Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and...Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and how H2A.Z interacts with other mechanisms of chromatin modification to regulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsis inflorescence. We showed that H2A.Z preferentially associated with H3K4me3 at promoters, while it was found with H3K27me3 at enhancers, and that H2A.Z deposition negatively correlated with gene expression. In addition, we demonstrated that H2A.Z represses gene expression by establishing low gene accessibility at ＋1 nucleosome and maintaining high gene accessibility at -1 nucleosome. We further showed that the high measures of gene responsiveness correlate with the H2A.Z-associated closed ＋1 nucleosome structure. Moreover, we found that H2A.Z represses enhancer activity by promoting H3K27me3 and preventing H3K4me3 histone modifications. This study provides a framework for future studies of H2A.Z functions and opens up new aspects for decoding the interplay between chromatin modification and histone variants in transcrip- tional control.展开更多
Camera traps serve as an important tool for monitoring species diversity. We used data from camera traps set for capturing snow leopards（Panthera uncia） in the Yanchiwan National Nature Reserve,Gansu Province,China,...Camera traps serve as an important tool for monitoring species diversity. We used data from camera traps set for capturing snow leopards（Panthera uncia） in the Yanchiwan National Nature Reserve,Gansu Province,China,to assess species richness with respect to mammal and birds species. We also assessed survey efficiency for species detection,and conducted an initial analysis of species interactions. The survey effort of 10,171 camera workdays yielded 2,868 suitable animal image events involving 17 mammal and 20 bird species. Among these,the dhole（Cuon alpinus） is considered to be Endangered,the snow leopard and white-lipped deer（Cervus albirostris） Vulnerable,and the Pallas＇ s cat（Feli smanul）,mountain weasel（Mustela altaica）,Himalayan griffon（Gyps himalayensis） and cinereous vulture（Aegypius monachus） Near Threatened under the IUCN red list. Fourteen species were also listed as key protected wild animals according to China national standards. Both the rarefaction curves and richness estimators suggested our sampling for mammal and pheasant species is sufficient,while more survey efforts are still needed to detect other bird species. With a focus on the dominant species Eurasian lynx（Lynx lynx）,occupancy models were used to estimate site use and detection probability for selected species,and to investigate predator-prey relationships between lynx on the one hand and woolly hare（Lepus oiostolus）,pika（Ochotona spp.）and Tibetan partridge（Perdix hodgsoniae） on the other. We give recommendations on how to increase efficiency in camera-based species inventory and biodiversity monitoring.展开更多
Background:Global climate change has had significant effects on animal distribution and population dynamics in mid-latitude alpine areas,but we know little about the basic ecology of high-altitude species due to the d...Background:Global climate change has had significant effects on animal distribution and population dynamics in mid-latitude alpine areas,but we know little about the basic ecology of high-altitude species due to the difficulties of conducting field research in the harsh climate and habitat present at high elevations.The Tibetan Snowcock(Tetraogallus tibetanus) is a little-known phasianid distributing in alpine areas at extremely high elevations in the mountains surrounding the Tibetan Plateau.Estimating the species occupancy rate and discussing the factors affecting its distribution based on infrared-triggered camera techniques would provide both a baseline to measure the influence of global warming and valuable information on its conservation and ecology.Methods:We used infrared-triggered cameras to investigate the Tibetan Snowcock on the western slope of Mt.Gongga from June to November 2016.We used the R package "overlap" to visualize its activity pattern,and used an occupancy model to both examine its habitat use as well as to determine the most influential variables affecting its habitat use.Results:Using 103 camera traps over 9213 camera-days,we recorded 428 instances of Tibetan Snowcock.The diel activity peaks of Tibetan Snowcock occurred during the periods of 8:00-10:00 am and 18:00-20:00 pm.The model estimate of occupancy for Tibetan Snowcock(0.830) was slightly higher than the na?ve site occupancy based on camera detections(0.663),indicating a wider use of habitat than the camera traps recorded.Elevation,slope,settlement density,road density,and EVI(enhanced vegetation index) were the most influential variables for its habitat use.Conclusions:The Tibetan Snowcock is confirmed to be diurnal.This species prefers an environment with a high elevation,gentle slope,and low EVI,apparently facing a trade-off between predator risk,foraging efficiency,and food availability.When human impact was low,there was a positive correlation between the habitat use of the Tibetan Snowcock and both its road and settlement den展开更多
