Long terminal repeat retrotransposons(LTR-RTs),a major type of class I transposable elements,are the most abundant repeat element in plants.The study of the interactions between LTR-RTs and the host genome relies on h...Long terminal repeat retrotransposons(LTR-RTs),a major type of class I transposable elements,are the most abundant repeat element in plants.The study of the interactions between LTR-RTs and the host genome relies on high-resolution characterization of LTR-RTs.However,for non-model species,this remains a challenge.To address this,we developed LTR_Stream for sublineage clustering of LTR-RTs in specific or closely related species,providing higher precision than current database-based lineage-level clustering.Using LTR_Stream,we analyzed Retand LTR-RTs in three Papaver species.Our findings show that high-resolution clustering reveals complex interactions between LTR-RTs and the host genome.For instance,we found that autonomous Retand elements could spread among the ancestors of different subgenomes,like retroviral pandemics,enriching genetic diversity.Additionally,we identified that specific truncated fragments containing transcription factor motifs such as TCP and bZIP may contribute to the generation of novel topologically associating domain-like(TAD-like)boundaries.Notably,our preallopolyploidization and post-allopolyploidization comparisons show that these effects diminished after allopolyploidization,suggesting that allopolyploidization may be one of the mechanisms by which Papaver species cope with LTR-RTs.We demonstrated the potential application of LTR_Stream and provided a reference case for studying the interactions between LTR-RTs and the host genome in non-model plant species.展开更多
The effects of bacterial strain, salinity and pH on the bioleaching of a complex ore using mesophilic and extremely thermophilic bacteria were investigated and the statistical analysis of the results was performed usi...The effects of bacterial strain, salinity and pH on the bioleaching of a complex ore using mesophilic and extremely thermophilic bacteria were investigated and the statistical analysis of the results was performed using ERGUN’s test. The extreme thermophiles were shown to display superior kinetics of dissolution of zinc compared with the mesophiles as confirmed by the statistical analysis. Bioleaching performance of the extreme thermophiles is found to improve in response to the increase in acidity (pH from 2.0 to 1.0) whilst the activity of the mesophiles is adversely affected by decreasing pH. Statistical analysis of the bioleaching data indicates that the effect of pH is insignificant in the range of pH 1.0-1.2 for the extreme thermophiles and pH 1.4-2.0 for the mesophiles. Salinity is shown to have a suppressing effect on the mesophiles. However, the extreme thermophiles appear to be halophilic in character as they could operate efficiently under saline conditions (1%-4%Cl- (w/v)).展开更多
Following an introduction, non-native species are exposed to environments that differ from those found in their native range; further, as these non-native species expand beyond the site of introduction, they must cons...Following an introduction, non-native species are exposed to environments that differ from those found in their native range; further, as these non-native species expand beyond the site of introduction, they must constantly adapt to novel environ- ments. Although introduced species are present across most ecosystems, few species have successfully established themselves on a truly global scale. One such species, the house sparrow Passer domesticus, is now one of the world＇s most broadly distributed vertebrate species and has been introduced to a great part of its current range. To date, work on four continents suggests both ge- netic and phenotypic variation exists between native and introduced ranges. As such, house sparrows represent an excellent op- portunity to study adaptations to novel environments and how these adaptations are derived. The global distribution of this spe- cies and the multiple independent introductions to geographically isolated sites allow researchers to ask questions regarding ge- netic variation and adaptation on a global scale. Here, we summarize the molecular studies of invasive house sparrows from the earliest work using allozymes through more recent work on epigenetics; using these studies, we discuss patterns of dispersal of this species. We then discuss future directions in techniques （e.g. next generation sequencing） and how they will provide new in- sight into questions that are fundamental to invasion biology. Finally, we discuss how continued research on the house sparrow in light of these genetic changes and adaptations will elucidate answers of adaptation, invasion biology, range expansion, and resi- lience in vertebrate systems generally展开更多
