, flexible, and inexpensive approach for the simultaneous quantification of multiple breast cancer related mRNA markers, with single tumor cell sensitivity.

关键词： Bar Codes coding sequence cancer cell Breast Cancer Cell Physiological Phenomena Circulating Neoplastic Cells Neoplastic Cell Messenger RNA

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MICROCELLULAR DIRECT-sequence SPREAD-SPECTRUM RADIO SYSTEM USING N-PATH RAKE RECEIVER

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IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS 1990年第5期8卷 772-780页

作者： GROB, U WELTI, AL ZOLLINGER, E KUNG, R KAUFMANN, H ASCOM ZELCOM AG RES DEPTCOMMUN GRPCH-8634 HOMBRECHTIKONSWITZERLAND SWISS FED INST TECHNOL INST COMMUN TECHNOLSPREAD SPECTRUM TECHNIQUES RES GRPCH-8092 ZURICHSWITZERLAND

A microcellular local area network (LAN) for indoor communications is proposed using code-division multiple access (CDMA) and differential phase-shift keying (DPSK) for data modulation. The pseudonoise (PN) codes in the transmitters of the base station are mutually synchronized. For this purpose, sets of Gold code sequences having low cross correlation have been found by an exhaustive computer search. Together with wideband measurements of the indoor radio channel at 900 MHz, a five-path RAKE receiver was designed to combat fading effects and to process the time diversity by using multipath signal reception. Each receiver path is demodulated independently. Several methods of diversity combining of these paths have been investigated. Acquisition and tracking of the spreading code in the receiver are controlled by a digital signal processor (DSP). Experimental results of the CDMA system are presented, showing the behavior in a multipath environment.

关键词： time diversity BASE STATION Cross correlation differential phase shift keying wireless channels pseudonoise codes diversity reception multipath signal signal reception Code division multiple access Receivers coding sequence Local Area Networks indoor communication CDMA mobile communications

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Isolation and sequencing of porcine fast skeletal muscle alkali myosin light chain 3 cDNA

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ANIMAL BIOTECHNOLOGY 1997年第2期8卷 179-185页

作者： Davoli, R Fontanesi, L Costosi, E Zambonelli, P Russo, V [a] Diproval Sezione di Allevamenti Zootecnici University of Bologna Reggio Emilia Italy

A cDNA coding for alkali myosin light chain 3 (MLC3(F)) was isolated from a porcine skeletal muscle library. This clone has an insert of 859 bp encompassing the complete CDS (coding sequence) plus the 5' and 3' untranslated regions. Computer analysis showed that porcine MLC3, cDNA is highly homologous to the corresponding cDNAs of human, rabbit and rat. Moreover, Northern analysis showed the presence of two bands that represent the mature mRNAs of the MLClF and MLC3(F) isoforms according to data observed in other species.

关键词： myosins nucleotide sequences messenger RNA skeletal muscle isolation light biotechnology pigs Sequencing Myosin Light Chains inserts Skeletal muscle Pigs coding sequence Messenger RNA

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Genetic evidence for an interaction between a picornaviral cis-acting RNA replication element and 3CD protein

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JOURNAL OF BIOLOGICAL CHEMISTRY 2004年第13期279卷 12659-12667页

作者： Yang, Y Rijnbrand, R Watowich, S Lemon, SM Univ Texas Med Branch Dept Microbiol & Immunol Galveston TX 77555 USA Univ Texas Med Branch Dept Human Biol Chem & Genet Galveston TX 77555 USA Univ Texas Med Branch Sealy Ctr Struct Biol Galveston TX 77555 USA

Internally located, cis-acting RNA replication elements, termed cres, are essential for replication of the genomes of picornaviruses such as human rhinovirus 14 (HRV-14) and poliovirus because they template uridylylation of the protein primer, VPg, by the polymerase 3D(pol). These cres form stem-loop structures sharing a common loop motif, and the HRV-14 cre can substitute functionally for the poliovirus cre in both uridylylation in vitro and RNA replication in vivo. We show, however, that the poliovirus cre is unable to support HRV-14 RNA replication. This lack of complementation maps to the stem of the poliovirus cre and was reversed by single nucleotide substitutions in the stem as well as the base of the loop. Replication-competent, revertant viruses rescued from dicistronic HRV-14 RNAs containing the poliovirus cre, or a chimeric cre containing the poliovirus stem, contained adaptive amino acid substitutions. These mapped to the surface of both the polymerase 3D(pol), at the tip of the "thumb" domain, and the protease 3C(pro), on the side opposing the active site and near the end of an extended strand segment implicated previously in RNA binding. These mutations substantially enhanced replication competence when introduced into HRV-14 RNAs containing the poliovirus cre, and they were additive in their effects. The data support a model in which 3CD or its derivatives 3C(pro) and 3D(pol) interact directly with the stem of the cre during uridylylation of VPg.

关键词： 3 untranslated region Poliovirus rna Vpg uridylylation Viral-rna Efficient replication Noncoding region Positive-strand coding sequence Rhinovirus 14 Genomicrna

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