A subfamily of four Phytochrome （phy）-Interacting bHLH transcription Factors （PIFs） collectively promote skotomorphogenic development in dark-grown seedlings. This activity is reversed upon exposure to light, by p...A subfamily of four Phytochrome （phy）-Interacting bHLH transcription Factors （PIFs） collectively promote skotomorphogenic development in dark-grown seedlings. This activity is reversed upon exposure to light, by photoacti- vated phy molecules that induce degradation of the PIFs, thereby triggering the transcriptional changes that drive a tran- sition to photomorphogenesis. The PIFs function both redundantly and partially differentially at the morphogenic level in this process, To identify the direct targets of PIF transcriptional regulation genome-wide, we analyzed the DNA-binding sites for all four PIFs by ChlP-seq analysis, and defined the genes transcriptionally regulated by each PIF, using RNA-seq analysis of pif mutants. Despite the absence of detectable differences in DNA-binding-motif recognition between the PIFs, the data show a spectrum of regulatory patterns, ranging from single PIF dominance to equal contributions by all four. Similarly, a broad array of promoter architectures was found, ranging from single PIF-binding sites, containing single sequence motifs, through multiple PIF-binding sites, each containing one or more motifs, with each site occupied prefer- entially by one to multiple PIFs. Quantitative analysis of the promoter occupancy and expression level induced by each PIF revealed an intriguing pattern. Although there is no robust correlation broadly across the target-gene population, examination of individual genes that are shared targets of multiple PIFs shows a gradation in correlation from strongly positive, through uncorrelated, to negative. This finding suggests a dual-layered mechanism of transcriptional regulation, comprising both a continuum of binding-site occupancy by each PIF and a superimposed layer of local regulation that acts differentially on each PIF, to modulate its intrinsic transcriptional activation capacity at each site, in a quantitative pattern that varies between the individual PIFs from gene to gene. These findings provide a framework for probing the mecha-展开更多
Energy simulation results for buildings have significantly deviated from actual consumption because of the uncertainty and randomness of occupant behavior.Such differences are mainly caused by the inaccurate estimatio...Energy simulation results for buildings have significantly deviated from actual consumption because of the uncertainty and randomness of occupant behavior.Such differences are mainly caused by the inaccurate estimation of occupancy in buildings.Therefore,the error between reality and prediction could be largely reduced by improving the accuracy level of occupancy prediction.Although various studies on occupancy have been conducted,there are still many differences in the approaches to detection,prediction,and validation.Reports published within this domain are reviewed in this article to discover the advantages and limitations of previous studies,and gaps in the research are identified for future investigation.Six methods of monitoring and their combinations are analyzed to provide effective guidance in choosing and applying a method.The advantages of deterministic schedules,stochastic schedules,and machine-learning methods for occupancy prediction are summarized and discussed to improve prediction accuracy in future work.Moreover,three applications of occupancy models—improving building simulation software,facilitating building operation control,and managing building energy use—are examined.This review provides theoretical guidance for building design and makes contributions to building energy conservation and thermal comfort through the implementation of intelligent control strategies based on occupancy monitoring and prediction.展开更多
Occupant behavior is an important factor affecting building energy consumption.Many studies have been conducted recently to model occupant behavior and analyze its impact on building energy use.However,to achieve a re...Occupant behavior is an important factor affecting building energy consumption.Many studies have been conducted recently to model occupant behavior and analyze its impact on building energy use.However,to achieve a reduction of energy consumption in buildings,the coordination between occupant behavior and energy-efficient technologies are essential to be considered simultaneously rather than separately considering the development of technologies and the analysis of occupant behavior.It is important to utilize energy-efficient technologies to guide the occupants to avoid unnecessary energy uses.This study,therefore,proposes a new concept,“technology-guided occupant behavior”to coordinate occupant behavior with energy-efficient technologies for building energy controls.The occupants are involved into the control loop of central air-conditioning systems by actively responding to their cooling needs.On-site tests are conducted in a Hong Kong campus building to analyze the performance of“technology-guided occupant behavior”on building energy use.According to the measured data,the occupant behavior guided by the technology could achieve“cooling on demand”principle and hence reduce the energy consumption of central air-conditioning system in the test building about 23.5%,which accounts for about 7.8%of total building electricity use.展开更多