The silver Y moth Autographa gamma undertakes windbome spring and fall migrations between winter breeding re- gions around the Mediterranean and summer breeding regions in northern Europe. Flight behaviors facilitatin...The silver Y moth Autographa gamma undertakes windbome spring and fall migrations between winter breeding re- gions around the Mediterranean and summer breeding regions in northern Europe. Flight behaviors facilitating these migrations include： （i） selection of seasonally-favorable tailwinds; （ii） flying at the altitude of the fastest winds; （iii） adopting flight headings that partially counteract crosswind drift; and （iv） seasonal reversal of preferred directions between spring and fall. In the UK, ra- dar measurements indicate that migratory activity is pronounced during the spring and fall, but is usually very low during mid- summer （July）. However, an atypically intense period of high-altitude flight was recorded during July 2006, and in this study we compare the flight behavior of A. gamma during these midsummer movements with the more typical spring and fall migrations. During July 2006, activity was most intense at significantly lower altitudes than occurred in spring or fall, and was not associated with the height of the fastest winds; consequently displacement speeds were significantly slower. The most striking difference was an absence of tailwind selectivity in July with windborne movements occurring on almost every night of the month and on tailwinds from all directions. Finally, orientation behavior was quantitatively different during July, with significantly greater dis- persion of flight headings and displacements than observed in spring and fall. We discuss mechanisms which could have caused these differences, and conclude that a lack of appropriate photopcriod cues during development of the summer generation resulted in randomly-oriented ＇dispersive＇ movements that were strikingly different from typical seasonal migrations .展开更多
This work presents a computational matrix framework in terms of tensor signal algebra for the formulation of discrete chirp Fourier transform algorithms. These algorithms are used in this work to estimate the point ta...This work presents a computational matrix framework in terms of tensor signal algebra for the formulation of discrete chirp Fourier transform algorithms. These algorithms are used in this work to estimate the point target functions （impulse response functions） of multiple-input multiple-output （MIMO） synthetic aperture radar （SAR） systems. This estimation technique is being studied as an alternative to the estimation of point target functions using the discrete cross-ambiguity function for certain types of environmental surveillance applications. The tensor signal algebra is presented as a mathematics environment composed of signal spaces, finite dimensional linear operators, and special matrices where algebraic methods are used to generate these signal transforms as computational estimators. Also, the tensor signal algebra contributes to analysis, design, and implementation of parallel algorithms. An instantiation of the framework was performed by using the MATLAB Parallel Computing Toolbox, where all the algorithms presented in this paper were implemented.展开更多
基金supported by the National Key R&D Program of China(Grant No.2022YFC3400300 to Kai Ye and Xiaofei Yang)the National Natural Science Foundation of China(Grant Nos.32125009 to Kai Ye,32070663 to Kai Ye,62172325 to Xiaofei Yang,and 32422019 to Xiaofei Yang)+2 种基金the Natural Science Foundation of Shaanxi Province(Grant No.2024JC-JCQN-28 to Xiaofei Yang)the Fundamental Research Funds for the Central Universities(Grant No.xzy012024088 to Xiaofei Yang)Funding for open access charge:National Key R&D Program of China.
文摘Long terminal repeat retrotransposons(LTR-RTs),a major type of class I transposable elements,are the most abundant repeat element in plants.The study of the interactions between LTR-RTs and the host genome relies on high-resolution characterization of LTR-RTs.However,for non-model species,this remains a challenge.To address this,we developed LTR_Stream for sublineage clustering of LTR-RTs in specific or closely related species,providing higher precision than current database-based lineage-level clustering.Using LTR_Stream,we analyzed Retand LTR-RTs in three Papaver species.Our findings show that high-resolution clustering reveals complex interactions between LTR-RTs and the host genome.For instance,we found that autonomous Retand elements could spread among the ancestors of different subgenomes,like retroviral pandemics,enriching genetic diversity.Additionally,we identified that specific truncated fragments containing transcription factor motifs such as TCP and bZIP may contribute to the generation of novel topologically associating domain-like(TAD-like)boundaries.Notably,our preallopolyploidization and post-allopolyploidization comparisons show that these effects diminished after allopolyploidization,suggesting that allopolyploidization may be one of the mechanisms by which Papaver species cope with LTR-RTs.We demonstrated the potential application of LTR_Stream and provided a reference case for studying the interactions between LTR-RTs and the host genome in non-model plant species.