We investigate the site occupancy and the interfacial energetics of TiAl-Ti3Al binary-phase system with H using a first-principles method. H energetically prefers to occupy the Ti-rich octahedral interstitial site bec...We investigate the site occupancy and the interfacial energetics of TiAl-Ti3Al binary-phase system with H using a first-principles method. H energetically prefers to occupy the Ti-rich octahedral interstitial site because H prefers to bond with Ti rather than with Al. The occupancy tendency of H in the binary phase TiAl-Ti3Al alloy from high to low is α2-Ti3Al to γ/α2 interface and 7-TiAl, because the decrease of the Ti local concentration is in the same order. We demonstrate that H can largely affect the mechanical properties of the TiAl-Ti3Al system. On the one hand, H at the interface reduces the interface energy with the H2 molecule as a reference, implying the TiAl/Ti3Al interface is stabilized. On the other hand, the ratio between the cleavage energy and the unstable stacking fault energy decreases after H-doping, indicating H will reduce the ductility of the TiAl/Ti3Al interface. Consequently, the mechanical property variation of TiA1 alloy due to the presence of H not only depends on the amount of TiAl/Ti3Al interfaces but also is related to the H concentration in the alloy.展开更多
Background:Disentangling the relative importance of environmental variables and interspecific interaction in modulating co-occurrence patterns of sympatric species is essential for understanding the mechanisms of comm...Background:Disentangling the relative importance of environmental variables and interspecific interaction in modulating co-occurrence patterns of sympatric species is essential for understanding the mechanisms of community assembly and biodiversity. For the two sympatric Galliformes, Silver Pheasants (Lophura nycthemera) and Whitenecklaced Partridges (Arborophila gingica), we know little about the role of habitat use and interspecific interactions in modulating their coexistence. Methods:We adopted a probabilistic approach incorporating habitat preference and interspecific interaction using occupancy model to account for imperfect detection,and used daily activity pattern analysis to investigate the cooccurrence pattern of these two sympatric Galliformes in wet and dry seasons. Results: We found that the detection probability of Silver Pheasant and White-necklaced Partridge were related to habitat variables and interspecific interaction. The presence of Silver Pheasant increases the detection probability of White-necklaced Partridge in both the wet and dry season. However, the presence of White-necklaced Partridges increases the detection probability of Silver Pheasants in the wet season, but decreases the probability in the dry season. Further, Silver Pheasants were detected frequently in the sites of high values of enhanced vegetable index (EVI) in both the wet and dry season, and in sites away from human residential settlement in the wet season. Whitenecklaced partridges were mainly detected in low EVI sites. The site use probabilities of two Galliformes were best explained by habitat variables, Silver Pheasants and White-necklaced Partridges preferred steeper areas during the wet and dry season. Both species mainly occurred in low EVI areas during the wet season and occupied sites away from the resident settlement during the dry season. Moreover, the site use probabilities of two species had opposite relationships with forest canopy coverage. Silver Pheasants preferred areas with high forest canopy coverage w展开更多
文摘Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and how H2A.Z interacts with other mechanisms of chromatin modification to regulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsis inflorescence. We showed that H2A.Z preferentially associated with H3K4me3 at promoters, while it was found with H3K27me3 at enhancers, and that H2A.Z deposition negatively correlated with gene expression. In addition, we demonstrated that H2A.Z represses gene expression by establishing low gene accessibility at ＋1 nucleosome and maintaining high gene accessibility at -1 nucleosome. We further showed that the high measures of gene responsiveness correlate with the H2A.Z-associated closed ＋1 nucleosome structure. Moreover, we found that H2A.Z represses enhancer activity by promoting H3K27me3 and preventing H3K4me3 histone modifications. This study provides a framework for future studies of H2A.Z functions and opens up new aspects for decoding the interplay between chromatin modification and histone variants in transcrip- tional control.
基金National Natural Science Foundation of China(31470567)
文摘Camera traps serve as an important tool for monitoring species diversity. We used data from camera traps set for capturing snow leopards（Panthera uncia） in the Yanchiwan National Nature Reserve,Gansu Province,China,to assess species richness with respect to mammal and birds species. We also assessed survey efficiency for species detection,and conducted an initial analysis of species interactions. The survey effort of 10,171 camera workdays yielded 2,868 suitable animal image events involving 17 mammal and 20 bird species. Among these,the dhole（Cuon alpinus） is considered to be Endangered,the snow leopard and white-lipped deer（Cervus albirostris） Vulnerable,and the Pallas＇ s cat（Feli smanul）,mountain weasel（Mustela altaica）,Himalayan griffon（Gyps himalayensis） and cinereous vulture（Aegypius monachus） Near Threatened under the IUCN red list. Fourteen species were also listed as key protected wild animals according to China national standards. Both the rarefaction curves and richness estimators suggested our sampling for mammal and pheasant species is sufficient,while more survey efforts are still needed to detect other bird species. With a focus on the dominant species Eurasian lynx（Lynx lynx）,occupancy models were used to estimate site use and detection probability for selected species,and to investigate predator-prey relationships between lynx on the one hand and woolly hare（Lepus oiostolus）,pika（Ochotona spp.）and Tibetan partridge（Perdix hodgsoniae） on the other. We give recommendations on how to increase efficiency in camera-based species inventory and biodiversity monitoring.
基金supported by the National Natural Science Foundation of China(No.31772478,31501851)the Administration of the Gongga Mountain National Nature Reserve
文摘Background:Global climate change has had significant effects on animal distribution and population dynamics in mid-latitude alpine areas,but we know little about the basic ecology of high-altitude species due to the difficulties of conducting field research in the harsh climate and habitat present at high elevations.The Tibetan Snowcock(Tetraogallus tibetanus) is a little-known phasianid distributing in alpine areas at extremely high elevations in the mountains surrounding the Tibetan Plateau.Estimating the species occupancy rate and discussing the factors affecting its distribution based on infrared-triggered camera techniques would provide both a baseline to measure the influence of global warming and valuable information on its conservation and ecology.Methods:We used infrared-triggered cameras to investigate the Tibetan Snowcock on the western slope of Mt.Gongga from June to November 2016.We used the R package "overlap" to visualize its activity pattern,and used an occupancy model to both examine its habitat use as well as to determine the most influential variables affecting its habitat use.Results:Using 103 camera traps over 9213 camera-days,we recorded 428 instances of Tibetan Snowcock.The diel activity peaks of Tibetan Snowcock occurred during the periods of 8:00-10:00 am and 18:00-20:00 pm.The model estimate of occupancy for Tibetan Snowcock(0.830) was slightly higher than the na?ve site occupancy based on camera detections(0.663),indicating a wider use of habitat than the camera traps recorded.Elevation,slope,settlement density,road density,and EVI(enhanced vegetation index) were the most influential variables for its habitat use.Conclusions:The Tibetan Snowcock is confirmed to be diurnal.This species prefers an environment with a high elevation,gentle slope,and low EVI,apparently facing a trade-off between predator risk,foraging efficiency,and food availability.When human impact was low,there was a positive correlation between the habitat use of the Tibetan Snowcock and both its road and settlement den
文摘A subfamily of four Phytochrome （phy）-Interacting bHLH transcription Factors （PIFs） collectively promote skotomorphogenic development in dark-grown seedlings. This activity is reversed upon exposure to light, by photoacti- vated phy molecules that induce degradation of the PIFs, thereby triggering the transcriptional changes that drive a tran- sition to photomorphogenesis. The PIFs function both redundantly and partially differentially at the morphogenic level in this process, To identify the direct targets of PIF transcriptional regulation genome-wide, we analyzed the DNA-binding sites for all four PIFs by ChlP-seq analysis, and defined the genes transcriptionally regulated by each PIF, using RNA-seq analysis of pif mutants. Despite the absence of detectable differences in DNA-binding-motif recognition between the PIFs, the data show a spectrum of regulatory patterns, ranging from single PIF dominance to equal contributions by all four. Similarly, a broad array of promoter architectures was found, ranging from single PIF-binding sites, containing single sequence motifs, through multiple PIF-binding sites, each containing one or more motifs, with each site occupied prefer- entially by one to multiple PIFs. Quantitative analysis of the promoter occupancy and expression level induced by each PIF revealed an intriguing pattern. Although there is no robust correlation broadly across the target-gene population, examination of individual genes that are shared targets of multiple PIFs shows a gradation in correlation from strongly positive, through uncorrelated, to negative. This finding suggests a dual-layered mechanism of transcriptional regulation, comprising both a continuum of binding-site occupancy by each PIF and a superimposed layer of local regulation that acts differentially on each PIF, to modulate its intrinsic transcriptional activation capacity at each site, in a quantitative pattern that varies between the individual PIFs from gene to gene. These findings provide a framework for probing the mecha-
基金This work is supported by the Nature Science Foundation of Tianjin(No.19JCQNJC07000)the National Nature Science Foundation of China(No.51678396).