文摘The effects of bacterial strain, salinity and pH on the bioleaching of a complex ore using mesophilic and extremely thermophilic bacteria were investigated and the statistical analysis of the results was performed using ERGUN’s test. The extreme thermophiles were shown to display superior kinetics of dissolution of zinc compared with the mesophiles as confirmed by the statistical analysis. Bioleaching performance of the extreme thermophiles is found to improve in response to the increase in acidity (pH from 2.0 to 1.0) whilst the activity of the mesophiles is adversely affected by decreasing pH. Statistical analysis of the bioleaching data indicates that the effect of pH is insignificant in the range of pH 1.0-1.2 for the extreme thermophiles and pH 1.4-2.0 for the mesophiles. Salinity is shown to have a suppressing effect on the mesophiles. However, the extreme thermophiles appear to be halophilic in character as they could operate efficiently under saline conditions (1%-4%Cl- (w/v)).
文摘Following an introduction, non-native species are exposed to environments that differ from those found in their native range; further, as these non-native species expand beyond the site of introduction, they must constantly adapt to novel environ- ments. Although introduced species are present across most ecosystems, few species have successfully established themselves on a truly global scale. One such species, the house sparrow Passer domesticus, is now one of the world＇s most broadly distributed vertebrate species and has been introduced to a great part of its current range. To date, work on four continents suggests both ge- netic and phenotypic variation exists between native and introduced ranges. As such, house sparrows represent an excellent op- portunity to study adaptations to novel environments and how these adaptations are derived. The global distribution of this spe- cies and the multiple independent introductions to geographically isolated sites allow researchers to ask questions regarding ge- netic variation and adaptation on a global scale. Here, we summarize the molecular studies of invasive house sparrows from the earliest work using allozymes through more recent work on epigenetics; using these studies, we discuss patterns of dispersal of this species. We then discuss future directions in techniques （e.g. next generation sequencing） and how they will provide new in- sight into questions that are fundamental to invasion biology. Finally, we discuss how continued research on the house sparrow in light of these genetic changes and adaptations will elucidate answers of adaptation, invasion biology, range expansion, and resi- lience in vertebrate systems generally
文摘The silver Y moth Autographa gamma undertakes windbome spring and fall migrations between winter breeding re- gions around the Mediterranean and summer breeding regions in northern Europe. Flight behaviors facilitating these migrations include： （i） selection of seasonally-favorable tailwinds; （ii） flying at the altitude of the fastest winds; （iii） adopting flight headings that partially counteract crosswind drift; and （iv） seasonal reversal of preferred directions between spring and fall. In the UK, ra- dar measurements indicate that migratory activity is pronounced during the spring and fall, but is usually very low during mid- summer （July）. However, an atypically intense period of high-altitude flight was recorded during July 2006, and in this study we compare the flight behavior of A. gamma during these midsummer movements with the more typical spring and fall migrations. During July 2006, activity was most intense at significantly lower altitudes than occurred in spring or fall, and was not associated with the height of the fastest winds; consequently displacement speeds were significantly slower. The most striking difference was an absence of tailwind selectivity in July with windborne movements occurring on almost every night of the month and on tailwinds from all directions. Finally, orientation behavior was quantitatively different during July, with significantly greater dis- persion of flight headings and displacements than observed in spring and fall. We discuss mechanisms which could have caused these differences, and conclude that a lack of appropriate photopcriod cues during development of the summer generation resulted in randomly-oriented ＇dispersive＇ movements that were strikingly different from typical seasonal migrations .
文摘This work presents a computational matrix framework in terms of tensor signal algebra for the formulation of discrete chirp Fourier transform algorithms. These algorithms are used in this work to estimate the point target functions （impulse response functions） of multiple-input multiple-output （MIMO） synthetic aperture radar （SAR） systems. This estimation technique is being studied as an alternative to the estimation of point target functions using the discrete cross-ambiguity function for certain types of environmental surveillance applications. The tensor signal algebra is presented as a mathematics environment composed of signal spaces, finite dimensional linear operators, and special matrices where algebraic methods are used to generate these signal transforms as computational estimators. Also, the tensor signal algebra contributes to analysis, design, and implementation of parallel algorithms. An instantiation of the framework was performed by using the MATLAB Parallel Computing Toolbox, where all the algorithms presented in this paper were implemented.