文摘Energy simulation results for buildings have significantly deviated from actual consumption because of the uncertainty and randomness of occupant behavior.Such differences are mainly caused by the inaccurate estimation of occupancy in buildings.Therefore,the error between reality and prediction could be largely reduced by improving the accuracy level of occupancy prediction.Although various studies on occupancy have been conducted,there are still many differences in the approaches to detection,prediction,and validation.Reports published within this domain are reviewed in this article to discover the advantages and limitations of previous studies,and gaps in the research are identified for future investigation.Six methods of monitoring and their combinations are analyzed to provide effective guidance in choosing and applying a method.The advantages of deterministic schedules,stochastic schedules,and machine-learning methods for occupancy prediction are summarized and discussed to improve prediction accuracy in future work.Moreover,three applications of occupancy models—improving building simulation software,facilitating building operation control,and managing building energy use—are examined.This review provides theoretical guidance for building design and makes contributions to building energy conservation and thermal comfort through the implementation of intelligent control strategies based on occupancy monitoring and prediction.
基金The work presented in this paper is financially supported by a strategic development special project of The Hong Kong Polytechnic University.
文摘Occupant behavior is an important factor affecting building energy consumption.Many studies have been conducted recently to model occupant behavior and analyze its impact on building energy use.However,to achieve a reduction of energy consumption in buildings,the coordination between occupant behavior and energy-efficient technologies are essential to be considered simultaneously rather than separately considering the development of technologies and the analysis of occupant behavior.It is important to utilize energy-efficient technologies to guide the occupants to avoid unnecessary energy uses.This study,therefore,proposes a new concept,“technology-guided occupant behavior”to coordinate occupant behavior with energy-efficient technologies for building energy controls.The occupants are involved into the control loop of central air-conditioning systems by actively responding to their cooling needs.On-site tests are conducted in a Hong Kong campus building to analyze the performance of“technology-guided occupant behavior”on building energy use.According to the measured data,the occupant behavior guided by the technology could achieve“cooling on demand”principle and hence reduce the energy consumption of central air-conditioning system in the test building about 23.5%,which accounts for about 7.8%of total building electricity use.
文摘We investigate the site occupancy and the interfacial energetics of TiAl-Ti3Al binary-phase system with H using a first-principles method. H energetically prefers to occupy the Ti-rich octahedral interstitial site because H prefers to bond with Ti rather than with Al. The occupancy tendency of H in the binary phase TiAl-Ti3Al alloy from high to low is α2-Ti3Al to γ/α2 interface and 7-TiAl, because the decrease of the Ti local concentration is in the same order. We demonstrate that H can largely affect the mechanical properties of the TiAl-Ti3Al system. On the one hand, H at the interface reduces the interface energy with the H2 molecule as a reference, implying the TiAl/Ti3Al interface is stabilized. On the other hand, the ratio between the cleavage energy and the unstable stacking fault energy decreases after H-doping, indicating H will reduce the ductility of the TiAl/Ti3Al interface. Consequently, the mechanical property variation of TiA1 alloy due to the presence of H not only depends on the amount of TiAl/Ti3Al interfaces but also is related to the H concentration in the alloy.
基金supported by the National Key Research and Development Program of China(2017YFC0503802)China Postdoctoral Science Foundation(2017M 620905)
文摘Background:Disentangling the relative importance of environmental variables and interspecific interaction in modulating co-occurrence patterns of sympatric species is essential for understanding the mechanisms of community assembly and biodiversity. For the two sympatric Galliformes, Silver Pheasants (Lophura nycthemera) and Whitenecklaced Partridges (Arborophila gingica), we know little about the role of habitat use and interspecific interactions in modulating their coexistence. Methods:We adopted a probabilistic approach incorporating habitat preference and interspecific interaction using occupancy model to account for imperfect detection,and used daily activity pattern analysis to investigate the cooccurrence pattern of these two sympatric Galliformes in wet and dry seasons. Results: We found that the detection probability of Silver Pheasant and White-necklaced Partridge were related to habitat variables and interspecific interaction. The presence of Silver Pheasant increases the detection probability of White-necklaced Partridge in both the wet and dry season. However, the presence of White-necklaced Partridges increases the detection probability of Silver Pheasants in the wet season, but decreases the probability in the dry season. Further, Silver Pheasants were detected frequently in the sites of high values of enhanced vegetable index (EVI) in both the wet and dry season, and in sites away from human residential settlement in the wet season. Whitenecklaced partridges were mainly detected in low EVI sites. The site use probabilities of two Galliformes were best explained by habitat variables, Silver Pheasants and White-necklaced Partridges preferred steeper areas during the wet and dry season. Both species mainly occurred in low EVI areas during the wet season and occupied sites away from the resident settlement during the dry season. Moreover, the site use probabilities of two species had opposite relationships with forest canopy coverage. Silver Pheasants preferred areas with high forest canopy coverage w
